subject:(long non coding RNA lncRNA )

Penn State University

1. Yetming, Kristen Dominique. BHLF1, a Lytic-Cycle Gene Encoding a Long Non-Coding RNA Contributes to Epstein-Barr Virus Latency.

Degree: 2017, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/13732kdy5005

► Epstein-Barr virus (EBV) is a lymphotropic, gammaherpesvirus which efficiently establishes a persistent, lifelong infection in humans. As is common with other herpesviruses, EBV has both… (more)

▼ Epstein-Barr virus (EBV) is a lymphotropic, gammaherpesvirus which efficiently establishes a persistent, lifelong infection in humans. As is common with other herpesviruses, EBV has both replicative (lytic) and latent cycles of infection. EBV latency, in which there is no virus production, can be subdivided into several distinct latency programs which are characterized by differential expression patterns of the viral latency-associated proteins: EBNA1, -2, -3A, -3B, -3C, -LP and LMP1, -2A, -2B. The major long-term reservoir of EBV is the memory B cell, and as latently-infected B cells progress from an initial state of EBV-driven cell proliferation to a state of long-term viral latency within the memory B-cell pool, there is a restriction in the expression of the viral latency proteins, due to the epigenetic silencing of the EBNA promoters Wp and Cp. This restriction in latency is essential for the persistence of EBV infection as cytotoxic T lymphocytes can remove infected B cells that continue to express several of the latency-associated proteins. Historically, it has been thought that latency-associated EBV gene products only contribute to the latent cycle, and lytic-cycle genes only function during lytic infection. However, it has recently been found that there is a subset of “lytic” genes that are expressed upon the initiation of latency, one of which is BHLF1. This, along with several other lines of evidence, suggests that BHLF1 may have a latency-associated function. Thus, the goal of the work presented in this dissertation was to elucidate whether BHLF1 has a role in the establishment or maintenance of EBV latency. Using recombinant EBV (rEBV), we observed that infection of an EBV-negative cell line, BL2, with a wild-type (WT) rEBV is capable of sustaining latency III, whereas infection with mutant rEBVs, in which BHLF1 has been deleted, results in a transition from latency III to latency I within 3 months post-infection at both the protein and mRNA levels. Disruption of BHLF1 did not significantly influence the expression of other genes near the locus; thus, the phenotype observed is likely a direct consequence of the loss of BHLF1 function. In addition to the mutant phenotype in BL2 cells, we also observed a decrease in the efficiency of immortalization upon infection of primary B cells with the mutant rEBVs. Although BHLF1 contains a predicted translational open reading frame (ORF), attempts to transiently express a protein from this ORF failed unless we co-expressed the EBV SM protein, whose expression is normally restricted to the lytic cycle. We therefore hypothesize that during latent infection, BHLF1 functions as a long non-coding RNA (lncRNA). The likelihood that BHLF1 primarily functions as an lncRNA is further supported by our recent observation and that of others that the ORF is not conserved among all EBV isolates. Furthermore, RT-PCR analysis of the 5' ends of the EBNA cDNAs indicated a higher frequency of intron retention, possibly resulting in nonsense-mediated decay. Overall, these data suggest… Advisors/Committee Members: Jeffery T. Sample, Dissertation Advisor/Co-Advisor, Jeffery T. Sample, Committee Chair/Co-Chair, Clare E. Sample, Committee Member, Todd D. Schell, Committee Member, Gregory S. Yochum, Outside Member, David J. Spector, Committee Member.

Subjects/Keywords: Epstein-Barr virus; EBV; BHLF1; long non-coding RNA; lncRNA; latency

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Yetming, K. D. (2017). BHLF1, a Lytic-Cycle Gene Encoding a Long Non-Coding RNA Contributes to Epstein-Barr Virus Latency. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/13732kdy5005

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Yetming, Kristen Dominique. “BHLF1, a Lytic-Cycle Gene Encoding a Long Non-Coding RNA Contributes to Epstein-Barr Virus Latency.” 2017. Thesis, Penn State University. Accessed March 05, 2021. https://submit-etda.libraries.psu.edu/catalog/13732kdy5005.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Yetming, Kristen Dominique. “BHLF1, a Lytic-Cycle Gene Encoding a Long Non-Coding RNA Contributes to Epstein-Barr Virus Latency.” 2017. Web. 05 Mar 2021.

Vancouver:

Yetming KD. BHLF1, a Lytic-Cycle Gene Encoding a Long Non-Coding RNA Contributes to Epstein-Barr Virus Latency. [Internet] [Thesis]. Penn State University; 2017. [cited 2021 Mar 05]. Available from: https://submit-etda.libraries.psu.edu/catalog/13732kdy5005.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Yetming KD. BHLF1, a Lytic-Cycle Gene Encoding a Long Non-Coding RNA Contributes to Epstein-Barr Virus Latency. [Thesis]. Penn State University; 2017. Available from: https://submit-etda.libraries.psu.edu/catalog/13732kdy5005

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of New South Wales

2. Quek, Xiucheng. Computational characterisation of the transcriptional landscape and long non-coding RNAs in cancer.

Degree: Garvan Institute of Medical Research, 2017, University of New South Wales

URL: http://handle.unsw.edu.au/1959.4/58668 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:46586/SOURCE02?view=true

► The recent rise of high-throughput sequencing technologies, paralleled with developments in computational biology, has provided an unprecedented amount of information on the roles of the… (more)

▼ The recent rise of high-throughput sequencing technologies, paralleled with developments in computational biology, has provided an unprecedented amount of information on the roles of the genome and transcriptome in human diseases. This has proven especially important for the treatment of cancer, where genomic diversity and acquired drug resistance are key challenges for development of successful therapies. In this thesis, we performed computational assessment of cancer transcriptomes, focusing on long non-coding RNAs (lncRNAs) as the master regulators of genome activity, in order to classify different types of skin cancer and examine mechanisms of adaptation to therapies.In our initial study, we performed the first whole-genome transcriptomic analysis of non-melanoma squamous cell carcinomas (NMSC-SCC) that distinguishes cancer types with similar clinical presentations. NMSC-SCC is a skin cancer that manifests as a spectrum of malignancies, ranging from actinic keratosis (AK) to intraepidermal carcinoma (IEC) and cutaneous squamous cell carcinoma (cSCC). We compared the transcriptomes of these malignancies, identified characteristic genes and pathways and defined IEC as a distinct malignancy. In addition, we characterised multiple lncRNAs, novel transcripts and fusion genes associated with NMSC-SCC pathogenesis.Next, we aimed to investigate development of resistance against targeted therapy in cancer over time. Targeted anti-cancer therapies work on specific parts of cancer pathways, but tumours develop resistance through stress-response pathways. To investigate the dynamics of these mechanisms, we studied a time course of resistance of two cancer cell-lines to four targeted therapies. Interestingly, resistant cells had initially downregulated DNA-repair genes and upregulated cell-proliferation genes followed by a complete reversal of their expression over time. This suggests that the fine-tuning of cancer genome mutation rates occurs as an adaptive strategy to treatment. Lastly, we identified several hypermutated genes with a role in development of resistance that present a potential target for novel cancer therapies.Finally, we provided the scientific community with a manually curated resource for lncRNAs with an experimentally proven function, lncRNAdb. This major update of the highly cited lncRNA database added a number of functional lncRNAs along with several usability upgrades, such as an inbuilt BLAST tool that allows database searches with nucleotide sequences. Updating lncRNAdb ensures its continuation as a reference database for lncRNAs research.Collectively, the thesis highlighted the application of computational method into the characterization of lncRNAs and cancer transcriptomics. Advisors/Committee Members: Dinger, Marcel, Garvan Institute of Medical Research, Faculty of Medicine, UNSW, Epstein, Richard John, Garvan Institute of Medical Research, Faculty of Medicine, UNSW.

Subjects/Keywords: long non-coding RNA; cancer trancriptomics; transcriptome; lncRNA; targeted therapy; resistant; squamous cell carcinoma; actinic keratosis; RNA Sequencing; intraepidermal carcinoma; lncRNAdb

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Quek, X. (2017). Computational characterisation of the transcriptional landscape and long non-coding RNAs in cancer. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/58668 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:46586/SOURCE02?view=true

Chicago Manual of Style (16^th Edition):

Quek, Xiucheng. “Computational characterisation of the transcriptional landscape and long non-coding RNAs in cancer.” 2017. Doctoral Dissertation, University of New South Wales. Accessed March 05, 2021. http://handle.unsw.edu.au/1959.4/58668 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:46586/SOURCE02?view=true.

MLA Handbook (7^th Edition):

Quek, Xiucheng. “Computational characterisation of the transcriptional landscape and long non-coding RNAs in cancer.” 2017. Web. 05 Mar 2021.

Vancouver:

Quek X. Computational characterisation of the transcriptional landscape and long non-coding RNAs in cancer. [Internet] [Doctoral dissertation]. University of New South Wales; 2017. [cited 2021 Mar 05]. Available from: http://handle.unsw.edu.au/1959.4/58668 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:46586/SOURCE02?view=true.

Council of Science Editors:

Quek X. Computational characterisation of the transcriptional landscape and long non-coding RNAs in cancer. [Doctoral Dissertation]. University of New South Wales; 2017. Available from: http://handle.unsw.edu.au/1959.4/58668 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:46586/SOURCE02?view=true

3. Smith, Jenna E. Investigation of the mRNP and Transcriptome Regulated by Nonsense-Mediated RNA Decay.

Degree: PhD, Biochemistry, 2015, Case Western Reserve University School of Graduate Studies

URL: http://rave.ohiolink.edu/etdc/view?acc_num=case1421428941

► Appropriate and accurate gene expression is critical for all organisms. One quality control pathway which exists to maintain the fidelity of gene expression is the… (more)

▼ Appropriate and accurate gene expression is critical for all organisms. One quality control pathway which exists to maintain the fidelity of gene expression is the nonsense-mediated RNA decay (NMD) pathway, responsible for recognizing and targeting for rapid degradation RNAs undergoing premature translation termination. Although this pathway is conserved throughout eukarya and essential in higher organisms, many mechanistic details underlying NMD are not understood.Proteins uniquely bound to NMD-sensitive mRNAs are predicted to facilitate their recognition as aberrant by the NMD pathway. To investigate differences between NMD-sensitive and NMD-insensitive RNAs, an efficient and highly-specific method to biochemically purify an individual mRNP from a whole-cell lysate was developed. This extensively optimized procedure will serve as a powerful tool to identify proteins preferentially associated with NMD-sensitive mRNAs to elucidate how NMD substrates are recognized. Furthermore, the mRNP pulldown protocol can be adapted to study other aspects of mRNA regulation.Because NMD is a strictly translation-dependent process, sensitivity to NMD can provide evidence for the translation of RNAs. An emerging class of poorly characterized RNAs, long non-coding RNAs (lncRNAs) are bioinformatically classified to lack protein-coding capacity. Unannotated RNAs (uRNAs) in yeast were specifically investigated for their capacity to associate with translating ribosomes based on co-sedimentation with polyribosomes, ribosome profiling, detection of encoded peptides, and sensitivity to NMD. These data demonstrated that many transcripts considered to lack protein-coding potential are, in fact, actively translated, and implicate NMD in regulating the activity or expression of a subset of lncRNAs.Finally, many endogenous mRNAs are sensitive to the NMD pathway, including specific mRNA isoforms. Genome-wide profiling of the yeast transcriptome by high-throughput sequencing globally identified mRNAs sensitive to NMD. These mRNAs were enriched for features common to NMD-sensitive RNAs, and also included indirect targets of NMD. A bioinformatic tool was developed to find NMD-sensitive regions of the yeast transcriptome independent of gene annotation or transcript structure, and identify NMD-sensitive RNA isoforms. This preliminary analysis of the NMD-sensitive transcriptome has revealed unappreciated complexity in RNA processing and expression in yeast. Advisors/Committee Members: Baker, Kristian (Advisor), Nilsen, Timothy (Committee Chair).

Subjects/Keywords: Molecular Biology; Biochemistry; nonsense-mediated RNA decay; NMD; mRNP; long non-coding RNA; lncRNA; transcriptome; translation

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Smith, J. E. (2015). Investigation of the mRNP and Transcriptome Regulated by Nonsense-Mediated RNA Decay. (Doctoral Dissertation). Case Western Reserve University School of Graduate Studies. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=case1421428941

Chicago Manual of Style (16^th Edition):

Smith, Jenna E. “Investigation of the mRNP and Transcriptome Regulated by Nonsense-Mediated RNA Decay.” 2015. Doctoral Dissertation, Case Western Reserve University School of Graduate Studies. Accessed March 05, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=case1421428941.

MLA Handbook (7^th Edition):

Smith, Jenna E. “Investigation of the mRNP and Transcriptome Regulated by Nonsense-Mediated RNA Decay.” 2015. Web. 05 Mar 2021.

Vancouver:

Smith JE. Investigation of the mRNP and Transcriptome Regulated by Nonsense-Mediated RNA Decay. [Internet] [Doctoral dissertation]. Case Western Reserve University School of Graduate Studies; 2015. [cited 2021 Mar 05]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=case1421428941.

Council of Science Editors:

Smith JE. Investigation of the mRNP and Transcriptome Regulated by Nonsense-Mediated RNA Decay. [Doctoral Dissertation]. Case Western Reserve University School of Graduate Studies; 2015. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=case1421428941

4. Barr, Jamie Ann, Ph.D. Regulation of the long non-coding RNA FAM83H-AS1 by human papillomavirus in cervical cancer.

Degree: PhD, Not Listed, 2019, West Virginia University

URL: https://doi.org/10.33915/etd.3926 ; https://researchrepository.wvu.edu/etd/3926

► Non-coding RNAs (NcRNAs), such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), have been found to be involved in a variety of critical biological… (more)

▼ Non-coding RNAs (NcRNAs), such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), have been found to be involved in a variety of critical biological processes, and dysregulation of ncRNAs have been involved with several human diseases including cancer. High-risk human papillomavirus (HPV) infection is one of the first events in the process of carcinogenesis in cervical and a subset of head and neck cancers. The expression of the viral oncoproteins E6 and E7 is essential in this process by inactivating the tumor suppressor proteins p53 and Rb, respectively, in addition to their interactions with other host proteins and regulation of ncRNAs. Our group identified novel regulation of host lncRNAs by HPV oncoprotein E6. More specifically, we discovered that a lncRNA known as FAM83H-AS1 is involved with proliferation, migration, and apoptosis in cervical cells, and high expression of this lncRNA correlates with poor overall cervical cancer patient survival. FAM83H-AS1 is a nuclear RNA, and mechanistically it is regulated through the E6-p300 pathway in a p53-independent manner. These findings provide knowledge of a specific lncRNA that could be studied further as a biomarker and/or therapeutic target not only in HPV-related cancers but also in other types of cancers where FAM83H-AS1 expression is dysregulated. In parallel with these studies, our group identified a specific subgroup of miRNAs that are induced during quiescence and processed by a non-canonical biogenesis pathway by using primary human cells. miRNA expression is dysregulated when cells undergo a reversible state of growth arrest known as quiescence. These primary (pri-)miRNAs are modified with a 2,2,7-trimethylguanosine (TMG)-cap such that they are processed downstream in an Exportin-1 (XPO1)-dependent manner, independent of the canonical Exportin-5 (XPO5) protein used for exportation to the cytoplasm. The discovery of a new alternative miRNA pathway in quiescent primary human cells opens the door to future studies in other types of cells, such as stem cells and cancer stem cells, where the state of quiescence is important in their biological functions. Advisors/Committee Members: J. Michael Ruppert, Laura F. Gibson, Laura F. Gibson.

Subjects/Keywords: FAM83H-AS1; long non-coding RNA; lncRNA; human papillomavirus; HPV; cervical cancer; Cancer Biology; Cell Biology; Molecular Biology; Oncology; Virus Diseases

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Barr, Jamie Ann, P. D. (2019). Regulation of the long non-coding RNA FAM83H-AS1 by human papillomavirus in cervical cancer. (Doctoral Dissertation). West Virginia University. Retrieved from https://doi.org/10.33915/etd.3926 ; https://researchrepository.wvu.edu/etd/3926

Chicago Manual of Style (16^th Edition):

Barr, Jamie Ann, Ph D. “Regulation of the long non-coding RNA FAM83H-AS1 by human papillomavirus in cervical cancer.” 2019. Doctoral Dissertation, West Virginia University. Accessed March 05, 2021. https://doi.org/10.33915/etd.3926 ; https://researchrepository.wvu.edu/etd/3926.

MLA Handbook (7^th Edition):

Barr, Jamie Ann, Ph D. “Regulation of the long non-coding RNA FAM83H-AS1 by human papillomavirus in cervical cancer.” 2019. Web. 05 Mar 2021.

Vancouver:

Barr, Jamie Ann PD. Regulation of the long non-coding RNA FAM83H-AS1 by human papillomavirus in cervical cancer. [Internet] [Doctoral dissertation]. West Virginia University; 2019. [cited 2021 Mar 05]. Available from: https://doi.org/10.33915/etd.3926 ; https://researchrepository.wvu.edu/etd/3926.

Council of Science Editors:

Barr, Jamie Ann PD. Regulation of the long non-coding RNA FAM83H-AS1 by human papillomavirus in cervical cancer. [Doctoral Dissertation]. West Virginia University; 2019. Available from: https://doi.org/10.33915/etd.3926 ; https://researchrepository.wvu.edu/etd/3926

University of Arizona

5. Forstedt, Joshua. Micropeptides Encoded by Non-Coding RNA .

Degree: 2020, University of Arizona

URL: http://hdl.handle.net/10150/650831

► Advancements in high throughput sequencing techniques have revealed different classes of non coding RNA contain short open reading frames (sORFS) with coding potential Similarly a… (more)

Subjects/Keywords: bifunctional RNA; lncRNA; micropeptide; ncRNA; Non-Coding RNA; Proteomics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Forstedt, J. (2020). Micropeptides Encoded by Non-Coding RNA . (Masters Thesis). University of Arizona. Retrieved from http://hdl.handle.net/10150/650831

Chicago Manual of Style (16^th Edition):

Forstedt, Joshua. “Micropeptides Encoded by Non-Coding RNA .” 2020. Masters Thesis, University of Arizona. Accessed March 05, 2021. http://hdl.handle.net/10150/650831.

MLA Handbook (7^th Edition):

Forstedt, Joshua. “Micropeptides Encoded by Non-Coding RNA .” 2020. Web. 05 Mar 2021.

Vancouver:

Forstedt J. Micropeptides Encoded by Non-Coding RNA . [Internet] [Masters thesis]. University of Arizona; 2020. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/10150/650831.

Council of Science Editors:

Forstedt J. Micropeptides Encoded by Non-Coding RNA . [Masters Thesis]. University of Arizona; 2020. Available from: http://hdl.handle.net/10150/650831

University of New South Wales

6. Mills, James. Human brain transcriptomic: towards understanding multiple system atrophy.

Degree: Biotechnology & Biomolecular Sciences, 2015, University of New South Wales

URL: http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true

► The human brain is a remarkably complex organ. It is a heterogeneous collection of billions of neurons and glial cells that are interconnected to form… (more)

▼ The human brain is a remarkably complex organ. It is a heterogeneous collection of billions of neurons and glial cells that are interconnected to form a finely tuned network capable of higher cognition. It is thought that the transcriptome may hold the key to understanding the complexity seen in the human brain. Next-generation sequencing allows the brain’s transcriptome to be probed at an unmatched resolution. This has uncovered a myriad of RNA elements, including RNA that does not code for protein, known as non-coding RNA (ncRNA). Originally, thought to be transcriptional noise, it is now appreciated that ncRNAs have numerous functional properties, with the ability to interact with DNA, other RNA molecules and proteins in different cellular compartments. It is thought that an increase in the number of ncRNAs being expressed throughout the brain, is a major driver of the increased intellectual capacity seen in humans and primates. The increase in the complexity of the human brain, also makes it prone to a number of different neurodegenerative and psychiatric diseases. These diseases are set to have dramatic economic and social impacts by the middle of the 21st century. To avert this looming epidemic an adequate understanding of the human brain is needed, so diagnostic tools and treatment targets can be developed. One such disorder is multiple system atrophy(MSA). MSA is a sporadic, rapidly progressing neurodegenerative disease. Currently no treatment exists and very little is known about the molecular basis of MSA. Before an understanding of the diseased brain can be reached an understanding of the healthy brain is necessary.Here, the transcriptome of grey matter (GM) and white matter (WM) from the superior frontal gyrus (SFG) of the healthy prefrontal cortex (PFC) was analysed. This revealed pervasive transcription and highlighted the differences in the transcriptome profiles of distinct cortical structures throughout the brain. A number of protein-coding genes were expressed exclusively in GM or WM, including gamma-aminobutyric acid A receptor, beta 2 (GABRB2) and P21 Protein (Cdc42/Rac)-Activated Kinase 2 (PAK2), respectively. Further, an interesting phenomenon known as isoform switching was detected in genes such as the G protein-coupled receptor 123 (GPR123). It was also revealed that in the healthy frontal cortex long intervening non-coding RNAs (lincRNAs), a subclass of long non-coding RNAs (lncRNAs), appear to be important drivers of tissue differentiation.To further establish the role of lincRNAs in the healthy human brain a comprehensive analysis of the oligodendrocyte maturation-associated lincRNA (OLMALINC) was carried out. It was found that OLMALINC is a recently evolved lincRNA with its highest expression levels in the human brain. OLMALINC was knocked down in human neurons and oligodendrocytes. Depletion of OLMALINC transcription revealed that it plays a role oligodendrocyte maturation. This study was one of the first functional characterisations of a lincRNA expressed in the human brain, and thus… Advisors/Committee Members: Janitz, Michael, Faculty of Science, UNSW.

Subjects/Keywords: Neurodegeneration; RNA-Seq; Long non-coding RNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Mills, J. (2015). Human brain transcriptomic: towards understanding multiple system atrophy. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true

Chicago Manual of Style (16^th Edition):

Mills, James. “Human brain transcriptomic: towards understanding multiple system atrophy.” 2015. Doctoral Dissertation, University of New South Wales. Accessed March 05, 2021. http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true.

MLA Handbook (7^th Edition):

Mills, James. “Human brain transcriptomic: towards understanding multiple system atrophy.” 2015. Web. 05 Mar 2021.

Vancouver:

Mills J. Human brain transcriptomic: towards understanding multiple system atrophy. [Internet] [Doctoral dissertation]. University of New South Wales; 2015. [cited 2021 Mar 05]. Available from: http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true.

Council of Science Editors:

Mills J. Human brain transcriptomic: towards understanding multiple system atrophy. [Doctoral Dissertation]. University of New South Wales; 2015. Available from: http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true

Freie Universität Berlin

7. Hanisch, Carlos. TFF3-dependent antiapoptotic effect is mediated by a miR-491-5p-PRINS-axis in human colorectal adenocarcinoma cells HT-29/B6.

Degree: 2017, Freie Universität Berlin

URL: http://dx.doi.org/10.17169/refubium-8050

► TFF3 is upregulated in mucosal injury, different ulcerative processes and cancer. It appears to have a relevance especially in the defense, maintenance and repair of… (more)

▼ TFF3 is upregulated in mucosal injury, different ulcerative processes and cancer. It appears to have a relevance especially in the defense, maintenance and repair of the intestinal epithelium and is also closely related to tumor invasion, resistance to apoptosis and metastasis. The over-expression of TFF3 in HT-29/B6 resulted in an increased protective effect against IFN-γ and TNF-α induced apoptosis and caused dysregulation of various non-coding RNAs. Anti- correlated expression pattern after transfection with miR-491-5p-mimic as well as reporter gene assays confirmed the direct interaction of miR-491-5p with the lncRNA PRINS in HT-29/B6/htff3. miR-491-5p was shown to inhibit PRINS- expression while PRINS had no discernible effect on miR-491-5p. Moreover, PRINS expression seemed to be controlled independently of TFF3 and miR-491-5p by IFN-γ- and TNF-α. Both non-coding RNAs hold an impact on the previously observed antiapoptotic phenotype. Compensation of the dysregulated noncoding RNAs increased the number of apoptotic cells after TRAIL-induced apoptosis. Mechanistically, Western blot analyzes confirmed the involvement of PI3K signaling pathway in this context. Regulation of miR-491-5p and PRINS by IFN-γ/TNF-α seemed to activate the PI3K signaling pathway independent of AKT through regulation of PDK1 and p70-S6K. In addition, the TFF3-mediated inhibitory effect on miR-491-5p was reversible by inhibition of the PI3K signaling pathway with small molecular inhibitors. PRINS and miR-491-5p had an impact on expression of a variety of mRNA that encode for pro-or anti- apoptotic proteins and the regulation of PMAIP1, FOXK1 and FOXK2 was confirmed at protein level, too. In further analyzes PRINS and PMAIP1 showed nuclear colocalization, indicating a direct interaction. PRINS revealed its influence on PMAIP1’s cellular localization in the nucleus especially in combination with TRAIL-induced apoptosis. PRINS seemed to be able to prevent the translocation of PMAIP1 from the nucleus to the cytoplasm. Finally, co- immunoprecipitation suggested PMAIP1’s direct binding on PRINS. In future, further mechanistic studies will be necessary in order to determine the impact of PRINS on regulation of PMAIP1. Analyzes under in vivo conditions will be indicated to prove the potential of PRINS as a therapeutic target in IBD, as a marker in metastatic cancers or as part of a TRAIL-based chemotherapy. Advisors/Committee Members: [email protected] (contact), m (gender), Prof. Dr. Dr. Ralf Einspanier (firstReferee), Prof. Dr. Tina Romeis (furtherReferee).

Subjects/Keywords: TFF3; ITF; micro RNA; long non coding RNA; miR; miR-491-5p; lncRNA; PRINS; colon cancer; apoptosis; PMAIP1; NOXA; 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

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APA (6^th Edition):

Hanisch, C. (2017). TFF3-dependent antiapoptotic effect is mediated by a miR-491-5p-PRINS-axis in human colorectal adenocarcinoma cells HT-29/B6. (Thesis). Freie Universität Berlin. Retrieved from http://dx.doi.org/10.17169/refubium-8050

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Hanisch, Carlos. “TFF3-dependent antiapoptotic effect is mediated by a miR-491-5p-PRINS-axis in human colorectal adenocarcinoma cells HT-29/B6.” 2017. Thesis, Freie Universität Berlin. Accessed March 05, 2021. http://dx.doi.org/10.17169/refubium-8050.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Hanisch, Carlos. “TFF3-dependent antiapoptotic effect is mediated by a miR-491-5p-PRINS-axis in human colorectal adenocarcinoma cells HT-29/B6.” 2017. Web. 05 Mar 2021.

Vancouver:

Hanisch C. TFF3-dependent antiapoptotic effect is mediated by a miR-491-5p-PRINS-axis in human colorectal adenocarcinoma cells HT-29/B6. [Internet] [Thesis]. Freie Universität Berlin; 2017. [cited 2021 Mar 05]. Available from: http://dx.doi.org/10.17169/refubium-8050.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Hanisch C. TFF3-dependent antiapoptotic effect is mediated by a miR-491-5p-PRINS-axis in human colorectal adenocarcinoma cells HT-29/B6. [Thesis]. Freie Universität Berlin; 2017. Available from: http://dx.doi.org/10.17169/refubium-8050

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Brno University of Technology

8. Abo Khayal, Layal. Transkriptomická charakterizace pomocí analýzy RNA-Seq dat: Transcriptomic Characterization Using RNA-Seq Data Analysis.

Degree: 2019, Brno University of Technology

URL: http://hdl.handle.net/11012/70129

► The high-throughputs sequence technologies produce a massive amount of data, that can reveal new genes, identify splice variants, and quantify gene expression genome-wide. However, the… (more)

Subjects/Keywords: RNA-Seq; diferenciální genová exprese (DGE); alternativní splicing; diferenciální použití exonů (DEU); dlouhá nekódující RNA (lncRNA); RNA-Seq; Differential Gene Expression (DGE); Alternative splicing; Differential Exon Usage (DEU); long non-coding RNA (lncRNA).

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Abo Khayal, L. (2019). Transkriptomická charakterizace pomocí analýzy RNA-Seq dat: Transcriptomic Characterization Using RNA-Seq Data Analysis. (Thesis). Brno University of Technology. Retrieved from http://hdl.handle.net/11012/70129

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Abo Khayal, Layal. “Transkriptomická charakterizace pomocí analýzy RNA-Seq dat: Transcriptomic Characterization Using RNA-Seq Data Analysis.” 2019. Thesis, Brno University of Technology. Accessed March 05, 2021. http://hdl.handle.net/11012/70129.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Abo Khayal, Layal. “Transkriptomická charakterizace pomocí analýzy RNA-Seq dat: Transcriptomic Characterization Using RNA-Seq Data Analysis.” 2019. Web. 05 Mar 2021.

Vancouver:

Abo Khayal L. Transkriptomická charakterizace pomocí analýzy RNA-Seq dat: Transcriptomic Characterization Using RNA-Seq Data Analysis. [Internet] [Thesis]. Brno University of Technology; 2019. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/11012/70129.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Abo Khayal L. Transkriptomická charakterizace pomocí analýzy RNA-Seq dat: Transcriptomic Characterization Using RNA-Seq Data Analysis. [Thesis]. Brno University of Technology; 2019. Available from: http://hdl.handle.net/11012/70129

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

West Virginia University

9. Brownmiller, Tayvia. Evidence of Y Chromosome Long Non-Coding RNAs involved in the Radiation Response of Male Non-Small Cell Lung Cancer Cells.

Degree: PhD, 2020, West Virginia University

URL: https://doi.org/10.33915/etd.7784 ; https://researchrepository.wvu.edu/etd/7784

► Non-small cell lung cancer (NSCLC) is the number one cause of cancer related mortality in the United States and worldwide. Advanced and therapeutically resistant… (more)

▼ Non-small cell lung cancer (NSCLC) is the number one cause of cancer related mortality in the United States and worldwide. Advanced and therapeutically resistant lung tumors contribute to the high rate of mortality from NSCLC, therefore there is a need for new methods of diagnosing and treating this disease. Long non-coding RNAs (lncRNAs) have been shown to be a crucial component of human molecular biology, regulating nearly every cellular pathway from chromatin condensation to transcription and translation. Furthermore, many lncRNAs have been classified as oncogenes or tumor suppressors, highlighting the various molecular mechanisms they are involved in regarding the formation and progression of cancer and their use as prognostic and diagnostic biomarkers has been proposed in numerous cancers, including NSCLC. Our group has discovered, for the first time, a three member family of Y chromosome lncRNAs (linc-SPRY3-2, lin-SPRY3-3, and linc-SPRY3-4) which regulate NSCLC cell response to ionizing radiation (IR). Briefly, the linc-SPRY3 family demonstrated a dose dependent induction of expression following exposure to IR in male radiosensitive NSCLC cell lines, but not in male radioresistant cell lines. This difference was revealed to be due to loss of the Y chromosome in the radioresistant cell lines. Using gain-of-function and loss-of-function experiments, we demonstrated statistically significant changes in cell viability and apoptosis in vitro. Furthermore, in vivo tumor growth delay assays showed a more radioresistant phenotype in tumors with knockdown of the linc-SPRY3 RNAs versus control tumors. We hypothesize linc-SPRY3-2/3/4 mediate their tumor suppressive effect via sequestration of the RNA binding protein IGF2BP3 demonstrated by CLIP and RNA degradation assays. Moreover, DNA FISH and bioinformatic analysis revealed a trending negative correlation in patient survival between loss of the Y chromosome and linc-SPRY3-2/3/4. These findings suggest that the linc-SPRY3 RNAs function as tumor suppressors by promoting cell death following IR through interactions with IGF2BP3, and could have potential as biomarkers in male NSCLC. Advisors/Committee Members: Elena Pugacheva, Scott Weed.

Subjects/Keywords: Long non-coding RNA; lncRNA; non-small cell lung cancer; NSCLC; radiation; radiosensitivity; radioresistance; Y chromosome; linc-SPRY3; Cancer Biology; Cell Biology; Genetics; Molecular Genetics; Radiation Medicine

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Brownmiller, T. (2020). Evidence of Y Chromosome Long Non-Coding RNAs involved in the Radiation Response of Male Non-Small Cell Lung Cancer Cells. (Doctoral Dissertation). West Virginia University. Retrieved from https://doi.org/10.33915/etd.7784 ; https://researchrepository.wvu.edu/etd/7784

Chicago Manual of Style (16^th Edition):

Brownmiller, Tayvia. “Evidence of Y Chromosome Long Non-Coding RNAs involved in the Radiation Response of Male Non-Small Cell Lung Cancer Cells.” 2020. Doctoral Dissertation, West Virginia University. Accessed March 05, 2021. https://doi.org/10.33915/etd.7784 ; https://researchrepository.wvu.edu/etd/7784.

MLA Handbook (7^th Edition):

Brownmiller, Tayvia. “Evidence of Y Chromosome Long Non-Coding RNAs involved in the Radiation Response of Male Non-Small Cell Lung Cancer Cells.” 2020. Web. 05 Mar 2021.

Vancouver:

Brownmiller T. Evidence of Y Chromosome Long Non-Coding RNAs involved in the Radiation Response of Male Non-Small Cell Lung Cancer Cells. [Internet] [Doctoral dissertation]. West Virginia University; 2020. [cited 2021 Mar 05]. Available from: https://doi.org/10.33915/etd.7784 ; https://researchrepository.wvu.edu/etd/7784.

Council of Science Editors:

Brownmiller T. Evidence of Y Chromosome Long Non-Coding RNAs involved in the Radiation Response of Male Non-Small Cell Lung Cancer Cells. [Doctoral Dissertation]. West Virginia University; 2020. Available from: https://doi.org/10.33915/etd.7784 ; https://researchrepository.wvu.edu/etd/7784

NSYSU

10. Tu, Ya-Ting. Identify Metastasis-related LncRNA in Breast Cancer by Microarray Approach.

Degree: Master, Biological Sciences, 2017, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0611117-145225

► Breast cancer occurs in mammary gland epithelial tissue and is the most commonly diagnosed cancer in women throughout the world. Previous studies indicated that invasion… (more)

▼ Breast cancer occurs in mammary gland epithelial tissue and is the most commonly diagnosed cancer in women throughout the world. Previous studies indicated that invasion of cancer cells was the major cause of the death, which had been a major challenge in the treatment of breast cancer. In human genome, recent studies reveal that there is < 2 % of the total genome sequence as protein-coding genes, however, at least 98 % of genome are transcribed into non-coding RNA (ncRNA). So far, the study of ncRNA is mainly concentrated on the microRNA (miRNA) and long non-coding RNA (lncRNA). An increasing number of researches reveal that ncRNAs have been shown to play an important role in gene regulation, normal cellular functions and disease processes. However, the detail biological function of lncRNA involving in breast metastasis is still unclear. In this study, we performed the expression profiles of two breast cancer cell lines, MB-231-P and MB-231-IV2-1, by microarray approach (Agilent SurePrint G3 Human V2 GE; including 34092 protein-coding genes and 8715 lncRNAs). After finishing the microarray profiling, we identified about 213 lncRNAs upregulated and 301 lncRNAs downregulated in MB-231-IV2-1 cell line compared to MB-231-P, respectively. Finally, we successfully identified several metastasis-related lncRNA candidates according microarray data and The Cancer Genome Atlas (TCGA). Among them, LINC01420 was selected for further study in this study. We assessed the expression levels of LINC01420 in breast cancer tissues by real-time PCR approach. Our data revealed that the expression levels of LINC01420 were significantly increased in breast cancer compared with adjacent normal tissues. We further identified the full length of LINC01420 by 5â and 3â rapid amplification of cDNA ends (RACE) in breast cancer cell. Our results revealed that LINC01420 could generate three splicing transcripts (V1, V2 and V3) via alternative splicing. Furthermore, knockdown of LINC01420 could suppress breast cancer cell growth by inducing cell cycle arrest at S phase. Interesting, the cell growth and the invasion ability of MB-231-IV2-1 cell significantly decreased after LINC01420-V1 and -V3 knockdown. These results implied that LINC01420-V1 and -V3 might be critical isoforms and exon 2 might be a functional oncogene region involving in modulating biological function in breast cancer. Our results suggest that LINC01420 might be a functional oncogene in breast tumorigenesis. Advisors/Committee Members: Kuo-Wang Tsai (committee member), Sung-Chou Li (chair), Huey-Wen Shyu (chair), Ming-Hong Tai (committee member).

Subjects/Keywords: Non-coding RNA; Metastasis; LINC01420; Long non-coding RNA; Breast cancer

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Tu, Y. (2017). Identify Metastasis-related LncRNA in Breast Cancer by Microarray Approach. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0611117-145225

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Tu, Ya-Ting. “Identify Metastasis-related LncRNA in Breast Cancer by Microarray Approach.” 2017. Thesis, NSYSU. Accessed March 05, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0611117-145225.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Tu, Ya-Ting. “Identify Metastasis-related LncRNA in Breast Cancer by Microarray Approach.” 2017. Web. 05 Mar 2021.

Vancouver:

Tu Y. Identify Metastasis-related LncRNA in Breast Cancer by Microarray Approach. [Internet] [Thesis]. NSYSU; 2017. [cited 2021 Mar 05]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0611117-145225.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Tu Y. Identify Metastasis-related LncRNA in Breast Cancer by Microarray Approach. [Thesis]. NSYSU; 2017. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0611117-145225

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

11. Gardner, Joseph Michael. The Contribution of Retrotransposons to the Transcriptomes of Murine Somatic Cells.

Degree: PhD, 2019, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/294025

► Retrotransposons comprise approximately 40% of the mouse genome. Once thought to be useless “junk” DNA, there is growing evidence that retrotransposons play crucial roles in… (more)

▼ Retrotransposons comprise approximately 40% of the mouse genome. Once thought to be useless “junk” DNA, there is growing evidence that retrotransposons play crucial roles in genome evolution and gene regulation, and contribute to the transcriptome. Several studies have found functional retrotransposon transcripts in the germline and during early development, but less is known about retrotransposon transcription in adult somatic cells. Retrotransposons are also responsible for generating gene copies in mammalian genomes (retrocopies), and there are several examples of retrocopies evolving into new genes, or being transcribed as non-coding RNA. Using computational approaches, I analyse RNA-seq data to assess the contribution of retrotransposons and retrocopies to the transcriptomes of adult mouse somatic cells, using purified naive B and T lymphocytes. First, I describe the transcriptomes generated using high-quality total RNA-seq data. Second, I quantify and characterise the retrotransposon content of these transcriptomes. Finally, I identify retrocopy transcripts and assess their relationship with the genes from which they originate. I found widespread inclusion of retrotransposons in somatic cell transcriptomes. These transcripts form distinct clusters based on retrotransposon sequence, with endogenous retroviruses being particularly prevalent in retrotransposon-rich transcripts. While these clusters are consistent between cell types, the individual retrotransposons transcribed show cell-type specificity. I also find evidence that retrotransposons may facilitate gene regulation by antisense transcripts. I demonstrate that a subset of retrocopies is transcribed, and the vast majority of these form RNA complementary to their parent mRNA, with high sequence identity. Using differential expression and proteome analysis, I present evidence for post-transcriptional regulation of parent transcripts by retrocopy RNA, possibly through stabilisation of the parent RNA. I also find that while retrocopy expression is not necessarily shared between cell types or mouse strains, certain parent transcripts tend to have an expressed retrocopy in multiple contexts. Overall, this thesis presents evidence of an important role for retrotransposons and retrocopies in the adult somatic transcriptome, and sets the stage for further investigation to experimentally elucidate the functions of these transcripts.

Subjects/Keywords: bioinformatics; RNA-seq; transcriptome; non-coding RNA; ncRNA; long non-coding RNA; lncRNA; retrotransposon; transposon; transposable element; retrogene; retrocopy; pseudogene; RNA; sequencing; antisense; endogenous retrovirus; LINE; SINE; LTR; transcriptomics; genome; epigenetics; lymphocytes; mouse; genetics

10 more images…

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gardner, J. M. (2019). The Contribution of Retrotransposons to the Transcriptomes of Murine Somatic Cells. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/294025

Chicago Manual of Style (16^th Edition):

Gardner, Joseph Michael. “The Contribution of Retrotransposons to the Transcriptomes of Murine Somatic Cells.” 2019. Doctoral Dissertation, University of Cambridge. Accessed March 05, 2021. https://www.repository.cam.ac.uk/handle/1810/294025.

MLA Handbook (7^th Edition):

Gardner, Joseph Michael. “The Contribution of Retrotransposons to the Transcriptomes of Murine Somatic Cells.” 2019. Web. 05 Mar 2021.

Vancouver:

Gardner JM. The Contribution of Retrotransposons to the Transcriptomes of Murine Somatic Cells. [Internet] [Doctoral dissertation]. University of Cambridge; 2019. [cited 2021 Mar 05]. Available from: https://www.repository.cam.ac.uk/handle/1810/294025.

Council of Science Editors:

Gardner JM. The Contribution of Retrotransposons to the Transcriptomes of Murine Somatic Cells. [Doctoral Dissertation]. University of Cambridge; 2019. Available from: https://www.repository.cam.ac.uk/handle/1810/294025

University of Cambridge

12. Gardner, Joseph Michael. The contribution of retrotransposons to the transcriptomes of murine somatic cells.

Degree: PhD, 2019, University of Cambridge

URL: https://doi.org/10.17863/CAM.41133 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.782867

► Retrotransposons comprise approximately 40% of the mouse genome. Once thought to be useless "junk" DNA, there is growing evidence that retrotransposons play crucial roles in… (more)

▼ Retrotransposons comprise approximately 40% of the mouse genome. Once thought to be useless "junk" DNA, there is growing evidence that retrotransposons play crucial roles in genome evolution and gene regulation, and contribute to the transcriptome. Several studies have found functional retrotransposon transcripts in the germline and during early development, but less is known about retrotransposon transcription in adult somatic cells. Retrotransposons are also responsible for generating gene copies in mammalian genomes (retrocopies), and there are several examples of retrocopies evolving into new genes, or being transcribed as non-coding RNA. Using computational approaches, I analyse RNA-seq data to assess the contribution of retrotransposons and retrocopies to the transcriptomes of adult mouse somatic cells, using purified naive B and T lymphocytes. First, I describe the transcriptomes generated using high-quality total RNA-seq data. Second, I quantify and characterise the retrotransposon content of these transcriptomes. Finally, I identify retrocopy transcripts and assess their relationship with the genes from which they originate. I found widespread inclusion of retrotransposons in somatic cell transcriptomes. These transcripts form distinct clusters based on retrotransposon sequence, with endogenous retroviruses being particularly prevalent in retrotransposon-rich transcripts. While these clusters are consistent between cell types, the individual retrotransposons transcribed show cell-type specificity. I also find evidence that retrotransposons may facilitate gene regulation by antisense transcripts. I demonstrate that a subset of retrocopies is transcribed, and the vast majority of these form RNA complementary to their parent mRNA, with high sequence identity. Using differential expression and proteome analysis, I present evidence for post-transcriptional regulation of parent transcripts by retrocopy RNA, possibly through stabilisation of the parent RNA. I also find that while retrocopy expression is not necessarily shared between cell types or mouse strains, certain parent transcripts tend to have an expressed retrocopy in multiple contexts. Overall, this thesis presents evidence of an important role for retrotransposons and retrocopies in the adult somatic transcriptome, and sets the stage for further investigation to experimentally elucidate the functions of these transcripts.

Subjects/Keywords: bioinformatics; RNA-seq; transcriptome; non-coding RNA; ncRNA; long non-coding RNA; lncRNA; retrotransposon; transposon; transposable element; retrogene; retrocopy; pseudogene; RNA; sequencing; antisense; endogenous retrovirus; LINE; SINE; LTR; transcriptomics; genome; epigenetics; lymphocytes; mouse; genetics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gardner, J. M. (2019). The contribution of retrotransposons to the transcriptomes of murine somatic cells. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.41133 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.782867

Chicago Manual of Style (16^th Edition):

Gardner, Joseph Michael. “The contribution of retrotransposons to the transcriptomes of murine somatic cells.” 2019. Doctoral Dissertation, University of Cambridge. Accessed March 05, 2021. https://doi.org/10.17863/CAM.41133 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.782867.

MLA Handbook (7^th Edition):

Gardner, Joseph Michael. “The contribution of retrotransposons to the transcriptomes of murine somatic cells.” 2019. Web. 05 Mar 2021.

Vancouver:

Gardner JM. The contribution of retrotransposons to the transcriptomes of murine somatic cells. [Internet] [Doctoral dissertation]. University of Cambridge; 2019. [cited 2021 Mar 05]. Available from: https://doi.org/10.17863/CAM.41133 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.782867.

Council of Science Editors:

Gardner JM. The contribution of retrotransposons to the transcriptomes of murine somatic cells. [Doctoral Dissertation]. University of Cambridge; 2019. Available from: https://doi.org/10.17863/CAM.41133 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.782867

Uppsala University

13. Elhorst, Paula. Regulation of TGFß signalling by the long noncoding RNA TGFß2-AS1.

Degree: Biology Education Centre, 2018, Uppsala University

URL: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-362083

► Long noncoding RNAs have been shown to regulate many signalling pathways and their expression has been linked to the development of many cancers. Here… (more)

Subjects/Keywords: TGFß; signalling; lncRNA; long non-coding RNA; regulation; TGFß2-AS1; cancer; PRC2; Polycomb Repressive Complex; EMT; eptihelial-to-mesenchymal transistion; Biochemistry and Molecular Biology; Biokemi och molekylärbiologi

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Elhorst, P. (2018). Regulation of TGFß signalling by the long noncoding RNA TGFß2-AS1. (Thesis). Uppsala University. Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-362083

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Elhorst, Paula. “Regulation of TGFß signalling by the long noncoding RNA TGFß2-AS1.” 2018. Thesis, Uppsala University. Accessed March 05, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-362083.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Elhorst, Paula. “Regulation of TGFß signalling by the long noncoding RNA TGFß2-AS1.” 2018. Web. 05 Mar 2021.

Vancouver:

Elhorst P. Regulation of TGFß signalling by the long noncoding RNA TGFß2-AS1. [Internet] [Thesis]. Uppsala University; 2018. [cited 2021 Mar 05]. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-362083.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Elhorst P. Regulation of TGFß signalling by the long noncoding RNA TGFß2-AS1. [Thesis]. Uppsala University; 2018. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-362083

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Manchester

14. Pettini, Tom. The role of novel long non-coding RNAs in Hox gene regulation.

Degree: 2013, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:190102

► Whole genome transcriptome analysis has revealed that a large proportion of the genome in higher metazoa is transcribed, yet only a small proportion of this… (more)

▼ Whole genome transcriptome analysis has revealed that a large proportion of the genome in higher metazoa is transcribed, yet only a small proportion of this transcription is protein-coding. One possible function of non-coding transcription is that it enables complex and diverse body plans to evolve through variation in deployment of a relatively common set of protein-coding genes. Functional studies suggest that long non-coding RNAs (lncRNAs) regulate gene expression via diverse mechanisms, operating in both cis and trans to activate or repress target genes. An emerging theme common to lncRNA function is interaction with proteins that modify chromatin and mediate epigenetic regulation. The Hox gene complexes are particularly rich in lncRNAs and require precise and fine-tuned expression to deploy Hox transcription factors throughout development. Here we identify and functionally characterize two novel lncRNAs within the D. melanogaster Hox complex, in the interval between Scr and Antp. We use nascent transcript fluorescent in-situ hybridization (ntFISH) to characterize the embryonic expression patterns of each lncRNA with respect to flanking Hox genes, and to analyze co-transcription within individual nuclei. We find that the transcription of one lncRNA, ncX, is an initial response to early transcription factors and may activate Scr expression, while transcription of the other lncRNA, ncPRE is consistent with activation and/or maintenance of Scr expression. ntFISH performed in D.virilis embryos revealed the presence of a lncRNA ortholog with highly similar expression to ncX, indicating functional conservation of lncRNA transcription across ~60 million years of evolution. We identify the ncPRE lncRNA locus as a binding site for multiple proteins associated with Polycomb/Trithorax response elements (PREs/TREs) and show that DNA encoding the ncPRE lncRNA functions as a bona fide PRE, mediating trans-interactions between chromosomes and silencing of nearby genes. We find that transcription through the ncPRE DNA relieves silencing, suggesting a role for endogenous transcription of the ncPRE lncRNA in relieving Polycomb-silencing and enabling Scr activation. We demonstrate that both lncRNA transcripts are required for proper Scr expression, and over-expression of either lncRNAs from ectopic genomic loci has no effect on Scr expression, but ectopic expression at the endogenous locus is associated with ectopic Scr activation, indicating that the lncRNA-mediated regulation functions locally at the site of transcription on the chromosome. ncX may mediate transvection effects previously observed at the Scr locus, independent of the protein Zeste. Together our results support a model of competing mechanisms in the regulation of Scr expression - a background of Polycomb repression acting from the ncPRE locus, which in the first thoracic segment is counteracted by lncRNA transcription and Trithorax binding to ncPRE, enabling activation and maintenance of Scr expression. This work provides a functional insight into the complex… Advisors/Committee Members: PAPALOPULU, NANCY A, Papalopulu, Nancy, Ronshaugen, Matthew.

Subjects/Keywords: long non-coding RNA; Hox genes

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Pettini, T. (2013). The role of novel long non-coding RNAs in Hox gene regulation. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:190102

Chicago Manual of Style (16^th Edition):

Pettini, Tom. “The role of novel long non-coding RNAs in Hox gene regulation.” 2013. Doctoral Dissertation, University of Manchester. Accessed March 05, 2021. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:190102.

MLA Handbook (7^th Edition):

Pettini, Tom. “The role of novel long non-coding RNAs in Hox gene regulation.” 2013. Web. 05 Mar 2021.

Vancouver:

Pettini T. The role of novel long non-coding RNAs in Hox gene regulation. [Internet] [Doctoral dissertation]. University of Manchester; 2013. [cited 2021 Mar 05]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:190102.

Council of Science Editors:

Pettini T. The role of novel long non-coding RNAs in Hox gene regulation. [Doctoral Dissertation]. University of Manchester; 2013. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:190102

15. Coyne, Victoria Lee. Characterization of long non-coding RNAs in the Hox Complex of Drosophila.

Degree: 2016, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:305935

► Long non-coding RNAs (lncRNAs) are often defined as transcripts >200nts that have no discernable protein-coding ability (Quinn and Chang, 2016). Although relatively little is understood… (more)

▼ Long non-coding RNAs (lncRNAs) are often defined as transcripts >200nts that have no discernable protein-coding ability (Quinn and Chang, 2016). Although relatively little is understood about the molecular mechanisms of lncRNA function, they have established roles in regulation of gene expression during development, cell differentiation and pluripotency (Fatica and Bozzoni, 2014; Luo et al., 2016; Quinn and Chang, 2016; Rinn and Chang, 2012) across vastly diverse organisms ranging from plants to humans (Ulitsky and Bartel, 2013). LncRNAs have also been associated with numerous pathological conditions, such as cancers (Brunner et al., 2012), cardiovascular disease and neurodegeneration (Chen et al., 2013). Investigations into lncRNAs in wide ranging organisms, have revealed that many influence gene activity by forming ribonucleoprotein complexes that affect the conformational state of chromatin (Rinn and Chang, 2012). A genomic region that has revealed several functional lncRNAs in diverse organisms is the Hox complex (Pauli et al., 2011; Pettini, 2012; Rinn et al., 2007). The Hox complex encodes a set of transcription factors (TFs), physically clustered in the genome, which provide morphological identity along the anterior to posterior axis of developing embryos (Mallo and Alonso, 2013), throughout the majority of bilatarian animals (Moreno et al., 2011). Misexpression or mutation of Hox genes causes morphological and pathophysiological defects (Quinonez and Innis, 2014). We investigated clustering of lncRNAs throughout the D. melanogaster genome using available annotations and carried out RNA-seq in D. virilis to expand the repertoire of lncRNAs and identify clusters of lncRNAs. We found the Hox complex to be heavily enriched with lncRNAs in both organisms, and syntenic transcripts from D. melanogaster could be identified in D. pseudoobscura and D. virilis. Several lncRNAs aligned with polycomb response elements (PREs); transcription of PREs has previously been linked to a switch in their activity (Herzog et al., 2014). However, we found that transcribed PREs in D. melanogaster move positions relative to the protein-coding genes in other drosophilids, whilst the transcriptional units remain in the same syntenic region. Conservation of syntenic transcripts without evidence of remaining a PRE suggest that the transcription is not linked to PRE function, agreeing with recent findings that transcription of PREs does not affect their function (Kassis and Muller, 2015). We investigated functions of a novel lncRNA and adjacent PRE in the Hox complex by ectopic expression and utilization of other genetic manipulation tools. Overexpression of either the lncRNA or PRE and partial duplication of the lncRNA caused phenotypes such as missing halteres and/or T3 legs, misshaped T3 legs or malformed abdominal segments. The observations that ectopic expression of this lncRNA and an adjacent regulatory element from the Hox complex causes phenotypes that can be linked to adjacent Hox gene misregulation, Antp and Ubx, suggest that they… Advisors/Committee Members: O'KEEFE, RAYMOND RT, GRIFFITHS-JONES, SAMUEL SR, O'Keefe, Raymond, Griffiths-Jones, Samuel, Ronshaugen, Matthew.

Subjects/Keywords: long non-coding RNA evolution development Hox

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APA (6^th Edition):

Coyne, V. L. (2016). Characterization of long non-coding RNAs in the Hox Complex of Drosophila. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:305935

Chicago Manual of Style (16^th Edition):

Coyne, Victoria Lee. “Characterization of long non-coding RNAs in the Hox Complex of Drosophila.” 2016. Doctoral Dissertation, University of Manchester. Accessed March 05, 2021. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:305935.

MLA Handbook (7^th Edition):

Coyne, Victoria Lee. “Characterization of long non-coding RNAs in the Hox Complex of Drosophila.” 2016. Web. 05 Mar 2021.

Vancouver:

Coyne VL. Characterization of long non-coding RNAs in the Hox Complex of Drosophila. [Internet] [Doctoral dissertation]. University of Manchester; 2016. [cited 2021 Mar 05]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:305935.

Council of Science Editors:

Coyne VL. Characterization of long non-coding RNAs in the Hox Complex of Drosophila. [Doctoral Dissertation]. University of Manchester; 2016. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:305935

University of Manchester

16. Pettini, Tom. The role of novel long non-coding RNAs in Hox gene regulation.

Degree: PhD, 2013, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/the-role-of-novel-long-noncoding-rnas-in-hox-gene-regulation(c8e44900-3ac0-40be-8ec6-b50179381d17).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.647365

► Whole genome transcriptome analysis has revealed that a large proportion of the genome in higher metazoa is transcribed, yet only a small proportion of this… (more)

▼ Whole genome transcriptome analysis has revealed that a large proportion of the genome in higher metazoa is transcribed, yet only a small proportion of this transcription is protein-coding. One possible function of non-coding transcription is that it enables complex and diverse body plans to evolve through variation in deployment of a relatively common set of protein-coding genes. Functional studies suggest that long non-coding RNAs (lncRNAs) regulate gene expression via diverse mechanisms, operating in both cis and trans to activate or repress target genes. An emerging theme common to lncRNA function is interaction with proteins that modify chromatin and mediate epigenetic regulation. The Hox gene complexes are particularly rich in lncRNAs and require precise and fine-tuned expression to deploy Hox transcription factors throughout development. Here we identify and functionally characterize two novel lncRNAs within the D. melanogaster Hox complex, in the interval between Scr and Antp. We use nascent transcript fluorescent in-situ hybridization (ntFISH) to characterize the embryonic expression patterns of each lncRNA with respect to flanking Hox genes, and to analyze co-transcription within individual nuclei. We find that the transcription of one lncRNA, ncX, is an initial response to early transcription factors and may activate Scr expression, while transcription of the other lncRNA, ncPRE is consistent with activation and/or maintenance of Scr expression. ntFISH performed in D.virilis embryos revealed the presence of a lncRNA ortholog with highly similar expression to ncX, indicating functional conservation of lncRNA transcription across ~60 million years of evolution. We identify the ncPRE lncRNA locus as a binding site for multiple proteins associated with Polycomb/Trithorax response elements (PREs/TREs) and show that DNA encoding the ncPRE lncRNA functions as a bona fide PRE, mediating trans-interactions between chromosomes and silencing of nearby genes. We find that transcription through the ncPRE DNA relieves silencing, suggesting a role for endogenous transcription of the ncPRE lncRNA in relieving Polycomb-silencing and enabling Scr activation. We demonstrate that both lncRNA transcripts are required for proper Scr expression, and over-expression of either lncRNAs from ectopic genomic loci has no effect on Scr expression, but ectopic expression at the endogenous locus is associated with ectopic Scr activation, indicating that the lncRNA-mediated regulation functions locally at the site of transcription on the chromosome. ncX may mediate transvection effects previously observed at the Scr locus, independent of the protein Zeste. Together our results support a model of competing mechanisms in the regulation of Scr expression - a background of Polycomb repression acting from the ncPRE locus, which in the first thoracic segment is counteracted by lncRNA transcription and Trithorax binding to ncPRE, enabling activation and maintenance of Scr expression. This work provides a functional insight into the complex…

Subjects/Keywords: 572.8; long non-coding RNA; Hox genes

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Pettini, T. (2013). The role of novel long non-coding RNAs in Hox gene regulation. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/the-role-of-novel-long-noncoding-rnas-in-hox-gene-regulation(c8e44900-3ac0-40be-8ec6-b50179381d17).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.647365

Chicago Manual of Style (16^th Edition):

Pettini, Tom. “The role of novel long non-coding RNAs in Hox gene regulation.” 2013. Doctoral Dissertation, University of Manchester. Accessed March 05, 2021. https://www.research.manchester.ac.uk/portal/en/theses/the-role-of-novel-long-noncoding-rnas-in-hox-gene-regulation(c8e44900-3ac0-40be-8ec6-b50179381d17).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.647365.

MLA Handbook (7^th Edition):

Pettini, Tom. “The role of novel long non-coding RNAs in Hox gene regulation.” 2013. Web. 05 Mar 2021.

Vancouver:

Pettini T. The role of novel long non-coding RNAs in Hox gene regulation. [Internet] [Doctoral dissertation]. University of Manchester; 2013. [cited 2021 Mar 05]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/the-role-of-novel-long-noncoding-rnas-in-hox-gene-regulation(c8e44900-3ac0-40be-8ec6-b50179381d17).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.647365.

Council of Science Editors:

Pettini T. The role of novel long non-coding RNAs in Hox gene regulation. [Doctoral Dissertation]. University of Manchester; 2013. Available from: https://www.research.manchester.ac.uk/portal/en/theses/the-role-of-novel-long-noncoding-rnas-in-hox-gene-regulation(c8e44900-3ac0-40be-8ec6-b50179381d17).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.647365

University of Houston

17. -9636-8146. Long Noncoding RNAs in Cardiac and Skeletal Muscle Differentiation during Mouse Embryogenesis.

Degree: PhD, Biology, 2017, University of Houston

URL: http://hdl.handle.net/10657/4789

► Development is a multistep process that involves a close co-ordination of gene regulatory networks. Lineage specification is a crucial step involved in embryogenesis and understanding… (more)

▼ Development is a multistep process that involves a close co-ordination of gene regulatory networks. Lineage specification is a crucial step involved in embryogenesis and understanding the significant steps involved in gene regulatory mechanisms is critical. Long non-coding RNAs, longer than 200 nucleotides have been identified as a new regulator of many molecular mechanisms involved in the development and pathological conditions. From the genome-wide transcriptome analysis of Mesp1-lineage reporter mouse ESC line (UH3), we identified mesoderm specific lncRNAs, from which we selected a subset of 12 lncRNAs for functional characterization. Of this, we identified lincRNA Platr14 to have a positive expression in vivo in cardiac plate and somites of E9.5 mouse embryos. Platr14 was seen enriched in vitro in the undifferentiated AB2.2 ES cell line, and the inhibition of Platr14 showed a decrease in the beating percentage of embryoid bodies which correlated with a deregulation of the mesoderm and cardiac-specific genes. Since Platr14 was enriched in the region of the myotome of E9.5 Embryos, we studied its role in myogenesis. Platr14 showed enrichment in skeletal muscle and the tongue in E15.5 embryonic mouse tissues. Knockdown of Platr14 in C2C12 mesenchymal cell line showed a deregulation of myogenic markers as well as a reduction in the fusion rate for the myotube formation. Though overexpression of Platr14 showed an up-regulation of the main myogenic markers, it did not show any significant change in the myotube formation rate. Strikingly, Platr14 overexpression in the terminal stages showed a repression in the expression of terminal myogenic markers. The whole transcriptome analysis by RNA-Sequencing of differentiating C2C12 myoblasts at day 2, showed a down-regulation of genes associated with the mesenchymal formation, somitogenesis, metabolism, cell migration, calcium transport and cell-cell signaling all related to developmental changes. In-silico analysis identified conservation of 3’ UTR of Platr14 across species as well as unique sites complementary to about 29 DNA binding sites of the mouse genome. Gene Ontology studies identified these DNA binding sites to have roles related to developmental processes. In this dissertation, we identified lincRNA Platr14, to have a novel role in mesoderm lineage driving the cardiac and skeletal myogenic differentiation. Advisors/Committee Members: Schwartz, Robert J. (advisor), Lin, Chin-Yo (committee member), Frigo, Daniel E. (committee member), Chen, Li (committee member), Cooney, Austin J. (committee member).

Subjects/Keywords: Long non coding RNA; RNA; Platr14; Cardiac; Skeletal myogenesis; Differentiation

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

-9636-8146. (2017). Long Noncoding RNAs in Cardiac and Skeletal Muscle Differentiation during Mouse Embryogenesis. (Doctoral Dissertation). University of Houston. Retrieved from http://hdl.handle.net/10657/4789

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Chicago Manual of Style (16^th Edition):

-9636-8146. “Long Noncoding RNAs in Cardiac and Skeletal Muscle Differentiation during Mouse Embryogenesis.” 2017. Doctoral Dissertation, University of Houston. Accessed March 05, 2021. http://hdl.handle.net/10657/4789.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

MLA Handbook (7^th Edition):

-9636-8146. “Long Noncoding RNAs in Cardiac and Skeletal Muscle Differentiation during Mouse Embryogenesis.” 2017. Web. 05 Mar 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

-9636-8146. Long Noncoding RNAs in Cardiac and Skeletal Muscle Differentiation during Mouse Embryogenesis. [Internet] [Doctoral dissertation]. University of Houston; 2017. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/10657/4789.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Council of Science Editors:

-9636-8146. Long Noncoding RNAs in Cardiac and Skeletal Muscle Differentiation during Mouse Embryogenesis. [Doctoral Dissertation]. University of Houston; 2017. Available from: http://hdl.handle.net/10657/4789

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Michigan State University

18. Achawanantakun, Rujira. Identification and analysis of non-coding RNAs in large scale genomic data.

Degree: 2014, Michigan State University

URL: http://etd.lib.msu.edu/islandora/object/etd:2757

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Thesis Ph. D. Michigan State University. Computer Science 2014.

The high-throughput sequencing technologies have created the opportunity of large-scale transcriptome analyses and intensify attention on… (more)

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Thesis Ph. D. Michigan State University. Computer Science 2014.

The high-throughput sequencing technologies have created the opportunity of large-scale transcriptome analyses and intensify attention on the study of non-coding RNAs (ncRNAs). NcRNAs pay important roles in many cellular processes. For example, transfer RNAs and ribosomal RNAs are involved in protein translation process; micro RNAs regulate gene expression; long ncRNAs are found to associate with many human diseases ranging from autism to cancer.Many ncRNAs function through both their sequences and secondary structures. Thus, accurate secondary structure prediction provides important information to understand the tertiary structures and thus the functions of ncRNAs.The state-of-the-art ncRNA identification tools are mainly based on two approaches. The first approach is a comparative structure analysis, which determines the consensus structure from homologous ncRNAs. Structure prediction is a costly process, because the size of the putative structures increases exponentially with the sequence length. Thus it is not practical for very long ncRNAs such as lncRNAs. The accuracy of current structure prediction tools is still not satisfactory, especially on sequences containing pseudoknots. An alternative identification approach that has been increasingly popular is sequence based expression analysis, which relies on next generation sequencing (NGS) technologies for quantifying gene expression on a genome-wide scale. The specific expression patterns are used to identify the type of ncRNAs. This method therefore is limited to ncRNAs that have medium to high expression levels and have the unique expression patterns that are different from other ncRNAs. In this work, we address the challenges presented in ncRNA identification using different approaches. To be specific, we have proposed four tools, grammar-string based alignment, KnotShape, KnotStructure, and lncRNA-ID. Grammar-string is a novel ncRNA secondary structure representation that encodes an ncRNA's sequence and secondary structure in the parameter space of a context-free grammar and a full RNA grammar including pseudoknots. It simplifies a complicated structure alignment to a simple grammar string-based alignment. Also, grammar-string-based alignment incorporates both sequence and structure into multiple sequence alignment. Thus, we can then enhance the speed of alignment and achieve an accurate consensus structure. KnotShape and KnotStructure focus on reducing the size of the structure search space to enhance the speed of a structure prediction process. KnotShape predicts the best shape by grouping similar structures together and applying SVM classification to select the best representative shape. KnotStructure improve the performance of structure prediction by using grammar-string based-alignment and the predicted shape output by KnotShape.lncRNA-ID is specially designed for lncRNA identification. It incorporates balanced random forest learning to construct a classification model to distinguish…

Advisors/Committee Members: Sun, Yanni, Brown, Titus, Tan, Pang-Ning, Cole, James.

Subjects/Keywords: Non-coding RNA – Identification; Non-coding RNA – Analysis; Genomics; Support vector machines; Non-coding RNA; Computer science; Biology; Random forest; Long non-coding RNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Achawanantakun, R. (2014). Identification and analysis of non-coding RNAs in large scale genomic data. (Thesis). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:2757

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Achawanantakun, Rujira. “Identification and analysis of non-coding RNAs in large scale genomic data.” 2014. Thesis, Michigan State University. Accessed March 05, 2021. http://etd.lib.msu.edu/islandora/object/etd:2757.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Achawanantakun, Rujira. “Identification and analysis of non-coding RNAs in large scale genomic data.” 2014. Web. 05 Mar 2021.

Vancouver:

Achawanantakun R. Identification and analysis of non-coding RNAs in large scale genomic data. [Internet] [Thesis]. Michigan State University; 2014. [cited 2021 Mar 05]. Available from: http://etd.lib.msu.edu/islandora/object/etd:2757.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Achawanantakun R. Identification and analysis of non-coding RNAs in large scale genomic data. [Thesis]. Michigan State University; 2014. Available from: http://etd.lib.msu.edu/islandora/object/etd:2757

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

19. Floriot, Océane. Virus de l’Hépatite B et transcription cellulaire : impact de la protéine HBx et de ses interactions avec les ARNs non-codants : Hepatits B virus and host cell transcription : impact of the HBx protein and its interaction with non coding RNA.

Degree: Docteur es, Infectiologie, 2018, Lyon

URL: http://www.theses.fr/2018LYSE1319

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Le virus de l'hépatite B (VHB) reste un problème de santé majeur dans le monde malgré la disponibilité du vaccin. Le VHB n’est pas éradiqué… (more)

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Le virus de l'hépatite B (VHB) reste un problème de santé majeur dans le monde malgré la disponibilité du vaccin. Le VHB n’est pas éradiqué par les thérapies actuelles et 240 millions de personnes infectées chroniquement restent à risque de développer une cirrhose du foie et un carcinome hépatocellulaire (CHC).Le VHB est un petit virus hépatotrope doté d'un génome à ADN double brin partiel (ADNrc). Après infection l'ADNrc est converti en ADN épisomal (ADNccc) qui est ensuite organisé en minichromosome viral, qui est le modèle pour la transcription et qui initie la réplication. La protéine de l'hépatite B x (HBx) est recrutée sur l'ADNccc pour initier et maintenir la transcription de l'ADN ccc. HBx cible aussi directement des gènes cellulaires impliqué dans le développement du CHC.Nous avons utilisé une approche ChIP-Seq pour identifier toutes les cibles génomiques de HBx dans les cellules qui répliquent le VHB. Les cibles HBx sont à la fois des gènes codant les protéines et des ARNnc (75 miARN et 34 lncRNA). Nous avons montré que HBx réprimait un sous-ensemble de miARNs qui réguleraient négativement la réplication virale (ex : miR-24) et des miARNs impliqués dans le développement du CHC (ex : miR-21). Parmi les lncARNs ciblés pour HBx, nous avons étudié DLEU2, qui est fortement surexprimé dans l’infection par le VHB et le CHC. Nous avons en outre montré que DLEU2 lie à la fois HBx et l’histone méthyltransférase Ezh2, la sous-unité catalytique du complexe répressif PRC2. L'interaction avec DLEU2 et HBx relie les fonctions Ezh2/PRC2 conduisant à l'activation constitutive d'un sous-ensemble de gènes cibles d'Ezh2 qui sont normalement conservés dans un état réprimé. Nous avons également montré que l’interaction de HBx avec DLEU2 se produisait sur le minichromosome de l’ADNccc où elle stimulait la transcription/réplication du virus. Enfin, nous avons caractérisé par ATAC-Seq les changements d'accessibilité de la chromatine imposés par HBV dans les hépatocytes humains primaires

Hepatitis B virus (HBV) remains a major health problem worldwide despite the availability of the vaccine. No cure is available for the 240 million peoples chronically infected with HBV that are at risk to develop liver cirrhosis and hepatocellular carcinoma (HCC). Viral suppression, achieved by long term treatment with nucleotides analogues (NUCs), impacts on liver fibrosis and prevents liver decompensation but HCC risk is not reduced in the first 5 years of treatment. HBV is a small hepatotropic virus with a partially double strand DNA (rcDNA) genome. After hepatocyte infection the rcDNA is converted into the cccDNA episome that is then organized into a viral minichromosome that is the template for all viral transcripts and initiates replication. The hepatitis B x protein (HBx) is recruited on the cccDNA and is required to launch and maintain cccDNA transcription. HBx has also been shown to directly target cellular genes and this has been related to HCC development.We used a ChIP-Seq approach to determine the full repertoire of HBx genomic…

Advisors/Committee Members: Levrero, Massimo (thesis director).

Subjects/Keywords: Virus de l’Hépatite B; HBx; Long non-coding RNA; Hepatitis B virus; HBx; Long non-coding RNA; 570

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Floriot, O. (2018). Virus de l’Hépatite B et transcription cellulaire : impact de la protéine HBx et de ses interactions avec les ARNs non-codants : Hepatits B virus and host cell transcription : impact of the HBx protein and its interaction with non coding RNA. (Doctoral Dissertation). Lyon. Retrieved from http://www.theses.fr/2018LYSE1319

Chicago Manual of Style (16^th Edition):

Floriot, Océane. “Virus de l’Hépatite B et transcription cellulaire : impact de la protéine HBx et de ses interactions avec les ARNs non-codants : Hepatits B virus and host cell transcription : impact of the HBx protein and its interaction with non coding RNA.” 2018. Doctoral Dissertation, Lyon. Accessed March 05, 2021. http://www.theses.fr/2018LYSE1319.

MLA Handbook (7^th Edition):

Floriot, Océane. “Virus de l’Hépatite B et transcription cellulaire : impact de la protéine HBx et de ses interactions avec les ARNs non-codants : Hepatits B virus and host cell transcription : impact of the HBx protein and its interaction with non coding RNA.” 2018. Web. 05 Mar 2021.

Vancouver:

Floriot O. Virus de l’Hépatite B et transcription cellulaire : impact de la protéine HBx et de ses interactions avec les ARNs non-codants : Hepatits B virus and host cell transcription : impact of the HBx protein and its interaction with non coding RNA. [Internet] [Doctoral dissertation]. Lyon; 2018. [cited 2021 Mar 05]. Available from: http://www.theses.fr/2018LYSE1319.

Council of Science Editors:

Floriot O. Virus de l’Hépatite B et transcription cellulaire : impact de la protéine HBx et de ses interactions avec les ARNs non-codants : Hepatits B virus and host cell transcription : impact of the HBx protein and its interaction with non coding RNA. [Doctoral Dissertation]. Lyon; 2018. Available from: http://www.theses.fr/2018LYSE1319

20. Rontani, Pauline. Caractérisation du long ARN non codant COSMOC dérégulé dans les troubles du spectre autistique : une approche transcriptomique sur cellules souches olfactives humaines : Characterization of the long non-coding RNA COSMOC in autism spectrum disorders : a transcriptomic approach on human olfactory stem cells.

Degree: Docteur es, Neurosciences, 2018, Aix Marseille Université

URL: http://www.theses.fr/2018AIXM0770

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L’autisme est un syndrome neuro-développemental hétérogène à l’étiologie génétique complexe. Afin d’identifier les dérèglements initiaux responsables de ce mal-développement cérébral, des travaux antérieurs au sein… (more)

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L’autisme est un syndrome neuro-développemental hétérogène à l’étiologie génétique complexe. Afin d’identifier les dérèglements initiaux responsables de ce mal-développement cérébral, des travaux antérieurs au sein de notre équipe se sont basés sur des cellules représentatives des stades précoces de l’ontogenèse : les cellules souches olfactives. Le gène MOCOS, codant pour la sulfurase du cofacteur à molybdène, a été trouvée sous-exprimé chez la majorité des patients autistes comparés à des sujets contrôles de même âge et du même sexe.Nous avons ensuite postulé que la dissection minutieuse des mécanismes moléculaires pouvant rendre compte de cette dérégulation aiderait à trouver des mécanismes sous-jacents contribuant aux troubles du spectre autistique (TSA). Ceci a conduit à l'identification de COSMOC, un long ARN non codant généré à partir d'une transcription divergente dans la région promotrice de MOCOS, dont l'expression est diminuée chez 10 des 11 patients autistes de notre cohorte. A l’aide de diverses techniques de biologie moléculaire, nous avons montré que la déplétion de COSMOC induit : (1) une sous-expression de MOCOS, (2) une déstabilisation de l'organisation de la chromatine, ce qui suggère une fonction de régulateur transcriptionnel, et (3) une altération du métabolisme des lipides et de l’homéostasie redox de la cellule, deux voies dérégulés dans les TSA. Par ailleurs, COSMOC régule de l’expression de la PTBP2 (polypirimidine track biding protein 2), un facteur d’épissage contrôlant l’expression de nombreuses protéines synaptiques. En conclusion, la dérégulation de COSMOC pourrait expliquer certains des dysfonctionnements observés dans les TSA.

Autism is a heterogeneous neuro-developmental syndrome with a complex genetic etiology. In order to unveil the initial disturbances responsible for this brain maldevelopment, previous works in our team relied on cells representative of the early stages of ontogenesis: olfactory stem cells. The MOCOS gene, coding for molybdenum cofactor sulfurase, was found under-expressed in most of autistic patients of our cohort when compared with age- and gender-matched control adults without any neuropsychiatric disorders. We postulated that the meticulous dissection of the molecular mechanisms involved this deregulation would help to unveil pathogenic mechanisms underlying autism spectrum disorders (ASD). This led to the identification of COSMOC, a long non-coding RNA, generated from a divergent transcription in the promoter region of MOCOS, whose expression is decreased in 10 out of 11 autistic patients in our cohort. Using various molecular biological techniques (interference RNA, DNA microarray, qPCR...), we showed that COSMOC depletion induces: (1) an under-expression of MOCOS, (2) a destabilization of chromatin organization, suggesting a transcriptional regulatory function, and (3) an alteration of cellular lipid metabolism and redox homeostasis, two deregulated pathways in ASD. In addition, COSMOC regulates the expression of PTBP2 (polypirimidine track biding…

Advisors/Committee Members: Féron, François (thesis director), Erard-Garcia, Madeleine (thesis director).

Subjects/Keywords: Autisme; ARN long non codant; Mocos; Cosmoc; Autism; Long non coding RNA; Mocos; Cosmoc

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Rontani, P. (2018). Caractérisation du long ARN non codant COSMOC dérégulé dans les troubles du spectre autistique : une approche transcriptomique sur cellules souches olfactives humaines : Characterization of the long non-coding RNA COSMOC in autism spectrum disorders : a transcriptomic approach on human olfactory stem cells. (Doctoral Dissertation). Aix Marseille Université. Retrieved from http://www.theses.fr/2018AIXM0770

Chicago Manual of Style (16^th Edition):

Rontani, Pauline. “Caractérisation du long ARN non codant COSMOC dérégulé dans les troubles du spectre autistique : une approche transcriptomique sur cellules souches olfactives humaines : Characterization of the long non-coding RNA COSMOC in autism spectrum disorders : a transcriptomic approach on human olfactory stem cells.” 2018. Doctoral Dissertation, Aix Marseille Université. Accessed March 05, 2021. http://www.theses.fr/2018AIXM0770.

MLA Handbook (7^th Edition):

Rontani, Pauline. “Caractérisation du long ARN non codant COSMOC dérégulé dans les troubles du spectre autistique : une approche transcriptomique sur cellules souches olfactives humaines : Characterization of the long non-coding RNA COSMOC in autism spectrum disorders : a transcriptomic approach on human olfactory stem cells.” 2018. Web. 05 Mar 2021.

Vancouver:

Rontani P. Caractérisation du long ARN non codant COSMOC dérégulé dans les troubles du spectre autistique : une approche transcriptomique sur cellules souches olfactives humaines : Characterization of the long non-coding RNA COSMOC in autism spectrum disorders : a transcriptomic approach on human olfactory stem cells. [Internet] [Doctoral dissertation]. Aix Marseille Université 2018. [cited 2021 Mar 05]. Available from: http://www.theses.fr/2018AIXM0770.

Council of Science Editors:

Rontani P. Caractérisation du long ARN non codant COSMOC dérégulé dans les troubles du spectre autistique : une approche transcriptomique sur cellules souches olfactives humaines : Characterization of the long non-coding RNA COSMOC in autism spectrum disorders : a transcriptomic approach on human olfactory stem cells. [Doctoral Dissertation]. Aix Marseille Université 2018. Available from: http://www.theses.fr/2018AIXM0770

21. Gautier-Isola, Marine. Caractérisation fonctionnelle de longs ARNs non codants induits par l’hypoxie et impliqués dans l’agressivité des cancers pulmonaires non à petites cellules : Functional characterization of long non coding RNA induced by hypoxia and associated with non small cell lung carcinoma aggressiveness.

Degree: Docteur es, Sciences de la vie et de la santé, 2020, Université Côte d'Azur

URL: http://www.theses.fr/2020COAZ6026

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Les cancers broncho-pulmonaires non à petites cellules, et plus particulièrement les adénocarcinomes (ADC), constituent la première cause de mortalité due au cancer dans les pays… (more)

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Les cancers broncho-pulmonaires non à petites cellules, et plus particulièrement les adénocarcinomes (ADC), constituent la première cause de mortalité due au cancer dans les pays développés. Malgré des prises en charge précoces, leur fort taux de récidive, nécessite l'identification de nouveaux marqueurs pronostics et de nouvelles cibles thérapeutiques. Dans cette optique, nous nous intéressons à l'hypoxie, un facteur d’agressivité tumoral, et à la famille émergente des longs ARNs non codants qui régulent l’expression génique par le biais de complexes ribonucléoprotéiques. Des analyses transcriptomiques de cohortes de patients d’ADC pulmonaires ont permis l’identification d'une quarantaine de longs ARNs non codants (lncARN) corrélés au statut hypoxique des tumeurs et/ou à un mauvais pronostic vital. Nous nous sommes focalisés sur deux candidats, NLUCAT1 et LINC01116, induits par l'hypoxie et associés à une diminution de la survie des patients. NLUCAT1 est un transcrit nucléaire de 9800 nt dont l’invalidation par le système CRISPR/Cas9 réduit les propriétés prolifératives et invasives des cellules et augmente la production de RLO et l'apoptose induite par le cisplatine ou un stress oxydatif. L’analyse comparative des transcriptomes de cellules invalidées ou non pour NLUCAT1 a révélé son implication dans la régulation du stress oxydatif via un rétrocontrôle positif sur des gènes de la réponse anti-oxydante. Par ailleurs, LINC01116 est cytosolique et exprimé conjointement dans les cellules cancéreuses et dans les cellules endothéliales du microenvironnement tumoral. J'ai montré que des siARNs réduisent l'adhésion et augmentent la perméabilité trans-endothéliale suggérant des défauts au niveau des contacts intercellulaires. J'ai ensuite entrepris l'étude du mode d'action de LINC01116 par l'identification de ses partenaires protéiques. Des expériences de "RNA pulldown" couplées à de la spectrométrie de masse ont permis d’identifier les protéines ILF3 et PABPC1. Ces interactions ont été validées par des expériences inverses d'immunoprécipitation d'ARN (RIP). L’implication de ces protéines dans le mode d’action de LINC01116 nécessite des études complémentaires.L’ensemble des résultats collectés durant ma thèse ont mis en évidence l’action pro-tumorale du transcrit NLUCAT1 dans les ADC et l'implication de LINC01116 dans la modification du microenvironnement vasculaire tumoral. Ces transcrits, associés à un mauvais pronostic des ADC, pourraient représenter des cibles thérapeutiques potentielles pour la prise en charge des patients.

Lung cancers, and notably Lung Adenocarcinomas (LUAD) are the leading cause of cancer death worldwide. Their high rate of recurrence despite early, requires new prognostic markers and new therapeutic targets. The combined study of local cohort (CHU of Nice) and large scale (TCGA) transcriptomes of LUAD allowed the identification of a shortlist of 28 long non-coding RNAs (lncRNA) correlated with hypoxia, a factor of tumor aggressiveness, and a poor prognosis. LncRNAs are transcripts that modulate…

Advisors/Committee Members: Rezzonico, Roger (thesis director).

Subjects/Keywords: Hypoxie; Long ARN non codant; Cancers broncho-pulmonaires; Hypoxia; Long non coding RNA; Lung cancer

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gautier-Isola, M. (2020). Caractérisation fonctionnelle de longs ARNs non codants induits par l’hypoxie et impliqués dans l’agressivité des cancers pulmonaires non à petites cellules : Functional characterization of long non coding RNA induced by hypoxia and associated with non small cell lung carcinoma aggressiveness. (Doctoral Dissertation). Université Côte d'Azur. Retrieved from http://www.theses.fr/2020COAZ6026

Chicago Manual of Style (16^th Edition):

Gautier-Isola, Marine. “Caractérisation fonctionnelle de longs ARNs non codants induits par l’hypoxie et impliqués dans l’agressivité des cancers pulmonaires non à petites cellules : Functional characterization of long non coding RNA induced by hypoxia and associated with non small cell lung carcinoma aggressiveness.” 2020. Doctoral Dissertation, Université Côte d'Azur. Accessed March 05, 2021. http://www.theses.fr/2020COAZ6026.

MLA Handbook (7^th Edition):

Gautier-Isola, Marine. “Caractérisation fonctionnelle de longs ARNs non codants induits par l’hypoxie et impliqués dans l’agressivité des cancers pulmonaires non à petites cellules : Functional characterization of long non coding RNA induced by hypoxia and associated with non small cell lung carcinoma aggressiveness.” 2020. Web. 05 Mar 2021.

Vancouver:

Gautier-Isola M. Caractérisation fonctionnelle de longs ARNs non codants induits par l’hypoxie et impliqués dans l’agressivité des cancers pulmonaires non à petites cellules : Functional characterization of long non coding RNA induced by hypoxia and associated with non small cell lung carcinoma aggressiveness. [Internet] [Doctoral dissertation]. Université Côte d'Azur; 2020. [cited 2021 Mar 05]. Available from: http://www.theses.fr/2020COAZ6026.

Council of Science Editors:

Gautier-Isola M. Caractérisation fonctionnelle de longs ARNs non codants induits par l’hypoxie et impliqués dans l’agressivité des cancers pulmonaires non à petites cellules : Functional characterization of long non coding RNA induced by hypoxia and associated with non small cell lung carcinoma aggressiveness. [Doctoral Dissertation]. Université Côte d'Azur; 2020. Available from: http://www.theses.fr/2020COAZ6026

22. BILAL UNAL. INVESTIGATING THE ROLE OF LONG NON-CODING RNAS IN INFLAMMATION.

Degree: 2018, National University of Singapore

URL: https://scholarbank.nus.edu.sg/handle/10635/153438

Subjects/Keywords: lncRNA; non-coding RNA; inflammation; NFkB; TNF; p38 pathway

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APA (6^th Edition):

UNAL, B. (2018). INVESTIGATING THE ROLE OF LONG NON-CODING RNAS IN INFLAMMATION. (Thesis). National University of Singapore. Retrieved from https://scholarbank.nus.edu.sg/handle/10635/153438

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

UNAL, BILAL. “INVESTIGATING THE ROLE OF LONG NON-CODING RNAS IN INFLAMMATION.” 2018. Thesis, National University of Singapore. Accessed March 05, 2021. https://scholarbank.nus.edu.sg/handle/10635/153438.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

UNAL, BILAL. “INVESTIGATING THE ROLE OF LONG NON-CODING RNAS IN INFLAMMATION.” 2018. Web. 05 Mar 2021.

Vancouver:

UNAL B. INVESTIGATING THE ROLE OF LONG NON-CODING RNAS IN INFLAMMATION. [Internet] [Thesis]. National University of Singapore; 2018. [cited 2021 Mar 05]. Available from: https://scholarbank.nus.edu.sg/handle/10635/153438.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

UNAL B. INVESTIGATING THE ROLE OF LONG NON-CODING RNAS IN INFLAMMATION. [Thesis]. National University of Singapore; 2018. Available from: https://scholarbank.nus.edu.sg/handle/10635/153438

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

23. MacDougall, Matthew Steven. Investigation of Myc-regulated Long Non-coding RNAs in Cell Cycle and Myc-dependent Transformation.

Degree: 2012, University of Toronto

URL: http://hdl.handle.net/1807/42402

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Myc deregulation critically contributes to many cancer etiologies. Recent work suggests that Myc and its direct interactors can confer a distinct epigenetic state. Our goal… (more)

Subjects/Keywords: c-Myc; long non-coding RNA; lncRNA; breast cancer; cancer biology; transcription; epigenetics; 0369; 0487; 0571

…Information non-coding RNA N-terminal domain nucleosome remodeling deacetylase open reading frame… …regulatory, non-coding RNA A finding that began to integrate the idea that Myc depended on… …regulatory ncRNAs called long non-coding RNAs (lncRNAs). For many years, this type of… …coding RNA genes could figure in prominently. As such, lncRNA biology could contribute to our… …observed on day 8 (Figure 5B, ‘Day 4’). 2.2 Global long non-coding gene expression…

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APA (6^th Edition):

MacDougall, M. S. (2012). Investigation of Myc-regulated Long Non-coding RNAs in Cell Cycle and Myc-dependent Transformation. (Masters Thesis). University of Toronto. Retrieved from http://hdl.handle.net/1807/42402

Chicago Manual of Style (16^th Edition):

MacDougall, Matthew Steven. “Investigation of Myc-regulated Long Non-coding RNAs in Cell Cycle and Myc-dependent Transformation.” 2012. Masters Thesis, University of Toronto. Accessed March 05, 2021. http://hdl.handle.net/1807/42402.

MLA Handbook (7^th Edition):

MacDougall, Matthew Steven. “Investigation of Myc-regulated Long Non-coding RNAs in Cell Cycle and Myc-dependent Transformation.” 2012. Web. 05 Mar 2021.

Vancouver:

MacDougall MS. Investigation of Myc-regulated Long Non-coding RNAs in Cell Cycle and Myc-dependent Transformation. [Internet] [Masters thesis]. University of Toronto; 2012. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/1807/42402.

Council of Science Editors:

MacDougall MS. Investigation of Myc-regulated Long Non-coding RNAs in Cell Cycle and Myc-dependent Transformation. [Masters Thesis]. University of Toronto; 2012. Available from: http://hdl.handle.net/1807/42402

University of Vermont

24. Zhang, Zhouwei. Investigation of DNA and RNA markers by novel technologies demonstrates DNA content intratumoral heterogeneity and long non-coding RNA aberrations in breast tumors.

Degree: MS, Pathology, 2014, University of Vermont

URL: https://scholarworks.uvm.edu/graddis/323

► BACKGROUND: Breast cancer is the most commonly diagnosed cancer and second leading cancer death cause among females in the U.S.A. About 1 in 8… (more)

▼ BACKGROUND: Breast cancer is the most commonly diagnosed cancer and second leading cancer death cause among females in the U.S.A. About 1 in 8 women in U.S will develop invasive breast cancer over the course of her lifetime. In 2013, 234,580 new invasive breast cancer cases are expected to occur in women within the US and approximately 64,640 non-invasive carcinomas in situ were diagnosed in 2013, most of which were ductal carcinoma in situ (DCIS). Along with technological advances, a wide variety of candidate biomarkers have been proposed for cancer diagnosis and prognosis, including DNA content and non-coding RNA. Current techniques for detecting DNA content abnormalities in formalin-fixed, paraffin-embedded (FFPE) tissue samples by flow cytometric analysis have used cells recovered from ≥50Âµm whole tissue sections. Here, in our first study, a novel core punch sampling method was investigated for assessing DNA content abnormalities and intratumoral heterogeneity in FFPE specimens. Secondly, long non-coding RNAs (lncRNAs) has been examined. LncRNA participates in a broad spectrum of biological activities by diverse mechanisms and its dysregulation is associated with tumorgenesis. Some lncRNAs may function as oncogenes (O) and others as tumor suppressor genes (TSG). To date, lncRNA has been investigated primarily by qRT-PCR and RNA sequencing. This study has examined the relationship of lncRNA expression patterns to breast tumor pathology by chromogenic in situ hybridization (CISH). METHODS: Firstly, FFPE breast carcinoma specimens were selectively targeted using 1.0 mm diameter punch needles. Extracted cores were assayed by flow cytometry using a modified-Headley method. Secondly, the lncRNA expression levels of 6 lncRNAs: HOTAIR, H19, KCNQ1OT1, MEG3, MALAT11 and Zfas1, was examined by RNAscope® CISH using FFPE breast tissue microarrays (TMAs) comprising normal adjacent epithelia (NA), DCIS, and invasive carcinoma (IC) from 46 patients. LncRNA associate polycomb complex protein EZH2 was evaluated by immunohistochemistry (IHC). LncRNA data was also compared to standard breast tumor data including ER, PR, Her2 and Ki67 IHC. SYSTAT version 11 statistical package was used to perform for all the tests. RESULTS: Following optimization experiments of the core punch flow cytometric approach, DNA index and percent S-phase fraction intratumoral heterogeneities were detected in 10/23 (44%) and 11/23 (47%) specimens respectively. The lncRNA CISH study utilized a TMA that contained 36 spots of NA breast tissues, 34 DCIS spots and 43 IC spots. HOTAIR CISH staining was significantly stronger in IC than DCIS (p CONCLUSION: Core-punching is an effective alternative to whole specimen sectioning and shows that macro-level genomic heterogeneity is common even within a single FFPE block. The interrelationship of DNA content heterogeneity to other forms of heterogeneity requires further study. RNAscope CISH supports bright-field microscopy investigations of… Advisors/Committee Members: Mark F. Evans, Donald L. Weaver, Nicholas H. Heintz.

Subjects/Keywords: Biomarker; Breast cancer; Intratumoral heterogeneity; Long non-coding RNA; Pathology

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APA (6^th Edition):

Zhang, Z. (2014). Investigation of DNA and RNA markers by novel technologies demonstrates DNA content intratumoral heterogeneity and long non-coding RNA aberrations in breast tumors. (Thesis). University of Vermont. Retrieved from https://scholarworks.uvm.edu/graddis/323

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Zhang, Zhouwei. “Investigation of DNA and RNA markers by novel technologies demonstrates DNA content intratumoral heterogeneity and long non-coding RNA aberrations in breast tumors.” 2014. Thesis, University of Vermont. Accessed March 05, 2021. https://scholarworks.uvm.edu/graddis/323.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Zhang, Zhouwei. “Investigation of DNA and RNA markers by novel technologies demonstrates DNA content intratumoral heterogeneity and long non-coding RNA aberrations in breast tumors.” 2014. Web. 05 Mar 2021.

Vancouver:

Zhang Z. Investigation of DNA and RNA markers by novel technologies demonstrates DNA content intratumoral heterogeneity and long non-coding RNA aberrations in breast tumors. [Internet] [Thesis]. University of Vermont; 2014. [cited 2021 Mar 05]. Available from: https://scholarworks.uvm.edu/graddis/323.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Zhang Z. Investigation of DNA and RNA markers by novel technologies demonstrates DNA content intratumoral heterogeneity and long non-coding RNA aberrations in breast tumors. [Thesis]. University of Vermont; 2014. Available from: https://scholarworks.uvm.edu/graddis/323

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

25. E. Oldoni. THE ROLE OF CELLULAR AND EXOSOMAL NEURAL-DERIVED LONG NON CODING RNA (LNCRNA) IN MULTIPLE SCLEROSIS: POTENTIAL BIOMARKERS OF DISEASE SUSCEPTIBILITY AND PROGRESSION.

Degree: 2018, Università degli Studi di Milano

URL: http://hdl.handle.net/2434/540356

► Long non-coding RNAs (lncRNAs) are a novel class of transcripts that are pervasively transcribed in the genome. Several lines of evidence correlate dysregulation of different… (more)

▼ Long non-coding RNAs (lncRNAs) are a novel class of transcripts that are pervasively transcribed in the genome. Several lines of evidence correlate dysregulation of different lncRNAs to human diseases including neurological and autoimmune disorders, but their expression has not been exhaustively investigated in MS so far. The main aim of this study was to identify a specific signature of cellular and neural-derived exosomal lncRNA expression. Regarding lncRNA expression levels from Peripheral Blood Mononuclear Cells (PBMC), we studied a discovery cohort of MS patients who were compared against controls. Results were validated in a larger cohort and further replicated in an independent Belgian population. LncRNA PCR arrays from System Bioscience (SBI) containing 90 common lncRNAs were used to screen lncRNA expression levels in PBMC from 5 patients with Relapsing Remitting (RR)-MS, 5 with Primary Progressive (PP)-MS and 5 age-matched controls. Results were validated by real time PCR in a further independent Italian cohort consisting of 30 PBMC samples from MS patients and 30 controls. Best hits were replicated using droplet digital PCR in a Belgian cohort consisting of 24 MS patients and 23 controls. In particular, in the Italian validation cohort ANRIL, TUG1, XIST (p<0.0001) and SOX2OT (p<0.001) were strongly down-regulated in RR-MS versus controls, while GOMAFU, HULC (p<0.0001) and BACE-1AS (p<0.001) showed a robust down-regulation both in RR and Progressive MS in comparison with controls. NRON and TUG1 downregulation in MS patients, compared with controls (p<0.05 and p<0.0001 respectively), was confirmed in the Belgian population. In addition, a protocol for the extraction and characterisation of neural-derived exosomes has been developed in order to investigate exosomal lncRNA expression levels. Using two types of commercial arrays, the human RT2 lncFinder array (QIAGEN) and the human RT2 lncRNA inflammation response and autoimmunity array (QIAGEN), generalised deregulation in exosomal lncRNA was observed. Moreover, the expression pattern of these molecules was different in RR-MS and in PP-MS. Precisely, results from the human RT2 lncFinder array (QIAGEN) analysis led to the identification of 7 most significantly deregulated lncRNAs, precisely AIRN (5.30-fold increase over controls, p=0.04); FAS-AS1 (4.76-fold increase over controls, p=0.02); HOTAIR (4.47-fold increase over controls, p=0.03); NAMA (13.24-fold increase over controls, p=0.01); TRERNA1 (5.84-fold increase over controls, p=0.01) and HOXA-AS2 (0.56-fold increase over controls, p=0.04). Six lncRNA were significantly deregulated in the RR-MS subgroup, precisely AIRN (10.77-fold increase over controls, p=0.04); DLX6-AS1 (46.95-fold increase over controls, p=0.01); FAS-AS1 (11.37-fold increase over controls, p=0.001); HOTAIR (9.31-fold increase over controls; p=0.02); and TRERNA1 (6.61-fold increase over controls, p=0.003). In PP-MS only SOX-2OT showed a significant upregulation (8.95-fold increase over controls, p=0.02). When we used the array… Advisors/Committee Members: tutor: E. A. Scarpini, co-tutor: D. Galimberti, C. Fenoglio, GHIDONI, RICCARDO.

Subjects/Keywords: multiple sclerosis, long non coding RNA, exosomes; Settore MED/26 - Neurologia

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Oldoni, E. (2018). THE ROLE OF CELLULAR AND EXOSOMAL NEURAL-DERIVED LONG NON CODING RNA (LNCRNA) IN MULTIPLE SCLEROSIS: POTENTIAL BIOMARKERS OF DISEASE SUSCEPTIBILITY AND PROGRESSION. (Thesis). Università degli Studi di Milano. Retrieved from http://hdl.handle.net/2434/540356

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Oldoni, E.. “THE ROLE OF CELLULAR AND EXOSOMAL NEURAL-DERIVED LONG NON CODING RNA (LNCRNA) IN MULTIPLE SCLEROSIS: POTENTIAL BIOMARKERS OF DISEASE SUSCEPTIBILITY AND PROGRESSION.” 2018. Thesis, Università degli Studi di Milano. Accessed March 05, 2021. http://hdl.handle.net/2434/540356.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Oldoni, E.. “THE ROLE OF CELLULAR AND EXOSOMAL NEURAL-DERIVED LONG NON CODING RNA (LNCRNA) IN MULTIPLE SCLEROSIS: POTENTIAL BIOMARKERS OF DISEASE SUSCEPTIBILITY AND PROGRESSION.” 2018. Web. 05 Mar 2021.

Vancouver:

Oldoni E. THE ROLE OF CELLULAR AND EXOSOMAL NEURAL-DERIVED LONG NON CODING RNA (LNCRNA) IN MULTIPLE SCLEROSIS: POTENTIAL BIOMARKERS OF DISEASE SUSCEPTIBILITY AND PROGRESSION. [Internet] [Thesis]. Università degli Studi di Milano; 2018. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2434/540356.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Oldoni E. THE ROLE OF CELLULAR AND EXOSOMAL NEURAL-DERIVED LONG NON CODING RNA (LNCRNA) IN MULTIPLE SCLEROSIS: POTENTIAL BIOMARKERS OF DISEASE SUSCEPTIBILITY AND PROGRESSION. [Thesis]. Università degli Studi di Milano; 2018. Available from: http://hdl.handle.net/2434/540356

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

26. Coyne, Victoria. Characterization of long non-coding RNAs in the Hox complex of Drosophila.

Degree: PhD, 2017, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/characterization-of-long-noncoding-rnas-in-the-hox-complex-of-drosophila(733e3dec-3f7b-4d6e-a1bc-674a8786246d).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.713612

► Long non-coding RNAs (lncRNAs) are often defined as transcripts >200nts that have no discernable protein-coding ability (Quinn and Chang, 2016). Although relatively little is understood… (more)

▼ Long non-coding RNAs (lncRNAs) are often defined as transcripts >200nts that have no discernable protein-coding ability (Quinn and Chang, 2016). Although relatively little is understood about the molecular mechanisms of lncRNA function, they have established roles in regulation of gene expression during development, cell differentiation and pluripotency (Fatica and Bozzoni, 2014; Luo et al., 2016; Quinn and Chang, 2016; Rinn and Chang, 2012) across vastly diverse organisms ranging from plants to humans (Ulitsky and Bartel, 2013). LncRNAs have also been associated with numerous pathological conditions, such as cancers (Brunner et al., 2012), cardiovascular disease and neurodegeneration (Chen et al., 2013). Investigations into lncRNAs in wide ranging organisms, have revealed that many influence gene activity by forming ribonucleoprotein complexes that affect the conformational state of chromatin (Rinn and Chang, 2012). A genomic region that has revealed several functional lncRNAs in diverse organisms is the Hox complex (Pauli et al., 2011; Pettini, 2012; Rinn et al., 2007). The Hox complex encodes a set of transcription factors (TFs), physically clustered in the genome, which provide morphological identity along the anterior to posterior axis of developing embryos (Mallo and Alonso, 2013), throughout the majority of bilatarian animals (Moreno et al., 2011). Misexpression or mutation of Hox genes causes morphological and pathophysiological defects (Quinonez and Innis, 2014). We investigated clustering of lncRNAs throughout the D. melanogaster genome using available annotations and carried out RNA-seq in D. virilis to expand the repertoire of lncRNAs and identify clusters of lncRNAs. We found the Hox complex to be heavily enriched with lncRNAs in both organisms, and syntenic transcripts from D. melanogaster could be identified in D. pseudoobscura and D. virilis. Several lncRNAs aligned with polycomb response elements (PREs); transcription of PREs has previously been linked to a switch in their activity (Herzog et al., 2014). However, we found that transcribed PREs in D. melanogaster move positions relative to the protein-coding genes in other drosophilids, whilst the transcriptional units remain in the same syntenic region. Conservation of syntenic transcripts without evidence of remaining a PRE suggest that the transcription is not linked to PRE function, agreeing with recent findings that transcription of PREs does not affect their function (Kassis and Muller, 2015). We investigated functions of a novel lncRNA and adjacent PRE in the Hox complex by ectopic expression and utilization of other genetic manipulation tools. Overexpression of either the lncRNA or PRE and partial duplication of the lncRNA caused phenotypes such as missing halteres and/or T3 legs, misshaped T3 legs or malformed abdominal segments. The observations that ectopic expression of this lncRNA and an adjacent regulatory element from the Hox complex causes phenotypes that can be linked to adjacent Hox gene misregulation, Antp and Ubx, suggest that they…

Subjects/Keywords: 572.8; long non-coding RNA evolution development Hox

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APA (6^th Edition):

Coyne, V. (2017). Characterization of long non-coding RNAs in the Hox complex of Drosophila. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/characterization-of-long-noncoding-rnas-in-the-hox-complex-of-drosophila(733e3dec-3f7b-4d6e-a1bc-674a8786246d).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.713612

Chicago Manual of Style (16^th Edition):

Coyne, Victoria. “Characterization of long non-coding RNAs in the Hox complex of Drosophila.” 2017. Doctoral Dissertation, University of Manchester. Accessed March 05, 2021. https://www.research.manchester.ac.uk/portal/en/theses/characterization-of-long-noncoding-rnas-in-the-hox-complex-of-drosophila(733e3dec-3f7b-4d6e-a1bc-674a8786246d).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.713612.

MLA Handbook (7^th Edition):

Coyne, Victoria. “Characterization of long non-coding RNAs in the Hox complex of Drosophila.” 2017. Web. 05 Mar 2021.

Vancouver:

Coyne V. Characterization of long non-coding RNAs in the Hox complex of Drosophila. [Internet] [Doctoral dissertation]. University of Manchester; 2017. [cited 2021 Mar 05]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/characterization-of-long-noncoding-rnas-in-the-hox-complex-of-drosophila(733e3dec-3f7b-4d6e-a1bc-674a8786246d).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.713612.

Council of Science Editors:

Coyne V. Characterization of long non-coding RNAs in the Hox complex of Drosophila. [Doctoral Dissertation]. University of Manchester; 2017. Available from: https://www.research.manchester.ac.uk/portal/en/theses/characterization-of-long-noncoding-rnas-in-the-hox-complex-of-drosophila(733e3dec-3f7b-4d6e-a1bc-674a8786246d).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.713612

Universitat Politècnica de València

27. Furió Tarí, Pedro. Development of bioinformatic tools for massive sequencing analysis .

Degree: 2020, Universitat Politècnica de València

URL: http://hdl.handle.net/10251/152485

► [EN] Transcriptomics is one of the most important and relevant areas of bioinformatics. It allows detecting the genes that are expressed at a particular moment… (more)

▼ [EN] Transcriptomics is one of the most important and relevant areas of bioinformatics. It allows detecting the genes that are expressed at a particular moment in time to explore the relation between genotype and phenotype. Transcriptomic analysis has been historically performed using microarrays until 2008 when high-throughput RNA sequencing (RNA-Seq) was launched on the market, replacing the old technique. However, despite the clear advantages over microarrays, it was necessary to understand factors such as the quality of the data, reproducibility and replicability of the analyses and potential biases. The first section of the thesis covers these studies. First, an R package called NOISeq was developed and published in the public repository "Bioconductor", which includes a set of tools to better understand the quality of RNA-Seq data, minimise the impact of noise in any posterior analyses and implements two new methodologies (NOISeq and NOISeqBio) to overcome the difficulties of comparing two different groups of samples (differential expression). Second, I show our contribution to the Sequencing Quality Control (SEQC) project, a continuation of the Microarray Quality Control (MAQC) project led by the US Food and Drug Administration (FDA, United States) that aims to assess the reproducibility and replicability of any RNA-Seq analysis. One of the most effective approaches to understand the different factors that influence the regulation of gene expression, such as the synergic effect of transcription factors, methylation events and chromatin accessibility, is the integration of transcriptomic with other omics data. To this aim, a file that contains the chromosomal position where the events take place is required. For this reason, in the second chapter, we present a new and easy to customise tool (RGmatch) to associate chromosomal positions to the exons, transcripts or genes that could regulate the events. Another aspect of great interest is the study of non-coding genes, especially long non-coding RNAs (lncRNAs). Not long ago, these regions were thought not to play a relevant role and were only considered as transcriptional noise. However, they represent a high percentage of the human genes and it was recently shown that they actually play an important role in gene regulation. Due to these motivations, in the last chapter we focus, first, in trying to find a methodology to find out the generic functions of every lncRNA using publicly available data and, second, we develop a new tool (spongeScan) to predict the lncRNAs that could be involved in the sequestration of micro-RNAs (miRNAs) and therefore altering their regulation task. Advisors/Committee Members: Conesa Cegarra, Ana (advisor).

Subjects/Keywords: Bioinformatics; RNA-Seq; LncRNAs; Long non-coding RNAs; Transcriptomics

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APA (6^th Edition):

Furió Tarí, P. (2020). Development of bioinformatic tools for massive sequencing analysis . (Doctoral Dissertation). Universitat Politècnica de València. Retrieved from http://hdl.handle.net/10251/152485

Chicago Manual of Style (16^th Edition):

Furió Tarí, Pedro. “Development of bioinformatic tools for massive sequencing analysis .” 2020. Doctoral Dissertation, Universitat Politècnica de València. Accessed March 05, 2021. http://hdl.handle.net/10251/152485.

MLA Handbook (7^th Edition):

Furió Tarí, Pedro. “Development of bioinformatic tools for massive sequencing analysis .” 2020. Web. 05 Mar 2021.

Vancouver:

Furió Tarí P. Development of bioinformatic tools for massive sequencing analysis . [Internet] [Doctoral dissertation]. Universitat Politècnica de València; 2020. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/10251/152485.

Council of Science Editors:

Furió Tarí P. Development of bioinformatic tools for massive sequencing analysis . [Doctoral Dissertation]. Universitat Politècnica de València; 2020. Available from: http://hdl.handle.net/10251/152485

University of Melbourne

28. Gradie, Paul Edward. Defining the master regulator of urethral closure in mouse.

Degree: 2017, University of Melbourne

URL: http://hdl.handle.net/11343/198127

► Hypospadias is the ectopic placement of the urethral opening on the underside of the penis and is one of the most common developmental abnormalities in… (more)

▼ Hypospadias is the ectopic placement of the urethral opening on the underside of the penis and is one of the most common developmental abnormalities in humans, occurring in approximately 1 in every 125 live male births. In addition, we have observed a doubling in the incidence of hypospadias over the past several decades suggesting an environmental component likely in the form of estrogen mimicking chemicals generally referred to as environmental endocrine disruptors (EEDs). Current models fail to explain these observations. The goal of this thesis is to produce a theory that describes the development and genetic regulation of urethral closure, and use it to explain the aetiology, spectrum, and rise in incidence of hypospadias observed in humans. The work presented in this thesis was performed using a novel mouse model (OVE442) with isolated hypospadias. This model was used to define the role of the urorectal septum (URS) during urethral closure. The process of urethral closure is generally thought to occur by tissue fusion. However, we provide immunohistological evidence that suggests the urethra is internalized by growth of the URS, which contributes tissue to the ventral aspect of the penis during embryonic development. The OVE442 model was next used to define a key regulator of the URS during urethral closure. Initial characterization of a genomic mutation in OVE442 model led us to discover a long non-coding RNA, designated Leat1, which was deleted near EfnB2. Loss of signalling through the EPHRINB2 protein was previously shown to cause severe hypospadias in mouse, however little is known about EfnB2 gene regulation during urethral closure. Leat1 was characterized, functionally examined, and shown to regulate EfnB2 expression through direct interaction with the EPHRINB2 protein. We further showed that Leat1 expression is differentially regulated in males and females, and that it is supressed by estrogen. These results showed that EfnB2 drives growth of the URS during urethral closure and provided the first experimental evidence revealing the genetic mechanism that causes male and female urethral anatomy to diverge. These observations were used together with our anatomical descriptions to produce a developmental theory that explains urethral formation in mouse. We extended our understanding further by using comparative time series RNA-Seq to describe global transcription and ChIP-Seq to identify genes actively regulated by estrogen and androgen during urethral. From these data, we identify potential urethral closure genes downstream of Leat1 and EfnB2 including genes that are likely responsive to sex hormones. This work has provided fundamental insights on the anatomy and genetic regulation of urethral closure. I have shown that male urethral closure is driven by growth of the URS and that this growth is regulated by the long non-coding RNA Leat1 in mouse. Furthermore, I have produced a list of potential EED targets that may lead to better understanding the causes of hypospadias. Through this work I have…

Subjects/Keywords: hypospadias; long non coding RNA; development; reproduction; urethra; urogenital; birth defect

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gradie, P. E. (2017). Defining the master regulator of urethral closure in mouse. (Doctoral Dissertation). University of Melbourne. Retrieved from http://hdl.handle.net/11343/198127

Chicago Manual of Style (16^th Edition):

Gradie, Paul Edward. “Defining the master regulator of urethral closure in mouse.” 2017. Doctoral Dissertation, University of Melbourne. Accessed March 05, 2021. http://hdl.handle.net/11343/198127.

MLA Handbook (7^th Edition):

Gradie, Paul Edward. “Defining the master regulator of urethral closure in mouse.” 2017. Web. 05 Mar 2021.

Vancouver:

Gradie PE. Defining the master regulator of urethral closure in mouse. [Internet] [Doctoral dissertation]. University of Melbourne; 2017. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/11343/198127.

Council of Science Editors:

Gradie PE. Defining the master regulator of urethral closure in mouse. [Doctoral Dissertation]. University of Melbourne; 2017. Available from: http://hdl.handle.net/11343/198127

University of Manchester

29. Nowicki-Osuch, Karol Piotr. Identification and characterisation of long non-coding RNAs expressed downstream of EGF-induced signalling programme.

Degree: 2016, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:296204

►

It has recently become apparent that cells encode a large number of novel non-protein-coding genes called long non-coding RNAs (lncRNAs). Whilst the biological function of… (more)

▼

It has recently become apparent that cells encode a large number of novel non-protein-coding genes called long non-coding RNAs (lncRNAs). Whilst the biological function of many lncRNAs remains unknown, recent evidence has suggested that lncRNAs may be important regulators of cellular growth, differentiation and may play a significant role in cancer. Epidermal growth factor (EGF) – an activator of the ERK1/2 signalling cascade – is an important spatio-temporal regulator of transcription and, ultimately, of cellular growth and movement. EGF stimulation triggers a wave-like expression of immediate-early genes (IE genes), followed by delayed-early genes (DE genes) and secondary-response genes (SR genes). Over the years, considerable effort has been made to unravel the regulatory loops downstream of EGF signalling. This study investigated whether lncRNAs are sensitive to EGF signalling and whether they play a role in the transcriptional programme associated with EGF signalling. In order to identify lncRNAs regulated by EGF signalling, I sequenced nuclear RNA in the presence or absence of EGF stimulation. RNA-seq data showed that 173 lncRNAs are upregulated by EGF, of which 89 were intergenic lncRNAs (lincRNAs). The time-dependent expression profile of EGF-upregulated lincRNAs followed the well-established expression pattern of IE genes. Finally, investigation of the expression of lincRNAs in primary breast and lung cancer cells showed that EGF-upregulated lincRNAs were differentially expressed in cancer. The EGF-dependent induction profile and cancer enrichment were particularly strong for one of the transcripts – EGF-induced lncRNA 1 (EIN1) – and I selected it for further studies.Firstly, using bioinformatics and biochemical approaches, I confirmed the non-coding status of the EIN1 transcript. Secondly, I confirmed that EIN1 transcription is ERK1/2-dependent and is independent of protein synthesis. Investigation of EIN1 expression in normal tissues showed its high enrichment in the human cardiovascular system. At the cellular level, the EIN1 transcript was predominantly found in the nucleus. Functionally, the depletion of endogenous EIN1 transcripts (using the newly developed CRISPRi approach) led to changes in the EGF-dependent transcription programme. EIN1 downregulation resulted in the addition of normally EGF-independent genes into the EGF-dependent expression programme.Collectively, these results show that EGF (via the ERK1/2 pathway) can regulate transcription of lincRNAs. The EIN1 example suggests that lincRNAs may play a crucial role in the modulation of the EGF-dependent expression programme by limiting of the scope of the programme.

All of the following files are available on the CD/DVDSupplementary file 1. The summary of the differential expression analysis of the high-depth nuclear RNA-seq.Supplementary file 2. The Ingenuity Pathway analysis output for the upstream regulators of EGF-regulated genes. Supplementary file 3. The average distribution of sequencing reads around TSSs of differentially expressed…

Advisors/Committee Members: JACKSON, DEAN DA, Jackson, Dean, Sharrocks, Andrew.

Subjects/Keywords: long non-coding RNA; EGF; Signalling; Expression; lcnRNA; EIN1; Immediate early

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Nowicki-Osuch, K. P. (2016). Identification and characterisation of long non-coding RNAs expressed downstream of EGF-induced signalling programme. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:296204

Chicago Manual of Style (16^th Edition):

Nowicki-Osuch, Karol Piotr. “Identification and characterisation of long non-coding RNAs expressed downstream of EGF-induced signalling programme.” 2016. Doctoral Dissertation, University of Manchester. Accessed March 05, 2021. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:296204.

MLA Handbook (7^th Edition):

Nowicki-Osuch, Karol Piotr. “Identification and characterisation of long non-coding RNAs expressed downstream of EGF-induced signalling programme.” 2016. Web. 05 Mar 2021.

Vancouver:

Nowicki-Osuch KP. Identification and characterisation of long non-coding RNAs expressed downstream of EGF-induced signalling programme. [Internet] [Doctoral dissertation]. University of Manchester; 2016. [cited 2021 Mar 05]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:296204.

Council of Science Editors:

Nowicki-Osuch KP. Identification and characterisation of long non-coding RNAs expressed downstream of EGF-induced signalling programme. [Doctoral Dissertation]. University of Manchester; 2016. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:296204

University of Toronto

30. Sukumar, Aravin Nirupan. Long Non-Coding RNAs in the Endothelial Cell Response to Shear Stress.

Degree: PhD, 2020, University of Toronto

URL: http://hdl.handle.net/1807/103175

► Endothelial cells (EC) act as professional sensors of shear stress, the frictional force of blood flow. In the absence of laminar (healthy) blood flow, ECs… (more)

Subjects/Keywords: atherosclerosis; cardiovascular; endothelial cell; epigenetics; hemodynamics; long non-coding RNA; 0307

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sukumar, A. N. (2020). Long Non-Coding RNAs in the Endothelial Cell Response to Shear Stress. (Doctoral Dissertation). University of Toronto. Retrieved from http://hdl.handle.net/1807/103175

Chicago Manual of Style (16^th Edition):

Sukumar, Aravin Nirupan. “Long Non-Coding RNAs in the Endothelial Cell Response to Shear Stress.” 2020. Doctoral Dissertation, University of Toronto. Accessed March 05, 2021. http://hdl.handle.net/1807/103175.

MLA Handbook (7^th Edition):

Sukumar, Aravin Nirupan. “Long Non-Coding RNAs in the Endothelial Cell Response to Shear Stress.” 2020. Web. 05 Mar 2021.

Vancouver:

Sukumar AN. Long Non-Coding RNAs in the Endothelial Cell Response to Shear Stress. [Internet] [Doctoral dissertation]. University of Toronto; 2020. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/1807/103175.

Council of Science Editors:

Sukumar AN. Long Non-Coding RNAs in the Endothelial Cell Response to Shear Stress. [Doctoral Dissertation]. University of Toronto; 2020. Available from: http://hdl.handle.net/1807/103175

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