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1.
Yang, Cheng.
An ab initio lncRNA identification and functional annotation tool based on deep learning.
Degree: PhD, Biomedical Engineering (Joint GT/Emory Department), 2018, Georgia Tech
URL: http://hdl.handle.net/1853/61121 
► Long noncoding RNAs (lncRNAs) play important biological roles and are implicated in human disease. To characterize lncRNAs, both identifying and functionally annotating them are essential…
(more)
▼ Long noncoding RNAs (lncRNAs) play important biological roles and are implicated in human disease. To characterize lncRNAs, both identifying and functionally annotating them are essential to be addressed. Despite the successes either in identifying from transcripts or predicting interacting proteins by a variety of tools, it continues to be interesting to develop novel ab initio methods to accurately identify and annotate lncRNAs. Moreover, a comprehensive construction for
lncRNA annotation is desired to facilitate the research in the field. In this dissertation, we propose a novel
lncRNA identification and functional annotation tool named LncADeep. For
lncRNA identification, LncADeep integrates sequence intrinsic features and homology features into a deep belief network (DBN) of deep learning algorithm and constructs models targeting both full- and partial-length transcripts. For functional annotation, LncADeep predicts a lncRNA’s interacting proteins based on deep neural networks (DNN) of deep learning algorithm, using both sequence and structure information. Furthermore, LncADeep integrates KEGG and Reactome pathway enrichment analysis and functional module detection with the predicted interacting proteins, and provides the enriched pathways and functional modules as functional annotations for lncRNAs. Test results show that LncADeep has outperformed state-of-the-art tools, both for
lncRNA identification and for
lncRNA-protein interaction prediction, and then presents a functional interpretation. We expect that LncADeep can contribute to identifying and annotating novel lncRNAs, and providing helpful information for biologists.
Advisors/Committee Members: Zhu, Huaiqiu (advisor), Wang, May D. (committee member), Lu, Zuhong (committee member), Xi, Jianzhong (committee member), Deng, Minghua (committee member).
Subjects/Keywords: RNA-seq; lncRNA identification; lncRNA-protein interaction; lncRNA functional annotation; Deep learning
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APA (6th Edition):
Yang, C. (2018). An ab initio lncRNA identification and functional annotation tool based on deep learning. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/61121
Chicago Manual of Style (16th Edition):
Yang, Cheng. “An ab initio lncRNA identification and functional annotation tool based on deep learning.” 2018. Doctoral Dissertation, Georgia Tech. Accessed February 27, 2021.
http://hdl.handle.net/1853/61121.
MLA Handbook (7th Edition):
Yang, Cheng. “An ab initio lncRNA identification and functional annotation tool based on deep learning.” 2018. Web. 27 Feb 2021.
Vancouver:
Yang C. An ab initio lncRNA identification and functional annotation tool based on deep learning. [Internet] [Doctoral dissertation]. Georgia Tech; 2018. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/1853/61121.
Council of Science Editors:
Yang C. An ab initio lncRNA identification and functional annotation tool based on deep learning. [Doctoral Dissertation]. Georgia Tech; 2018. Available from: http://hdl.handle.net/1853/61121
Harvard University
2.
Froberg, John E.
The Spatial Organization of the X-chromosome and its Impact on X-inactivation.
Degree: PhD, 2018, Harvard University
URL: http://nrs.harvard.edu/urn-3:HUL.InstRepos:41121361
► Female mammals have two X-chromosomes, males have one X-chromosome. X-chromosome inactivation (XCI) is a process where most genes on one female X-chromosome is transcriptionally silenced…
(more)
▼ Female mammals have two X-chromosomes, males have one X-chromosome. X-chromosome inactivation (XCI) is a process where most genes on one female X-chromosome is transcriptionally silenced in order to balance gene dosage on the X-chromosome between males and females. It has been known since the discovery of the Barr body in the 1940’s that the active (Xa) and inactive (Xi) X-chromosomes fold differently. However, the precise structures adopted by the two Xs, the mechanisms that cause the Xa and Xi to fold differently, and the role of the unique structure of the Xi in silencing were unknown. In this thesis, I describe our work defining the structures of the Xa and the Xi, the role of Xist RNA and cohesin proteins in shaping the organization of the Xi, and testing whether the “super-structure” of the Xi is necessary for gene silencing. I performed allele-specific Hi-C to map the structures of the Xa and Xi at high resolution and found that while the Xa is organized into megabase-sized topologically associated domains (TADs) like all the other chromosomes, the Xi is largely devoid of TADs. Allele-specific ChIP-seq showed that cohesin proteins, which are necessary for folding chromosomes into TADs, are depleted from the Xi. Deletion of Xist allows partial restoration of both cohesin binding and TADs across large regions of the Xi, suggesting that Xist RNA removes cohesin from chromatin and breaks down TADs on the Xi.
Although the Xi lacks TADs, it folds into two very large “megadomains”, each tens of megabases in size. There is an unusual tandem repeat locus called Dxz4 at the border between the two megadomains. Dxz4 also forms a ~25 Mb looping interaction with another tandem repeat called Firre specifically on the Xi. I generated single and double deletions of Dxz4 and Firre in mouse embryonic stem cells. Deletion of Dxz4 prevented megadomain formation and deletion of Firre partially disrupted interactions within megadomains. However, deletion of Dxz4, Firre or both loci had no impact on the ability of XCI to initiate, suggesting that the large-scale organization of the Xi is not needed for gene silencing.
Medical Sciences
Advisors/Committee Members: Kingston, Robert (advisor), Hochedlinger, Konrad (committee member), Mostoslavsky, Raul (committee member), Bach, Ingolf (committee member).
Subjects/Keywords: Chromatin conformation; X-inactivation; X-chromosome; Hi-C; 4C; ChIP-seq; chromatin; cohesin; CTCF; tandem repeat; chromatin; epigenetics; genomics; Dxz4; Firre; Xist; proteomics; RNA; lncRNA; long noncoding RNA; Barr Body
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APA ·
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APA (6th Edition):
Froberg, J. E. (2018). The Spatial Organization of the X-chromosome and its Impact on X-inactivation. (Doctoral Dissertation). Harvard University. Retrieved from http://nrs.harvard.edu/urn-3:HUL.InstRepos:41121361
Chicago Manual of Style (16th Edition):
Froberg, John E. “The Spatial Organization of the X-chromosome and its Impact on X-inactivation.” 2018. Doctoral Dissertation, Harvard University. Accessed February 27, 2021.
http://nrs.harvard.edu/urn-3:HUL.InstRepos:41121361.
MLA Handbook (7th Edition):
Froberg, John E. “The Spatial Organization of the X-chromosome and its Impact on X-inactivation.” 2018. Web. 27 Feb 2021.
Vancouver:
Froberg JE. The Spatial Organization of the X-chromosome and its Impact on X-inactivation. [Internet] [Doctoral dissertation]. Harvard University; 2018. [cited 2021 Feb 27].
Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:41121361.
Council of Science Editors:
Froberg JE. The Spatial Organization of the X-chromosome and its Impact on X-inactivation. [Doctoral Dissertation]. Harvard University; 2018. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:41121361
3.
Lebo, Kevin J.
The role of the TLC1 RNA flexible scaffold in yeast telomerase function.
Degree: 2014, Johns Hopkins University
URL: http://jhir.library.jhu.edu/handle/1774.2/38007
► In eukaryotic cells, the ends of the chromosomes are capped by structures known as telomeres, comprised of repeated DNA segments bound by proteins. Many organisms…
(more)
▼ In eukaryotic cells, the ends of the chromosomes are capped by structures known as telomeres, comprised of repeated DNA segments bound by proteins. Many organisms employ a ribonucleoprotein (RNP) complex, telomerase, to counteract the telomere DNA shortening that occurs during each cell cycle. Telomerase is minimally composed of a telomerase reverse transcriptase (TERT) and a telomerase
RNA component, although other accessory protein subunits are required for telomere maintenance in vivo. In the budding yeast Saccharomyces cerevisiae, the telomerase
RNA is the 1157-nt TLC1. TLC1 forms a Y-shaped overall secondary structure, with three long arms radiating out from a central catalytic core. Yeast TERT (Est2) localizes to the central core, while accessory proteins, including Est1, Ku, and Sm7, each bind to the tip of a different
RNA arm. TLC1 organizes the telomerase RNP by serving as a flexible scaffold, in which accessory protein binding sites can be relocated on the
RNA with retention of function. My research has focused on understanding how the TLC1 flexible scaffold regulates telomerase function. By designing a version of TLC1 with stiffened
RNA arms, I have demonstrated that physical flexibility in the
RNA is not required for telomerase function. This suggests that rather than allowing the proteins to “flex to position,” TLC1 organizes the RNP as “beads on a string,” without specific orientations required for accessory protein function. Furthermore, I identified a Second Essential Est1-arm Domain (SEED) in the Est1-binding arm of TLC1, which has an essential function independent of Est1 protein. This indicates that portions of the flexible scaffold
RNA have roles beyond passive scaffolding. Next, while designing a version of TLC1 that would fold competently for function both in vivo and in vitro, I uncovered a previously unknown role for the Ku-binding arm
RNA in
RNA structure and abundance. Finally, I identified a region of the terminal arm
of TLC1 that helps to regulate telomerase
RNA levels in the cell. Overall, my research has advanced the flexible scaffold model for telomerase
RNA, and suggests that the flexible scaffold RNP may best be viewed as a series of functional modules, which includes both proteins and
RNA domains, all tethered together by intervening segments of
RNA in non-specific positions within the RNP holoenzyme.
Advisors/Committee Members: Zappulla, David C (advisor).
Subjects/Keywords: lncRNA;
scaffold;
TLC1;
telomere;
yeast;
Telomerase;
RNA
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APA ·
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APA (6th Edition):
Lebo, K. J. (2014). The role of the TLC1 RNA flexible scaffold in yeast telomerase function. (Thesis). Johns Hopkins University. Retrieved from http://jhir.library.jhu.edu/handle/1774.2/38007
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Lebo, Kevin J. “The role of the TLC1 RNA flexible scaffold in yeast telomerase function.” 2014. Thesis, Johns Hopkins University. Accessed February 27, 2021.
http://jhir.library.jhu.edu/handle/1774.2/38007.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Lebo, Kevin J. “The role of the TLC1 RNA flexible scaffold in yeast telomerase function.” 2014. Web. 27 Feb 2021.
Vancouver:
Lebo KJ. The role of the TLC1 RNA flexible scaffold in yeast telomerase function. [Internet] [Thesis]. Johns Hopkins University; 2014. [cited 2021 Feb 27].
Available from: http://jhir.library.jhu.edu/handle/1774.2/38007.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Lebo KJ. The role of the TLC1 RNA flexible scaffold in yeast telomerase function. [Thesis]. Johns Hopkins University; 2014. Available from: http://jhir.library.jhu.edu/handle/1774.2/38007
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
4.
지, 별아.
Profiling of long non-coding RNA in hepatocellular carcinoma.
Degree: 2017, Ajou University
URL: http://repository.ajou.ac.kr/handle/201003/16405
;
http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000025972
► Hepatocellular carcinoma (HCC) is the predominant subject of liver malignancies which provoke global concern. Previous studies have shown that long non-coding RNAs (lncRNAs) are differentially…
(more)
▼ Hepatocellular carcinoma (HCC) is the predominant subject of liver malignancies which provoke global concern. Previous studies have shown that long non-coding RNAs (lncRNAs) are differentially expressed in HCC, which have distinct functional roles in the pathogenesis of HCC. Recent advance of high-throughput RNA sequencing have revealed that numerous non-coding RNAs are expressed in cancers. Here, to deleineate functional lncRNAs in HCC, RNA-seq profiling was performed. I found 23 differentially expressed lncRNAs in the HCCs compared to non-tumoral tissues. Of these, 15 lncRNAs showed the correlated expression between antisense and sense lncRNAs, inclduding HAND2-AS1 and HAND2. The functional effects of HAND2-AS1 or HAND2 expression in liver cancers were further evaluated. Overexpression of HAND2-AS1 or HAND2 inhibited the proliferation and migration of liver cancer cells in vitro. The xenografted in vivo mouse model also showed significant reduction of tumor size by knockdown of HAND2. In addition, I found that the HAND2 mRNA expression was induced by HAND2-AS1 overexpression. This HAND2-AS1-mediated HAND2 expression was mediated throguht phosphorylation of CREB transcription factor. In summary, genome-wide noncoding RNA profiling analysis could identify that HAND2-AS1 can play pivotal roles in liver cancer progression.
Long non coding RNA 는 단백질로 번역되지 않는 200 bp 이상의 전사체로 정의되며 lncRNA 는 그 개수만큼이나 역할이나 기전도 다양할 것으로 추정되고 있다. 그러나 근래 들어 다양한 종류의 lncRNA 에서 기전이 하나 둘씩 알려짐에 따라 lncRNA 에 대한 관심이 점차 높아지고 있으며, 특히 암과 연관이 있다는 점이 밝혀지면서 lncRNA 를 통해 암의 발생과 전이 기전을 설명할 수 있을 것으로 기대를 모으고 있다. 이에 본 연구에서는 간암과 연관된 lncRNA 를 찾고자 하였다. 이를 위해, 본 연구에서는 간암환자의 시료 및 주변 정상조직을 이용하여 RNA 시컨싱을 수행하였으며 이 데이터를 바탕으로 전사체 프로파일링을 수행하여 간암에서의 antisense lncRNAs 발현 변화를 밝히고자 하였다. 간암시료에서 특이적으로 발현되는 23 개의 antisense lncRNAs 발굴하였다. 이 중 antisense 및 antisense RNA 의 역방향으로 인접한 전사체의 발현량의 상관분석을 통해, HAND2-AS1 과 HAND2 두 유전자의 발현이 밀접한 상관관계가 있음을 확인하였다. 간암 세포주를 대상으로 한 실험적 검증을 통해 HAND2 와 HAND2-AS1 이 세포의 증식, 전이를 억제시킴을 확인하였다. 또한, HAND2-AS1 이 과발현된 간암세포주에서 특이적으로 HAND2 mRNA 발현이 증가됨을 관찰하였으며, 이는 HAND2-AS1 가 전사단계 수준에서 HAND2 발현을 조절하고 있음을 시사한다. 이를 검증하기 위해, HAND2-AS1 이 과발현하는 간암세포주에서, HAND2 와 HAND2-AS1 사이에 존재하는 CREB 결합부위를 대상으로 luciferase assay 를 수행한 결과, CREB 결합부위가 HAND2 및 HAND2-AS 의 발현을 조절함을 관찰하였다. 이상의 연구에서, HAND2-AS1 를 포함한 비암호화 유전자 (ncRNA) 발현이 간암의 종양형성에 중요한 역할을 하고 있음을 제시하였다.
I. INTORDUCTION 1
II. MATERIALS AND METHODS 3
1. Cell culture 3
2. Clinical samples 3
3. RNA isolation, DNA library preparation and sequencing 3
4. Gene expression constructs and lentiviral vector transfection 4
5. quantitative RTPCR 5
6. Western Blotting 5
7. Colony formation assay 6
8. Migration assay 6
9. Xenograft Mouse model 7
10. Construction of luciferase reporter plasmid 7
11. Luciferase reporter assay 8
12. Estimation of transcript expression 8
13. Analysis of public data 9
14. Statistical analysis 9
III. RESULTS 10
1. Overall distribution of whole transcripts in hepatocellular carcinoma by RNAseq 10
2. Differentially expressed antisense lncRNAs in HCC 15
3. Clinical…
Advisors/Committee Members: 대학원 의생명과학과, 201224132, 지, 별아.
Subjects/Keywords: Hepatocellular carcinoma (HCC); Transcripts expression profiling; Long noniicoding RNA (lncRNA); Antisense RNA; 간암; 비암호화 유전자(lncRNA); Antisense lncRNA; HAND2; HAND2-AS1
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APA ·
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MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
지, . (2017). Profiling of long non-coding RNA in hepatocellular carcinoma. (Thesis). Ajou University. Retrieved from http://repository.ajou.ac.kr/handle/201003/16405 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000025972
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
지, 별아. “Profiling of long non-coding RNA in hepatocellular carcinoma.” 2017. Thesis, Ajou University. Accessed February 27, 2021.
http://repository.ajou.ac.kr/handle/201003/16405 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000025972.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
지, 별아. “Profiling of long non-coding RNA in hepatocellular carcinoma.” 2017. Web. 27 Feb 2021.
Vancouver:
지 . Profiling of long non-coding RNA in hepatocellular carcinoma. [Internet] [Thesis]. Ajou University; 2017. [cited 2021 Feb 27].
Available from: http://repository.ajou.ac.kr/handle/201003/16405 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000025972.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
지 . Profiling of long non-coding RNA in hepatocellular carcinoma. [Thesis]. Ajou University; 2017. Available from: http://repository.ajou.ac.kr/handle/201003/16405 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000025972
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
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)
▼ 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 combination of bioinformatic tools and experimental data have identified that sORFs are in fact translated to small proteins called micropeptides. Thus non-coding
RNA previously annotated as non-protein forming, seem to have newly identified coding ability and therefore need to be reclassified as bifunctional
RNA. This review discusses the changing paradigms of ncRNA classification to include its coding functions, methods to identify sORFs within these classes, and the functional relevance of micropeptides. It also aims to highlight the potential application of micropeptides in therapeutic and agronomic interventions. Finally, it provides future research perspectives in this nascent but promising field of micropeptide biology.
Advisors/Committee Members: McCarthy, Fiona (advisor), Hagen, Darren (committeemember), Mosher, Rebecca (committeemember).
Subjects/Keywords: bifunctional RNA;
lncRNA;
micropeptide;
ncRNA;
Non-Coding RNA;
Proteomics
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APA ·
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APA (6th 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 (16th Edition):
Forstedt, Joshua. “Micropeptides Encoded by Non-Coding RNA
.” 2020. Masters Thesis, University of Arizona. Accessed February 27, 2021.
http://hdl.handle.net/10150/650831.
MLA Handbook (7th Edition):
Forstedt, Joshua. “Micropeptides Encoded by Non-Coding RNA
.” 2020. Web. 27 Feb 2021.
Vancouver:
Forstedt J. Micropeptides Encoded by Non-Coding RNA
. [Internet] [Masters thesis]. University of Arizona; 2020. [cited 2021 Feb 27].
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
6.
Le Béguec, Céline.
Analyse intégrative des ARN longs non-codants chez le chien et leurs implications dans le mélanome oral canin, modèle des mélanomes humains : Integrative analysis of long non-coding RNAs in dogs and their implications in canine oral melanoma, human melanoma model.
Degree: Docteur es, Génétique, Génomique, Bioinformatique, 2018, Rennes 1
URL: http://www.theses.fr/2018REN1B030
► Les ARN longs non-codants (lncRNAs) constituent une famille d'ARN hétérogènes qui jouent un rôle majeur dans de nombreux cancers et notamment dans les mélanomes. Le…
(more)
▼ Les ARN longs non-codants (lncRNAs) constituent une famille d'ARN hétérogènes qui jouent un rôle majeur dans de nombreux cancers et notamment dans les mélanomes. Le chien est un modèle naturel et spontané pour l’analyse génétique comparée des cancers et, l'annotation du génome canin a récemment été enrichie avec l'identification de plus 10 000 lncRNAs. Afin de réaliser des prédictions fonctionnelles bioinformatiques des lncRNAs, nous avons caractérisé les profils d'expression des lncRNAs canins à partir de 26 tissus distincts. Nous avons défini la spécificité tissulaire de l’expression des lncRNAs et inféré leur fonctionnalité potentielle par des analyses de génomique et de transcriptomique comparatives avec des données humaines issues du projet ENCODE (ENCyclopedia Of DNA Elements). Comme chez l'homme et la souris, une grande proportion de lncRNAs canins (44 %) est exprimée de manière spécifique au sein d’un tissu. Par une approche de génomique comparative, nous avons identifié plus de 900 lncRNAs orthologues entre l’homme et le chien et pour 26 % d’entre eux, des patrons d'expression entre tissus significativement conservés (p < 0,05). Dans le cadre de l'étude des mélanomes canins, nous avons analysé les données de RNA-seq de 52 échantillons tumeurs/contrôles de mélanomes oraux. Nous avons identifié plus de 750 lncRNAs différentiellement exprimés entre la tumeur et le contrôle (FDR < 0,01), dont plus de 100 conservés avec l’homme. Ces lncRNAs constituent de bons candidats pour étudier la régulation de la progression tumorale des mélanomes chez le chien et pourront être évalués pour leurs potentiels diagnostic et thérapeutique en médecine humaine et vétérinaire.
Long non-coding RNAs (lncRNAs) are a family of heterogeneous RNAs that play a major role in many cancers, particularly in melanomas. The dog is a natural and spontaneous model for the comparative genetic analysis of cancers and, the annotation of the canine genome has recently been enriched with the identification of over 10,000 lncRNAs. In order to perform functional bioinformatic predictions of lncRNAs, we have characterized the expression patterns of canine lncRNAs from 26 distinct tissues representative of the major functions of the organism. We defined the tissue specificity of lncRNAs expression and inferred their potential functionality by comparative genomic and transcriptomic analyses with human data from the ENCODE project (ENCyclopedia Of DNA Elements). As in humans and mice, we show that a large proportion of canine lncRNAs (44%) are expressed specifically within a tissue. Using a comparative genomic approach, we have identified more than 900 orthologue lncRNAs between humans and dogs, and we show that for 26% of them, tissue expression patterns are also significantly conserved (p < 0.05). In the study of canine melanomas, we investigated the lncRNAs from RNA-seq data from 52 tumour/control samples of oral melanoma. We identified more than 750lncRNAs differentially expressed between tumour…
Advisors/Committee Members: Hitte, Christophe (thesis director), Derrien, Thomas (thesis director).
Subjects/Keywords: LncRNA; Chien; RNA-Seq; Transcriptome; Génomique comparative; Élémenttransposable; Cancers; LncRNA; Dog; RNA-Seq; Transcriptome; Comparative genomics; Transposableelement; Cancers
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Le Béguec, C. (2018). Analyse intégrative des ARN longs non-codants chez le chien et leurs implications dans le mélanome oral canin, modèle des mélanomes humains : Integrative analysis of long non-coding RNAs in dogs and their implications in canine oral melanoma, human melanoma model. (Doctoral Dissertation). Rennes 1. Retrieved from http://www.theses.fr/2018REN1B030
Chicago Manual of Style (16th Edition):
Le Béguec, Céline. “Analyse intégrative des ARN longs non-codants chez le chien et leurs implications dans le mélanome oral canin, modèle des mélanomes humains : Integrative analysis of long non-coding RNAs in dogs and their implications in canine oral melanoma, human melanoma model.” 2018. Doctoral Dissertation, Rennes 1. Accessed February 27, 2021.
http://www.theses.fr/2018REN1B030.
MLA Handbook (7th Edition):
Le Béguec, Céline. “Analyse intégrative des ARN longs non-codants chez le chien et leurs implications dans le mélanome oral canin, modèle des mélanomes humains : Integrative analysis of long non-coding RNAs in dogs and their implications in canine oral melanoma, human melanoma model.” 2018. Web. 27 Feb 2021.
Vancouver:
Le Béguec C. Analyse intégrative des ARN longs non-codants chez le chien et leurs implications dans le mélanome oral canin, modèle des mélanomes humains : Integrative analysis of long non-coding RNAs in dogs and their implications in canine oral melanoma, human melanoma model. [Internet] [Doctoral dissertation]. Rennes 1; 2018. [cited 2021 Feb 27].
Available from: http://www.theses.fr/2018REN1B030.
Council of Science Editors:
Le Béguec C. Analyse intégrative des ARN longs non-codants chez le chien et leurs implications dans le mélanome oral canin, modèle des mélanomes humains : Integrative analysis of long non-coding RNAs in dogs and their implications in canine oral melanoma, human melanoma model. [Doctoral Dissertation]. Rennes 1; 2018. Available from: http://www.theses.fr/2018REN1B030
Vanderbilt University
7.
Collier, Sarah Parker.
TMEVPG1, a long noncoding RNA within the immune system.
Degree: PhD, Microbiology and Immunology, 2014, Vanderbilt University
URL: http://hdl.handle.net/1803/10859
► Thousands of genes encoding long noncoding RNAs were identified throughout the genome; however, less than 1% of known long noncoding RNAs have been assigned a…
(more)
▼ Thousands of genes encoding long noncoding RNAs were identified throughout the genome; however, less than 1% of known long noncoding RNAs have been assigned a biologic function. At present, long noncoding RNAs mediate positive or negative regulation target gene transcription within nearly all developmental systems establishing an additional layer of noncoding regulation of protein-coding genes. Within the immune system we identified TMEVPG1, an enhancer
lncRNA that contributes to the Th1 differentiation program of key adaptive immune cells resulting in the expression of the pleiotropic cytokine interferon gamma. As with other developmental programs, our results demonstrate that a
lncRNA plays an essential role in Th1 cell biology.
Advisors/Committee Members: Andrew Link (committee member), Anthony Weil (committee member), Jim Patton (committee member), Amy Major (committee member), Thomas Aune (committee member), Eric Sebzda (Committee Chair).
Subjects/Keywords: lincRNA; lncRNA; interferon gamma; gene regulation; noncoding RNA
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APA (6th Edition):
Collier, S. P. (2014). TMEVPG1, a long noncoding RNA within the immune system. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/10859
Chicago Manual of Style (16th Edition):
Collier, Sarah Parker. “TMEVPG1, a long noncoding RNA within the immune system.” 2014. Doctoral Dissertation, Vanderbilt University. Accessed February 27, 2021.
http://hdl.handle.net/1803/10859.
MLA Handbook (7th Edition):
Collier, Sarah Parker. “TMEVPG1, a long noncoding RNA within the immune system.” 2014. Web. 27 Feb 2021.
Vancouver:
Collier SP. TMEVPG1, a long noncoding RNA within the immune system. [Internet] [Doctoral dissertation]. Vanderbilt University; 2014. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/1803/10859.
Council of Science Editors:
Collier SP. TMEVPG1, a long noncoding RNA within the immune system. [Doctoral Dissertation]. Vanderbilt University; 2014. Available from: http://hdl.handle.net/1803/10859
Penn State University
8.
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 ·
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CSE |
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to Zotero / EndNote / Reference
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APA (6th 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 (16th 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 February 27, 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 (7th Edition):
Yetming, Kristen Dominique. “BHLF1, a Lytic-Cycle Gene Encoding a Long Non-Coding RNA Contributes to Epstein-Barr Virus Latency.” 2017. Web. 27 Feb 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 Feb 27].
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
Harvard University
9.
Broadbent, Kate Mariel.
The regulatory capacity of long non-coding RNA in Plasmodium falciparum malaria.
Degree: PhD, Systems Biology, 2014, Harvard University
URL: http://nrs.harvard.edu/urn-3:HUL.InstRepos:13065005
► The mechanisms underpinning gene regulation in P. falciparum malaria remain largely elusive, though mounting evidence suggests a major role for epigenetic feedback. Interestingly, long non-(protein)-coding…
(more)
▼ The mechanisms underpinning gene regulation in P. falciparum malaria remain largely elusive, though mounting evidence suggests a major role for epigenetic feedback. Interestingly, long non-(protein)-coding RNAs (lncRNAs) have been found to play a dominant role in initiating and guiding the transcriptional, epigenetic, and post-transcriptional status of specific loci across a broad range of organisms. LncRNAs are uniquely poised to act co-transcriptionally on neighboring loci, and/or to remain physically tethered at their site of origin, and through sequence-specific binding activities can impart temporal and spatial specificity to ubiquitously expressed nuclear protein complexes. Proteins, on the other hand, must be translated in the cytoplasm, and hence lose memory of their transcriptional origins. Encouraged by these features of lncRNAs, we set out to investigate the regulatory capacity of P. falciparum lncRNAs on a genome-wide scale.
First, we surveyed transcriptional activity across approximately one quarter of the P. falciparum genome using a custom high-density DNA tiling array. We predicted a set of 60 developmentally regulated intergenic lncRNAs, and found that many of these novel loci neighbored genes involved in parasite survival or virulence pathways. Remarkably, upon further analysis of intergenic
lncRNA properties, we discovered a family of twenty-two telomere-associated lncRNAs encoded in the telomere-associated repetitive element (TARE) region of P. falciparum chromosome ends. We found that each
lncRNA-TARE was encoded adjacent and divergent to a subtelomeric var virulence gene. Moreover, we found that
lncRNA-TARE expression was sharply induced between the parasite DNA replication and cell division cycles, that
lncRNA-TARE loci contained numerous transcription factor binding sites only otherwise found in subtelomeric var promoter regions, and that the GC content and evolutionary sequence conservation of
lncRNA-TAREs was similar to that of P. falciparum ribosomal
RNA.
Next, we set out to assemble P. falciparum intergenic
lncRNA and antisense
RNA transcript structures using state-of-the-art deep sequencing and computational tools. Towards this end, we harvested an unprecedented sample set that finely maps temporal changes across 56 hours of P. falciparum blood stage development, and developed and validated strand-specific, non-polyA-selected
RNA sequencing methods. This enabled the annotation of over one thousand high-confidence, bona fide
lncRNA transcript models, and their comprehensive global analysis. We discovered an enrichment of negatively correlated, tail-to-tail overlapping sense-antisense transcript pairs, suggesting a conserved role for antisense-mediated transcriptional interference in P. falciparum gene regulation. We also discovered a highly correlated spliced antisense counterpart to a gene required for sexual commitment, that the expression of an intriguing subset of antisense transcripts significantly dropped during parasite invasion, and that
lncRNA-TARE and 'sterile' var virulence…
Advisors/Committee Members: Rinn, John L (advisor), Murray, Andrew (committee member), Wirth, Dyann (committee member), Niles, Jacquin (committee member), Marti, Matthias (committee member).
Subjects/Keywords: Parasitology; Genetics; Bioinformatics; antisense; lncRNA; malaria; plasmodium; RNA; telomere
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CSE |
Export
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APA (6th Edition):
Broadbent, K. M. (2014). The regulatory capacity of long non-coding RNA in Plasmodium falciparum malaria. (Doctoral Dissertation). Harvard University. Retrieved from http://nrs.harvard.edu/urn-3:HUL.InstRepos:13065005
Chicago Manual of Style (16th Edition):
Broadbent, Kate Mariel. “The regulatory capacity of long non-coding RNA in Plasmodium falciparum malaria.” 2014. Doctoral Dissertation, Harvard University. Accessed February 27, 2021.
http://nrs.harvard.edu/urn-3:HUL.InstRepos:13065005.
MLA Handbook (7th Edition):
Broadbent, Kate Mariel. “The regulatory capacity of long non-coding RNA in Plasmodium falciparum malaria.” 2014. Web. 27 Feb 2021.
Vancouver:
Broadbent KM. The regulatory capacity of long non-coding RNA in Plasmodium falciparum malaria. [Internet] [Doctoral dissertation]. Harvard University; 2014. [cited 2021 Feb 27].
Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:13065005.
Council of Science Editors:
Broadbent KM. The regulatory capacity of long non-coding RNA in Plasmodium falciparum malaria. [Doctoral Dissertation]. Harvard University; 2014. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:13065005
10.
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
► 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)
▼ 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 is to better understand the Myc-conferred epigenetic status of cells. We have previously identified the long non-coding RNA (lncRNA), H19, as a target of Myc regulation and shown it to be important for transformation in lung and breast cells. These results prompted further analysis to identify similarly important Myc-regulated lncRNAs. Myc-regulated lncRNAs associated with the cell cycle and transformation have been identified by microarray analysis. A small number of candidate lncRNAs that were differentially expressed in both the cell cycle and transformation have been validated. Given the increasing importance of lncRNAs and epigenetics to cancer biology, the discovery of Myc-induced, growth associated lncRNAs could provide insight into the mechanisms behind Myc-related epigenetic signatures in both normal and disease states.
MAST
Advisors/Committee Members: Marsden, Philip A., Penn, Linda Z., Laboratory Medicine and Pathobiology.
Subjects/Keywords: c-Myc; long non-coding RNA; lncRNA; breast cancer; cancer biology; transcription; epigenetics; 0369; 0487; 0571
…coding RNA genes could figure in prominently. As such, lncRNA biology could
contribute to our… …Information
non-coding RNA
N-terminal domain
nucleosome remodeling deacetylase
open reading frame… …transcript
viii
1
Chapter 1
Introduction
c-Myc (Myc) is a major player in many… …now called cellular Myc (c-Myc or Myc)
(24). The family of Myc also… …includes c-Myc, L-Myc, N-Myc, S-Myc, and B-Myc (25, 26, 27,
28, 28, 29). The…
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APA ·
Chicago ·
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Export
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APA (6th 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 (16th 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 February 27, 2021.
http://hdl.handle.net/1807/42402.
MLA Handbook (7th Edition):
MacDougall, Matthew Steven. “Investigation of Myc-regulated Long Non-coding RNAs in Cell Cycle and Myc-dependent Transformation.” 2012. Web. 27 Feb 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 Feb 27].
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
11.
Ali, Mohamad.
Cell cycle regulation in cancer: A noncoding perspective.
Degree: 2019, University of Gothenburg / Göteborgs Universitet
URL: http://hdl.handle.net/2077/61690
► The cell cycle progression is tightly regulated to ensure error-free cell replication. The complexity of the transcriptional machinery aids to function in a spatiotemporal pattern…
(more)
▼ The cell cycle progression is tightly regulated to ensure error-free cell replication. The complexity of the transcriptional machinery aids to function in a spatiotemporal pattern across different phases and genomic loci. However, the cell cycle regulation has always been associated with a “protein-centric” view that implicates an intricate network of closely related proteins and transcription factors. This view neglects the fact that only 2 ̶ 2.3% of the human genome codes for proteins. On the other hand, more than 70% of the human genome undergoes pervasive transcription of, most likely, regulatory non-coding RNA (ncRNA) counterparts. Thus, the interrogation of the intimate functional relationship of ncRNAs to cell cycle progression and tumor homeostasis in different cancer types is indispensable. To this end, in the first study of the current thesis, we optimized a nascent RNA capture assay coupled with high throughput sequencing that enables high-resolution mapping of ongoing RNA transcriptional events. The study revealed the temporal separation between DNA replication and RNA transcription, where replication timing has an inverse correlation with transcription.
Given that the DNA replication is the most critical process during cellular division, the regulatory elements governing the S phase progression would be of great importance for cell survival. Thus, in the second study, we utilized our optimized nascent RNA capture assay to identify the long noncoding RNAs (lncRNAs), which are enriched in different compartments of the S phase in HeLa cells. Then, we analyzed the expression patterns of the identified lncRNAs across the cancer genome atlas (TCGA) datasets and determined their clinical relevance in different types of cancer. We uncoupled the function of an uncharacterized lncRNA, termed as SCAT7, which harbored oncogenic properties that promote cell cycle progression. Transcriptome-wide analysis of cells depleted of SCAT7 demonstrated its role in activating FGF/FGFR signaling and the downstream PI3K-AKT pathway in different cancer models, including lung adenocarcinoma (LUAD) and renal cell carcinoma. The SCAT7-mediated activation of PI3K/AKT signaling depends on the lncRNA interaction with a protein complex comprising hnRNPK and YBX1 proteins. Therefore, the therapeutic targeting of SCAT7 in mouse xenografts and PDX models reduced tumors progression significantly.
In the third study, we uncoupled the DNA replication-related functions of SCAT7. Using a combination of immuno-precipitation, immuno-fluorescence, and DNA combing assays, we report that SCAT7 physically interacts and regulates the topoisomerase I (TOP1) turnover via protein ubiquitination. The depletion of SCAT7 induces accumulation of TOP1 that creates replication stress and double-stranded breaks. However, SCAT7 abrogation also interferes with DNA homology-directed repair and inhibits the phosphorylation of ATM protein. Subsequently, the TOP1-induced DNA damage persists, causing further replication stress and cellular death. We also uncover the…
Subjects/Keywords: Long Noncoding RNA; lncRNA; Cell cycle; S phase; Mitosis; Checkpoint; Cancer; SCAT7; LY6K-AS
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Ali, M. (2019). Cell cycle regulation in cancer: A noncoding perspective. (Thesis). University of Gothenburg / Göteborgs Universitet. Retrieved from http://hdl.handle.net/2077/61690
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Ali, Mohamad. “Cell cycle regulation in cancer: A noncoding perspective.” 2019. Thesis, University of Gothenburg / Göteborgs Universitet. Accessed February 27, 2021.
http://hdl.handle.net/2077/61690.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Ali, Mohamad. “Cell cycle regulation in cancer: A noncoding perspective.” 2019. Web. 27 Feb 2021.
Vancouver:
Ali M. Cell cycle regulation in cancer: A noncoding perspective. [Internet] [Thesis]. University of Gothenburg / Göteborgs Universitet; 2019. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/2077/61690.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Ali M. Cell cycle regulation in cancer: A noncoding perspective. [Thesis]. University of Gothenburg / Göteborgs Universitet; 2019. Available from: http://hdl.handle.net/2077/61690
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Melbourne
12.
Chen, Yu.
Hormone-responsive networks influence urethral closure and phallus growth.
Degree: 2018, University of Melbourne
URL: http://hdl.handle.net/11343/221906
► Phallus development in mammals is androgen-dependent but can be affected by oestrogen. Many genes that are important in regulating phallus development in mice are also…
(more)
▼ Phallus development in mammals is androgen-dependent but can be affected by oestrogen. Many genes that are important in regulating phallus development in mice are also androgen and/or oestrogen responsive. The balance between androgen receptor (AR) and oestrogen receptor α (ERα) activity is important to maintain normal penile development. Interfering this balance either by treating with sex steroids or AR inhibitors, such as flutamide, induces abnormal phallus phenotype in mice and rat. However, very few studies have looked into the global regulation of gene networks on phallus development under the direct effects of sex steroids. Different from eutherian mammals, tammar wallaby has a unique phallus developmental process, where the phallus differentiation occurs postnatally. Such unique postnatal development allows us to observe the direct effects of sex hormones on phallus development without considering maternal physiology and placental transfer. In this thesis, male tammar wallabies were treated with oestrogen and females were treated with the adiol from day 20-40 postpartum (pp) during the established androgen imprinting window (day 25-30 pp). Another group of male tammars were castrated at day 25 pp. Phalluses were collected for morphological comparison at day 150 pp, when urethral closure was almost completed, and for transcriptomic analysis at day 50 pp when they first become sexually dimorphic to examine changes in multiple signalling pathways, including SHH/WNT signalling pathways, IGF1 signalling pathway and AP-1 signalling pathway, as well as to identify novel hormonal responsive lncRNAs, such as, lnc-BMP5, lnc- ZBTB16 and lnc-RSPO4, during phallus development in the tammar.
Administration of oestrogen to males inhibited phallus elongation but had no effect on urethral closure and did not significantly depress testicular androgen synthesis. Androgen treatment during the imprinting window in females did not promote phallus elongation but did initiate urethral closure. Along with multiple stage hormonal treatments conducted by Leihy, et al., (2004) in the tammar phallus, the data suggests that short-term exposure of androgen during the window of sensitivity is necessary for urethral closure, but a constant level of androgen is required to maintain later phallus elongation.
Hormonal manipulation altered gene expression in multiple signalling pathways during tammar phallus development. Adiol treatment suppressed SHH expression and its associated genes, including MAFB, WNT5A and RSPO4, but upregulated IGF1 and AP 1 genes in male phalluses at day 50 pp. After day 50 pp, SHH was transiently increased in male phalluses, which might be regulated by the increase level of IGF2 in the liver. The androgen-SHH switch might be the signalling constraint for the timing of phallus differentiation. While, the later activation of both endocrine IGF2-SHH and androgen- IGF1 signalling may be required to trigger and maintain male urethral closure. More interestingly, the activation of androgen dependent window (day…
Subjects/Keywords: hypospadias; lncRNA; RNA-Seq; WGCNA; marsupial; androstanediol; phallus; androgen receptor; oestrogen receptor; castration
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Chen, Y. (2018). Hormone-responsive networks influence urethral closure and phallus growth. (Doctoral Dissertation). University of Melbourne. Retrieved from http://hdl.handle.net/11343/221906
Chicago Manual of Style (16th Edition):
Chen, Yu. “Hormone-responsive networks influence urethral closure and phallus growth.” 2018. Doctoral Dissertation, University of Melbourne. Accessed February 27, 2021.
http://hdl.handle.net/11343/221906.
MLA Handbook (7th Edition):
Chen, Yu. “Hormone-responsive networks influence urethral closure and phallus growth.” 2018. Web. 27 Feb 2021.
Vancouver:
Chen Y. Hormone-responsive networks influence urethral closure and phallus growth. [Internet] [Doctoral dissertation]. University of Melbourne; 2018. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/11343/221906.
Council of Science Editors:
Chen Y. Hormone-responsive networks influence urethral closure and phallus growth. [Doctoral Dissertation]. University of Melbourne; 2018. Available from: http://hdl.handle.net/11343/221906
13.
Diaz-Miranda, Maria Alejandra.
Transcript Diversity In The Protozoan Parasite Toxoplasma Gondii.
Degree: 2017, University of Pennsylvania
URL: https://repository.upenn.edu/edissertations/2256
► Technological advances have made possible to sequence RNA transcripts at unprecedented depth, enabling deep profiling of abundance and diversity under a variety of conditions. Such…
(more)
▼ Technological advances have made possible to sequence RNA transcripts at unprecedented depth, enabling deep profiling of abundance and diversity under a variety of conditions. Such information permits refinement of draft genome annotation originally generated in the absence of transcript coverage data, and provides new insights into organismal biology and regulatory mechanisms. This dissertation provides an extensive analysis of mRNA-seq data from the obligate intracellular protozoan parasite Toxoplasma gondii, a ubiquitous pathogen of humans and other vertebrates. We produced and sequenced 24 strand-specific RNA libraries from several parasite strains and developmental stages, and examined these in con�junction with 45 additional mRNA-seq libraries produced by other groups.
The current reference genome annotation for T. gondii, generated using de novo methods informed by cDNA sequencing prior to mRNA-seq, identifies ~8300 protein-coding genes, fragmented by ~40K introns. Untranslated regions are incompletely defined, few alternatively-spliced transcripts are described, and non-coding transcripts remain largely unexplored. mRNA-seq datasets presented in this dissertation define a total of 2.7M introns, most observed at vanishingly low abundance. Using current annotation to define parameters minimizing false discovery yields ~60K likely splice junctions. Comparing the frequency of intron-spanning reads to the abundance of transcripts to which introns belong provides a reliable metric for estimating intron excision, readily distinguishing introns that are (i) universally used, (ii) alternatively-spliced, or (iii) likely insignificant. Genome-wide analysis suggests ~3000 annotated introns that should be deleted from the reference genome, ~1400 to be added as alternative isoforms, ~3100 as additions to existing annotation (often within UTRs) and ~3400 associated with novel transcripts. Transcriptomic expression is consis�tent with biological and phenotypic variation across the complex parasite life cycle, including undescribed differences in gene expression during intracellular tachyzoite replication. Strong circumstantial evidence also suggests that lncRNAs may play an important role in regulating stage-specific expression during sexual differentia�tion and sporogony. These results provide the basis for revising the reference T. gondii genome annotation available at ToxoDB.org and GenBank. Strategies developed in this dissertation also provide the basis for defining annotation criteria for other species, including related parasites responsible for malaria and conceivably other eukaryotes as well.
Subjects/Keywords: Alternative splicing; Eukaryotic genome annotation; lncRNA; RNA-seq; Toxoplasma gondii; Transcriptomics; Biology
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APA (6th Edition):
Diaz-Miranda, M. A. (2017). Transcript Diversity In The Protozoan Parasite Toxoplasma Gondii. (Thesis). University of Pennsylvania. Retrieved from https://repository.upenn.edu/edissertations/2256
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Diaz-Miranda, Maria Alejandra. “Transcript Diversity In The Protozoan Parasite Toxoplasma Gondii.” 2017. Thesis, University of Pennsylvania. Accessed February 27, 2021.
https://repository.upenn.edu/edissertations/2256.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Diaz-Miranda, Maria Alejandra. “Transcript Diversity In The Protozoan Parasite Toxoplasma Gondii.” 2017. Web. 27 Feb 2021.
Vancouver:
Diaz-Miranda MA. Transcript Diversity In The Protozoan Parasite Toxoplasma Gondii. [Internet] [Thesis]. University of Pennsylvania; 2017. [cited 2021 Feb 27].
Available from: https://repository.upenn.edu/edissertations/2256.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Diaz-Miranda MA. Transcript Diversity In The Protozoan Parasite Toxoplasma Gondii. [Thesis]. University of Pennsylvania; 2017. Available from: https://repository.upenn.edu/edissertations/2256
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Duke University
14.
Huynh, Nguyen Phuong Thao.
Bioinformatics and Molecular Approaches for the Construction of Biological Artificial Cartilage
.
Degree: 2018, Duke University
URL: http://hdl.handle.net/10161/18214
► Osteoarthritis (OA) is one of the leading causes of disability in the United States, afflicting over 27 million Americans and imposing an economic burden…
(more)
▼ Osteoarthritis (OA) is one of the leading causes of disability in the United States, afflicting over 27 million Americans and imposing an economic burden of more than $128 billion each year (1, 2). OA is characterized by progressive degeneration of articular cartilage together with sub-chondral bone remodeling and synovial joint inflammation. Currently, OA treatments are limited, and inadequate to restore the joint to its full functionality. Over the years, progresses have been made to create biologic cartilage substitutes. However, the repair of degenerated cartilage remains challenging due to its complex architecture and limited capability to integrate with surrounding tissues. Hence, there exists a need to create not only functional chondral constructs, but functional osteochondral constructs, which could potentially enhance affixing properties of cartilage implants utilizing the underlying bone. Furthermore, the molecular mechanisms driving chondrogenesis are still not fully understood. Therefore, detailed transcriptomic profiling would bring forth the progression of not only genes, but gene entities and networks that orchestrate this process. Bone-marrow derived mesenchymal stem cells (MSCs) are routinely utilized to create cartilage constructs in vitro for the study of chondrogenesis. In this work, we set out to examine the underlying mechanisms of these cells, as well as the intricate gene correlation networks over the time course of lineage development. We first asked the question of how transforming growth factors are determining MSC differentiation, and subsequently utilized genetic engineering to manipulate this pathway to create an osteochondral construct. Next, we performed high-throughput next-generation sequencing to profile the dynamics of MSC transcriptomes over the time course of chondrogenesis. Bioinformatics analyses of these big data have yielded a multitude of information: the chondrogenic functional module, the associated gene ontologies, and finally the elucidation of GRASLND and its crucial function in chondrogenesis. We extended our results with a detailed molecular characterization of GRASLND and its underlying mechanisms. We showed that GRASLND could enhance chondrogenesis, and thus proposed its therapeutic use in cartilage tissue engineering as well as in the treatment of OA.
Advisors/Committee Members: Guilak, Farshid (advisor), Capel, Blanche (advisor).
Subjects/Keywords: Bioengineering;
Bioinformatics;
Molecular biology;
Cartilage tissue engineering;
Chondrogenesis;
GRASLND;
lncRNA;
Mesenchymal stem cells;
RNA-Seq
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APA (6th Edition):
Huynh, N. P. T. (2018). Bioinformatics and Molecular Approaches for the Construction of Biological Artificial Cartilage
. (Thesis). Duke University. Retrieved from http://hdl.handle.net/10161/18214
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Huynh, Nguyen Phuong Thao. “Bioinformatics and Molecular Approaches for the Construction of Biological Artificial Cartilage
.” 2018. Thesis, Duke University. Accessed February 27, 2021.
http://hdl.handle.net/10161/18214.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Huynh, Nguyen Phuong Thao. “Bioinformatics and Molecular Approaches for the Construction of Biological Artificial Cartilage
.” 2018. Web. 27 Feb 2021.
Vancouver:
Huynh NPT. Bioinformatics and Molecular Approaches for the Construction of Biological Artificial Cartilage
. [Internet] [Thesis]. Duke University; 2018. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/10161/18214.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Huynh NPT. Bioinformatics and Molecular Approaches for the Construction of Biological Artificial Cartilage
. [Thesis]. Duke University; 2018. Available from: http://hdl.handle.net/10161/18214
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
15.
Muret, Kévin.
Annotation des ARN longs non-codants chez la poule et les espèces d’élevage : Focus sur les ARNlnc régulateurs du métabolisme des lipides : Long noncoding RNAs annotation in chicken and livestock species : Focus on lncRNAs regulating lipid metabolism.
Degree: Docteur es, Génétique, génomique et bio-informatique, 2018, Rennes, Agrocampus Ouest
URL: http://www.theses.fr/2018NSARC139
► L’annotation des génomes est un défi majeur pour lier les génotypes aux phénotypes. Identifier les ARN longs non-codants (ARNlnc) dans les génomes fait partie de…
(more)
▼ L’annotation des génomes est un défi majeur pour lier les génotypes aux phénotypes. Identifier les ARN longs non-codants (ARNlnc) dans les génomes fait partie de ce défi ; d’expression relativement faible, ils n’ont été mis en évidence que récemment (2012) par l’avènement des technologies de séquençage haut débit. Ces travaux de recherche ont permis à partir de données RNA-seq, de mettre en lumière un grand nombre d’ARNlnc chez les espèces d’élevage et en particulier chez la poule chez qui aucun ARNlnc n’était décrit au début de cette thèse (2015). Un premier travail a consisté à identifier ces ARNlnc en utilisant des échantillons de foie et tissu adipeux puis nous avons amélioré ce catalogue par intégration d’autres bases de données publiques d’ARNlnc disparates. De plus, d’après la littérature, les ARNlnc ont été décrits comme intervenant dans la régulation de tous les processus biologiques :de la structure cellulaire à l’expression des gènes. La problématique de l’équipe étant associée à la compréhension de la régulation du métabolisme des lipides chez la poule, mon second travail a consisté à établir la liste des ARNlnc connus dans le règne animal comme étant impliqués dans ce métabolisme ou dans le processus de stockage et de formation du tissu adipeux, l’adipogenèse. Les analyses de conservation par synténie ont permis de retrouver une vingtaine de ces ARNlnc chez la poule. Enfin, à partir de lignées divergentes pour le poids de gras abdominal, j’ai également mis en évidence de nouveaux ARNlnc potentiellement régulateurs de ce métabolisme lipidique.
Genome annotation is a major challenge in connecting genotypes with phenotypes. Identifying long noncoding RNAs (lncRNA) in genomes is part of this challenge; they are relatively low-expressed and have only been highlighted in 2012 thanks to the development of high throughput sequencing technologies. This research work has led to the identification of a large number of lncRNAs in livestock species, particularly in the chicken, in which no lncRNA had yet been described at the beginning of this thesis (2015). First, my aim was to identify these lncRNAs using liver and adipose tissue and to improve this catalogue by integrating other existing lncRNA public databases.Moreover, according to the literature, lncRNAs are involved in the regulation of any biological process, from gene expression to cell structure. One of the goals of our team is to understand the regulation of lipid metabolism in the chicken, I thus established the list of all lncRNAs known within the animal kingdom and involved in this metabolism or in adipogenesis, the process of storage and formation of adipose tissue. The conservation by synteny analyses revealed around twenty conserved lncRNAs in the chicken. From divergent abdominal fat weight chicken lines, I lastly identified new lncRNAs that potentially regulate this lipid metabolism.
Advisors/Committee Members: Lagarrigue, Sandrine (thesis director).
Subjects/Keywords: ARNlnc; RNA-Seq; Modélisation; Annotation; Conservation; Métabolisme des lipides; Adipogenèse; LncRNA; RNA-Seq; Modeling; Annotation; Conservation; Lipid metabolism; Adipogenesis
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Muret, K. (2018). Annotation des ARN longs non-codants chez la poule et les espèces d’élevage : Focus sur les ARNlnc régulateurs du métabolisme des lipides : Long noncoding RNAs annotation in chicken and livestock species : Focus on lncRNAs regulating lipid metabolism. (Doctoral Dissertation). Rennes, Agrocampus Ouest. Retrieved from http://www.theses.fr/2018NSARC139
Chicago Manual of Style (16th Edition):
Muret, Kévin. “Annotation des ARN longs non-codants chez la poule et les espèces d’élevage : Focus sur les ARNlnc régulateurs du métabolisme des lipides : Long noncoding RNAs annotation in chicken and livestock species : Focus on lncRNAs regulating lipid metabolism.” 2018. Doctoral Dissertation, Rennes, Agrocampus Ouest. Accessed February 27, 2021.
http://www.theses.fr/2018NSARC139.
MLA Handbook (7th Edition):
Muret, Kévin. “Annotation des ARN longs non-codants chez la poule et les espèces d’élevage : Focus sur les ARNlnc régulateurs du métabolisme des lipides : Long noncoding RNAs annotation in chicken and livestock species : Focus on lncRNAs regulating lipid metabolism.” 2018. Web. 27 Feb 2021.
Vancouver:
Muret K. Annotation des ARN longs non-codants chez la poule et les espèces d’élevage : Focus sur les ARNlnc régulateurs du métabolisme des lipides : Long noncoding RNAs annotation in chicken and livestock species : Focus on lncRNAs regulating lipid metabolism. [Internet] [Doctoral dissertation]. Rennes, Agrocampus Ouest; 2018. [cited 2021 Feb 27].
Available from: http://www.theses.fr/2018NSARC139.
Council of Science Editors:
Muret K. Annotation des ARN longs non-codants chez la poule et les espèces d’élevage : Focus sur les ARNlnc régulateurs du métabolisme des lipides : Long noncoding RNAs annotation in chicken and livestock species : Focus on lncRNAs regulating lipid metabolism. [Doctoral Dissertation]. Rennes, Agrocampus Ouest; 2018. Available from: http://www.theses.fr/2018NSARC139
University of New South Wales
16.
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 (6th 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 (16th 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 February 27, 2021.
http://handle.unsw.edu.au/1959.4/58668 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:46586/SOURCE02?view=true.
MLA Handbook (7th Edition):
Quek, Xiucheng. “Computational characterisation of the transcriptional landscape and long non-coding RNAs in cancer.” 2017. Web. 27 Feb 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 Feb 27].
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
17.
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 (6th 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 (16th 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 February 27, 2021.
http://rave.ohiolink.edu/etdc/view?acc_num=case1421428941.
MLA Handbook (7th Edition):
Smith, Jenna E. “Investigation of the mRNP and Transcriptome Regulated by
Nonsense-Mediated RNA Decay.” 2015. Web. 27 Feb 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 Feb 27].
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
Brno University of Technology
18.
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)
▼ 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 volume and the complexity of data from
RNA-seq experiments necessitate a scalable, and mathematical analysis based on a robust statistical model. Therefore, it is challenging to design integrated workflow, that incorporates the various analysis procedures. Particularly, the comparative transcriptome analysis is complicated due to several sources of measurement variability and poses numerous statistical challenges. In this research, we performed an integrated transcriptional profiling pipeline, which generates novel reproducible codes to obtain biologically interpretable results. Starting with the annotation of
RNA-seq data and quality assessment, we provided a set of codes to serve the quality assessment visualization needed for establishing the
RNA-Seq data analysis experiment. Additionally, we performed comprehensive differential gene expression analysis, presenting descriptive methods to interpret the
RNA-Seq data. For implementing alternative splicing and differential exons usage analysis, we improved the performance of the Bioconductor package DEXSeq by defining the open reading frame of the exonic regions, which are differentially used between biological conditions due to the alternative splicing of the transcripts. Furthermore, we present a new methodology to analyze the differentially expressed long non-coding
RNA, by finding the functional correlation of the long non-coding
RNA with neighboring differential expressed protein coding genes. Thus, we obtain a clearer view of the regulation mechanism, and give a hypothesis about the role of long non-coding
RNA in gene expression regulation.
Advisors/Committee Members: Provazník, Ivo (advisor), Babula, Petr (referee), Lexa,, Matej (referee).
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 (6th 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 (16th 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 February 27, 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 (7th Edition):
Abo Khayal, Layal. “Transkriptomická charakterizace pomocí analýzy RNA-Seq dat: Transcriptomic Characterization Using RNA-Seq Data Analysis.” 2019. Web. 27 Feb 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 Feb 27].
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
Universiteit Utrecht
19.
Cordeiro Machado Rodrigues, R.J.
Noncoding RNAs and Chromatin.
Degree: 2013, Universiteit Utrecht
URL: http://dspace.library.uu.nl:8080/handle/1874/261346
► During embryonic development organisms need to establish different cell types to carry out specific functions. Gene expression regulation through chromatin changes has more and more…
(more)
▼ During embryonic development organisms need to establish different cell types to carry out specific functions. Gene expression regulation through chromatin changes has more and more been found to play a major role in cellular differentiation.
RNA has also been found to be a player in gene expression regulation through mechanisms like
RNA interference. Recent studies show a great connection between
RNA and chromatin, though this field is in a very early stage. Here I discuss these recent findings in the
RNA and chromatin fields, focusing in noncoding RNAs. I will go through the mechanisms by which noncoding RNAs can regulate chromatin and gene expression. Through examples I will argue in favour that noncoding RNAs are important general players in chromatin remodelling and gene expression.
Advisors/Committee Members: Ketting, R.F..
Subjects/Keywords: RNAi; RNAe; lncRNA; chromatin; silencing; noncoding; long noncoding; siRNA; piwi; piRNA; 21U; 22G; Swi6; epigenetic; RNA
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APA (6th Edition):
Cordeiro Machado Rodrigues, R. J. (2013). Noncoding RNAs and Chromatin. (Masters Thesis). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/261346
Chicago Manual of Style (16th Edition):
Cordeiro Machado Rodrigues, R J. “Noncoding RNAs and Chromatin.” 2013. Masters Thesis, Universiteit Utrecht. Accessed February 27, 2021.
http://dspace.library.uu.nl:8080/handle/1874/261346.
MLA Handbook (7th Edition):
Cordeiro Machado Rodrigues, R J. “Noncoding RNAs and Chromatin.” 2013. Web. 27 Feb 2021.
Vancouver:
Cordeiro Machado Rodrigues RJ. Noncoding RNAs and Chromatin. [Internet] [Masters thesis]. Universiteit Utrecht; 2013. [cited 2021 Feb 27].
Available from: http://dspace.library.uu.nl:8080/handle/1874/261346.
Council of Science Editors:
Cordeiro Machado Rodrigues RJ. Noncoding RNAs and Chromatin. [Masters Thesis]. Universiteit Utrecht; 2013. Available from: http://dspace.library.uu.nl:8080/handle/1874/261346
20.
Andersen, Rebecca Ellen.
The novel long noncoding RNA Pnky regulates neurogenesis and neural stem cell maintenance in vivo.
Degree: Developmental and Stem Cell Biology, 2019, University of California – San Francisco
URL: http://www.escholarship.org/uc/item/2c0846rw
► While it is now appreciated that certain long noncoding RNAs (lncRNAs) have important functions in cell biology, relatively few have been shown to regulate development…
(more)
▼ While it is now appreciated that certain long noncoding RNAs (lncRNAs) have important functions in cell biology, relatively few have been shown to regulate development in vivo, particularly with genetic strategies that establish cis versus trans mechanisms. We have identified Pinky (Pnky) as a lncRNA that regulates neurogenesis in the embryonic and postnatal mouse brain. Pnky is a nuclear-enriched lncRNA that is divergent to the neighboring proneural transcription factor Pou3f2. In postnatal neural stem cells (NSCs) from the ventricular-subventricular zone (V-SVZ), Pnky knockdown promotes neuronal lineage commitment and expands the transit amplifying cell population, increasing neuron production several-fold. In the embryonic cortex, Pnky knockdown increases neuronal differentiation and depletes the NSC population prematurely. Furthermore, genetic deletion of Pnky results in the aberrant production of neuronal masses along the postnatal V-SVZ. In the developing cortex, Pnky regulates the production of projection neurons from NSCs in a cell-autonomous manner, and loss of Pnky alters postnatal cortical lamination. Surprisingly, Pou3f2 expression is not disrupted by deletion of the entire Pnky gene. Moreover, expression of Pnky from a bacterial artificial chromosome (BAC) transgene rescues the differential gene expression and increased neurogenesis of Pnky-knockout NSCs, as well as the developmental phenotypes of Pnky-deletion in vivo. Thus, despite being transcribed divergently from a key developmental transcription factor, the lncRNA Pnky regulates neural development in trans.
Subjects/Keywords: Developmental biology; Neurosciences; Molecular biology; cortical development; lncRNA knockout mouse; long noncoding RNA; neural stem cells; neurogenesis; trans rescue
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APA ·
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MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Andersen, R. E. (2019). The novel long noncoding RNA Pnky regulates neurogenesis and neural stem cell maintenance in vivo. (Thesis). University of California – San Francisco. Retrieved from http://www.escholarship.org/uc/item/2c0846rw
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Andersen, Rebecca Ellen. “The novel long noncoding RNA Pnky regulates neurogenesis and neural stem cell maintenance in vivo.” 2019. Thesis, University of California – San Francisco. Accessed February 27, 2021.
http://www.escholarship.org/uc/item/2c0846rw.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Andersen, Rebecca Ellen. “The novel long noncoding RNA Pnky regulates neurogenesis and neural stem cell maintenance in vivo.” 2019. Web. 27 Feb 2021.
Vancouver:
Andersen RE. The novel long noncoding RNA Pnky regulates neurogenesis and neural stem cell maintenance in vivo. [Internet] [Thesis]. University of California – San Francisco; 2019. [cited 2021 Feb 27].
Available from: http://www.escholarship.org/uc/item/2c0846rw.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Andersen RE. The novel long noncoding RNA Pnky regulates neurogenesis and neural stem cell maintenance in vivo. [Thesis]. University of California – San Francisco; 2019. Available from: http://www.escholarship.org/uc/item/2c0846rw
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
21.
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 (6th 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 (16th 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 February 27, 2021.
https://doi.org/10.33915/etd.3926 ; https://researchrepository.wvu.edu/etd/3926.
MLA Handbook (7th Edition):
Barr, Jamie Ann, Ph D. “Regulation of the long non-coding RNA FAM83H-AS1 by human papillomavirus in cervical cancer.” 2019. Web. 27 Feb 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 Feb 27].
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 Hawaii
22.
Zhao, Tianying.
IDENTIFICATION OF LNCRNA BIOMARKERS FOR LUNG CANCR THROUGH INTEGRATIVE CROSS-PLATFORM DATA ANALYSIS.
Degree: 2020, University of Hawaii
URL: http://hdl.handle.net/10125/69023
Subjects/Keywords: Bioinformatics; lncRNA; lung cancer; microarray; RNA-Seq
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APA ·
Chicago ·
MLA ·
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CSE |
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to Zotero / EndNote / Reference
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APA (6th Edition):
Zhao, T. (2020). IDENTIFICATION OF LNCRNA BIOMARKERS FOR LUNG CANCR THROUGH INTEGRATIVE CROSS-PLATFORM DATA ANALYSIS. (Thesis). University of Hawaii. Retrieved from http://hdl.handle.net/10125/69023
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Zhao, Tianying. “IDENTIFICATION OF LNCRNA BIOMARKERS FOR LUNG CANCR THROUGH INTEGRATIVE CROSS-PLATFORM DATA ANALYSIS.” 2020. Thesis, University of Hawaii. Accessed February 27, 2021.
http://hdl.handle.net/10125/69023.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Zhao, Tianying. “IDENTIFICATION OF LNCRNA BIOMARKERS FOR LUNG CANCR THROUGH INTEGRATIVE CROSS-PLATFORM DATA ANALYSIS.” 2020. Web. 27 Feb 2021.
Vancouver:
Zhao T. IDENTIFICATION OF LNCRNA BIOMARKERS FOR LUNG CANCR THROUGH INTEGRATIVE CROSS-PLATFORM DATA ANALYSIS. [Internet] [Thesis]. University of Hawaii; 2020. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/10125/69023.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Zhao T. IDENTIFICATION OF LNCRNA BIOMARKERS FOR LUNG CANCR THROUGH INTEGRATIVE CROSS-PLATFORM DATA ANALYSIS. [Thesis]. University of Hawaii; 2020. Available from: http://hdl.handle.net/10125/69023
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
23.
UFUK DEGIRMENCI.
SILENCING AN INSULIN-INDUCED LNCRNA, LNCASIR IMPAIRS THE TRANSCRIPTIONAL RESPONSE TO INSULIN SIGNALLING IN ADIPOCYTES.
Degree: 2018, National University of Singapore
URL: http://scholarbank.nus.edu.sg/handle/10635/149805
Subjects/Keywords: lncRNA; noncoding RNA; adipose; adipocyte; insulin; metabolism
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Chicago ·
MLA ·
Vancouver ·
CSE |
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to Zotero / EndNote / Reference
Manager
APA (6th Edition):
DEGIRMENCI, U. (2018). SILENCING AN INSULIN-INDUCED LNCRNA, LNCASIR IMPAIRS THE TRANSCRIPTIONAL RESPONSE TO INSULIN SIGNALLING IN ADIPOCYTES. (Thesis). National University of Singapore. Retrieved from http://scholarbank.nus.edu.sg/handle/10635/149805
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
DEGIRMENCI, UFUK. “SILENCING AN INSULIN-INDUCED LNCRNA, LNCASIR IMPAIRS THE TRANSCRIPTIONAL RESPONSE TO INSULIN SIGNALLING IN ADIPOCYTES.” 2018. Thesis, National University of Singapore. Accessed February 27, 2021.
http://scholarbank.nus.edu.sg/handle/10635/149805.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
DEGIRMENCI, UFUK. “SILENCING AN INSULIN-INDUCED LNCRNA, LNCASIR IMPAIRS THE TRANSCRIPTIONAL RESPONSE TO INSULIN SIGNALLING IN ADIPOCYTES.” 2018. Web. 27 Feb 2021.
Vancouver:
DEGIRMENCI U. SILENCING AN INSULIN-INDUCED LNCRNA, LNCASIR IMPAIRS THE TRANSCRIPTIONAL RESPONSE TO INSULIN SIGNALLING IN ADIPOCYTES. [Internet] [Thesis]. National University of Singapore; 2018. [cited 2021 Feb 27].
Available from: http://scholarbank.nus.edu.sg/handle/10635/149805.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
DEGIRMENCI U. SILENCING AN INSULIN-INDUCED LNCRNA, LNCASIR IMPAIRS THE TRANSCRIPTIONAL RESPONSE TO INSULIN SIGNALLING IN ADIPOCYTES. [Thesis]. National University of Singapore; 2018. Available from: http://scholarbank.nus.edu.sg/handle/10635/149805
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
24.
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 ·
Chicago ·
MLA ·
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CSE |
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to Zotero / EndNote / Reference
Manager
APA (6th 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 (16th Edition):
UNAL, BILAL. “INVESTIGATING THE ROLE OF LONG NON-CODING RNAS IN INFLAMMATION.” 2018. Thesis, National University of Singapore. Accessed February 27, 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 (7th Edition):
UNAL, BILAL. “INVESTIGATING THE ROLE OF LONG NON-CODING RNAS IN INFLAMMATION.” 2018. Web. 27 Feb 2021.
Vancouver:
UNAL B. INVESTIGATING THE ROLE OF LONG NON-CODING RNAS IN INFLAMMATION. [Internet] [Thesis]. National University of Singapore; 2018. [cited 2021 Feb 27].
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
25.
ZHU BOWEN.
IDENTIFICATION AND CHARACTERIZATION OF REGULATORY NON-CODING RNAS IN THE HIPPO-YAP/TAZ SIGNALING PATHWAY.
Degree: 2019, National University of Singapore
URL: https://scholarbank.nus.edu.sg/handle/10635/169732
Subjects/Keywords: Hippo-YAP/TAZ Signalling; Noncoding RNA; LncRNA; microRNA; Cancer
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
BOWEN, Z. (2019). IDENTIFICATION AND CHARACTERIZATION OF REGULATORY NON-CODING RNAS IN THE HIPPO-YAP/TAZ SIGNALING PATHWAY. (Thesis). National University of Singapore. Retrieved from https://scholarbank.nus.edu.sg/handle/10635/169732
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
BOWEN, ZHU. “IDENTIFICATION AND CHARACTERIZATION OF REGULATORY NON-CODING RNAS IN THE HIPPO-YAP/TAZ SIGNALING PATHWAY.” 2019. Thesis, National University of Singapore. Accessed February 27, 2021.
https://scholarbank.nus.edu.sg/handle/10635/169732.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
BOWEN, ZHU. “IDENTIFICATION AND CHARACTERIZATION OF REGULATORY NON-CODING RNAS IN THE HIPPO-YAP/TAZ SIGNALING PATHWAY.” 2019. Web. 27 Feb 2021.
Vancouver:
BOWEN Z. IDENTIFICATION AND CHARACTERIZATION OF REGULATORY NON-CODING RNAS IN THE HIPPO-YAP/TAZ SIGNALING PATHWAY. [Internet] [Thesis]. National University of Singapore; 2019. [cited 2021 Feb 27].
Available from: https://scholarbank.nus.edu.sg/handle/10635/169732.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
BOWEN Z. IDENTIFICATION AND CHARACTERIZATION OF REGULATORY NON-CODING RNAS IN THE HIPPO-YAP/TAZ SIGNALING PATHWAY. [Thesis]. National University of Singapore; 2019. Available from: https://scholarbank.nus.edu.sg/handle/10635/169732
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Harvard University
26.
Davis, Christopher.
Analysis of Noncoding RNA Function at Specific Genomic Loci.
Degree: PhD, 2017, Harvard University
URL: http://nrs.harvard.edu/urn-3:HUL.InstRepos:42061481
► Long noncoding RNAs (lncRNAs) have emerged as important effectors of gene expression, due to their interactions with chromatin regulatory complexes and their implication in developmental…
(more)
▼ Long noncoding RNAs (lncRNAs) have emerged as important effectors of gene expression, due to their interactions with chromatin regulatory complexes and their implication in developmental processes such as genomic imprinting, dosage compensation, and maintenance of pluripotency. However, despite numerous studies suggesting regulatory roles for lncRNAs in gene expression, there is limited mechanistic insight into how lncRNAs can target and regulate specific sets of genes.
To better understand the regulatory effects of lncRNAs, I explored factors contributing to interactions between lncRNAs and specific genomic loci. To this end, I analyzed genomic binding sites for two highly abundant RNAs, NEAT1 and MALAT1. NEAT1 and MALAT1 bind hundreds of genomic sites in trans, primarily localizing to active genes. NEAT1 and MALAT1 colocalize to many of these loci, but display distinct gene body binding patterns, suggesting independent but complementary functions for these RNAs. Mass spectrometry analysis of lncRNA-associated proteins identified numerous proteins enriched by both lncRNAs, supporting complementary binding and function. Transcriptional inhibition or stimulation alters genome-wide localization of NEAT1, implying that underlying DNA sequence does not target NEAT1 to chromatin and that localization is instead responsive to the process of transcription.
In addition to examining lncRNAs associated with active genes, I characterized the impact of lncRNAs on gene repression at specific loci. I focused on a human lncRNA expressed during neural differentiation, CAT7, whose locus is composed primarily of tandem repeats and is proximal to the Polycomb Repressive Complex 1 (PRC1) target genes SHH and MNX1. RNA immunoprecipitation experiments indicate CAT7 directly interacts with PRC1 in vivo. Loss of the CAT7 tandem repeats leads to derepression of MNX1 and reduced PRC1 binding to the locus. Coincident with loss of gene repression, perturbation of CAT7 leads to diminished long-range genomic contacts between MNX1 and other cis-localized PRC1-bound loci. These results suggest a role for CAT7 in maintenance of a localized region of gene repression near its site of transcription. Overall, these studies support a model wherein lncRNAs aid in the organization of subnuclear domains that coordinate the activation or repression of specific sets of genomic loci.
Medical Sciences
Advisors/Committee Members: Kuroda, Mitzi (committee member), Adelman, Karen (committee member), Fazzio, Thomas (committee member).
Subjects/Keywords: lncRNA; chromatin
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APA ·
Chicago ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Davis, C. (2017). Analysis of Noncoding RNA Function at Specific Genomic Loci. (Doctoral Dissertation). Harvard University. Retrieved from http://nrs.harvard.edu/urn-3:HUL.InstRepos:42061481
Chicago Manual of Style (16th Edition):
Davis, Christopher. “Analysis of Noncoding RNA Function at Specific Genomic Loci.” 2017. Doctoral Dissertation, Harvard University. Accessed February 27, 2021.
http://nrs.harvard.edu/urn-3:HUL.InstRepos:42061481.
MLA Handbook (7th Edition):
Davis, Christopher. “Analysis of Noncoding RNA Function at Specific Genomic Loci.” 2017. Web. 27 Feb 2021.
Vancouver:
Davis C. Analysis of Noncoding RNA Function at Specific Genomic Loci. [Internet] [Doctoral dissertation]. Harvard University; 2017. [cited 2021 Feb 27].
Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:42061481.
Council of Science Editors:
Davis C. Analysis of Noncoding RNA Function at Specific Genomic Loci. [Doctoral Dissertation]. Harvard University; 2017. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:42061481
27.
ZHANG, BING.
Mechanistic Analysis of The Function of A Long
Non-codingRNA.
Degree: PhD, Biochemistry, 2015, Case Western Reserve University School of Graduate Studies
URL: http://rave.ohiolink.edu/etdc/view?acc_num=case1427212306
► The ubiquitous presence of long non-coding RNAs (lncRNAs) in higher eukaryotes points to the importance of understanding the mechanism of their functions. Currently, a large…
(more)
▼ The ubiquitous presence of long non-coding RNAs
(lncRNAs) in higher eukaryotes points to the importance of
understanding the mechanism of their functions. Currently, a large
number of studies on the mechanism of lncRNAs’ functions have been
focused on identifying the correlative relationships between
lncRNAs and a variety of cellular processes and diseases. In
contrast, very few cases of studies on the detailed molecular
mechanism of lncRNAs’ functions have been reported. To gain insight
into the mechanistic actions of lncRNAs, we selected an example
(
lncRNA BORG) from this
lncRNA group and performed detailed a
mechanistic analysis on its functions.BORG is an intergenic
lncRNA
that was originally discovered as a target gene of the Bone
Morphogenetic Protein (BMP) pathway. In order to gain insight into
the mechanism of action of nuclear
lncRNA BORG, we first analyzed
the sequence requirements for its nuclear localization. Our study
showed that the subcellular localization of BORG was not dependent
on the context or level of its expression or decay, but rather
depended on the primary sequence of the mature, spliced transcript.
Mutational analyses indicated that nuclear localization of BORG was
mediated through a novel
RNA motif. Interestingly, the presence of
this motif in other cellular RNAs showed a direct correlation with
nuclear localization. After that, we explored the mechanism of
action of BORG in cellular stress response. The expression of BORG
can be induced by stressful stimuli in several neuronal and
non-neuronal cell types, including cells of mesodermal and
ectodermal origin. After exposure to stress, BORG knockdown cells
exhibited an impaired cellular stress response and a much lower
survival rate compared to controls, while the BORG overexpression
cells showed an elevated level of stress response and a cellular
stress-resistant phenotype. Analysis of the stress response factors
indicated that some, but not all, heat shock proteins had a higher
basal level in the overexpression cells even in the absence of
stress and thus, the elevated expression of the
lncRNA seemed to
“pre-condition” the cells for tolerance to stress. Interestingly,
in the BORG knockdown cells, the induction of heat shock proteins
after stress was both delayed and reduced in magnitude.
RNA
pull-down assay and mass spectrometry showed that BORG is
associated with the Replication Protein A (RPA) complex in vivo.
Knockdown of RPA1 or HSF1 abolished the protective effect of BORG
overexpression and blocked the induction of heat shock proteins.
These data indicate that BORG plays an important role in regulation
of the stress response and cellular survival under stressful
conditions, likely through modulation of the function of RPA
complex and HSF1. In summary, our study has identified a novel
RNA
nuclear localization motif and clarified the function of
lncRNA
BORG in the cellular stress response. These findings have
demonstrated how the sequence of RNAs mediates their function and
how lncRNAs can play critical roles in regulating fundamental…
Advisors/Committee Members: VALADKHAN, SABA (Advisor).
Subjects/Keywords: Biochemistry; lncRNA
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
ZHANG, B. (2015). Mechanistic Analysis of The Function of A Long
Non-codingRNA. (Doctoral Dissertation). Case Western Reserve University School of Graduate Studies. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=case1427212306
Chicago Manual of Style (16th Edition):
ZHANG, BING. “Mechanistic Analysis of The Function of A Long
Non-codingRNA.” 2015. Doctoral Dissertation, Case Western Reserve University School of Graduate Studies. Accessed February 27, 2021.
http://rave.ohiolink.edu/etdc/view?acc_num=case1427212306.
MLA Handbook (7th Edition):
ZHANG, BING. “Mechanistic Analysis of The Function of A Long
Non-codingRNA.” 2015. Web. 27 Feb 2021.
Vancouver:
ZHANG B. Mechanistic Analysis of The Function of A Long
Non-codingRNA. [Internet] [Doctoral dissertation]. Case Western Reserve University School of Graduate Studies; 2015. [cited 2021 Feb 27].
Available from: http://rave.ohiolink.edu/etdc/view?acc_num=case1427212306.
Council of Science Editors:
ZHANG B. Mechanistic Analysis of The Function of A Long
Non-codingRNA. [Doctoral Dissertation]. Case Western Reserve University School of Graduate Studies; 2015. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=case1427212306
Freie Universität Berlin
28.
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 ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th 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 (16th 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 February 27, 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 (7th 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. 27 Feb 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 Feb 27].
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
University of California – San Francisco
29.
Asundi, Aarati.
Noncanonical roles for RNA in maintaining genomic stability and influencing organismal physiology.
Degree: Biomedical Sciences, 2018, University of California – San Francisco
URL: http://www.escholarship.org/uc/item/76244248
► It is becoming increasingly clear that sensory neurons are able to integrate information about environmental changes to regulate aspects of an organism’s physiology. The L’Etoile…
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▼ It is becoming increasingly clear that sensory neurons are able to integrate information about environmental changes to regulate aspects of an organism’s physiology. The L’Etoile lab has gathered evidence suggesting that mobile small RNAs may represent a previously unidentified endocrine signal and thus, might regulate various physiological outputs. My thesis work used different models and experimental approaches to test the hypothesis that small RNA machinery acts as a regulator of mitotic signals to ensure genomic integrity in proliferative cell populations. The proliferative germ cells (PGCs) in the C. elegans nematode and MCF10As, a human derived, non-tumorgenic breast epithelial cell line, are complementary models that are ideal to study how the small RNA pathway might regulate mitosis.I discovered that loss of NRDE2, a nuclear RNAi-dependent protein, induces DNA damage accumulation specifically under conditions of stress, such as high cultivation temperature in C. elegans or Aurora B Kinase oncogenic overexpression in MCF10A cells. I found that NRDE2 interacts with β-actin in unstressed mammalian cells. This interaction is dramatically reduced upon DNA damage and increased in the absence of RNA. I propose a model by which NRDE2 associates with actin only when DNA is intact and the bulk of nuclear actin is monomeric. Thus, NRDE2 may dissociate from actin when it becomes filamentous as a result of DNA damage. This implies that, NRDE2, in its role as a heterochromatin factor, binds to monomeric actin, protecting the genome from DNA damage in stressful conditions.I have also gathered preliminary data showing that the AWC olfactory sensory neurons are required to regulate brood size and egg laying pattern in C. elegans. Furthermore, my preliminary evidence indicates that SID-1, an import channel required for RNAi spreading, is required to regulate brood size and germ cell proliferation. This suggests that mobile RNAs could act as hormones to allow for gene specific regulation of distant target cells, providing a novel pathway for scientists to understand regulation of cell-cell communication and the subsequent consequences of its dysfunction.This thesis work lays groundwork for further studies into small RNAs as regulators for epigenetic inheritance, cancer, reproduction and mental health.
Subjects/Keywords: Biology; C. elegans; mitosis; NRDE2; RNA
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APA (6th Edition):
Asundi, A. (2018). Noncanonical roles for RNA in maintaining genomic stability and influencing organismal physiology. (Thesis). University of California – San Francisco. Retrieved from http://www.escholarship.org/uc/item/76244248
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Asundi, Aarati. “Noncanonical roles for RNA in maintaining genomic stability and influencing organismal physiology.” 2018. Thesis, University of California – San Francisco. Accessed February 27, 2021.
http://www.escholarship.org/uc/item/76244248.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Asundi, Aarati. “Noncanonical roles for RNA in maintaining genomic stability and influencing organismal physiology.” 2018. Web. 27 Feb 2021.
Vancouver:
Asundi A. Noncanonical roles for RNA in maintaining genomic stability and influencing organismal physiology. [Internet] [Thesis]. University of California – San Francisco; 2018. [cited 2021 Feb 27].
Available from: http://www.escholarship.org/uc/item/76244248.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Asundi A. Noncanonical roles for RNA in maintaining genomic stability and influencing organismal physiology. [Thesis]. University of California – San Francisco; 2018. Available from: http://www.escholarship.org/uc/item/76244248
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Cambridge
30.
Rees, Alice.
Investigating the role of the IP3 signalling pathway in RNA interference in C. elegans.
Degree: PhD, 2020, University of Cambridge
URL: https://doi.org/10.17863/CAM.55509
;
https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.810025
► Both inositol 1,4,5-trisphosphate (IP3) mediated signalling and RNA interference are widespread processes with fundamental roles in animal cell function. In the nematode C. elegans these…
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▼ Both inositol 1,4,5-trisphosphate (IP3) mediated signalling and RNA interference are widespread processes with fundamental roles in animal cell function. In the nematode C. elegans these two pathways have been shown to intersect such that IP3 signalling mutants display an altered exogenous RNAi response. IP3 is a key second messenger in the transduction of intracellular signals. Produced by the hydrolysis of membrane phospholipid PIP2 by phospholipase C (PLC), IP3 triggers Ca2+ release from internal stores by binding to the IP3 receptor, a ligand gated calcium channel in the ER, thus triggering downstream calcium signalling pathways. It has been previously shown that loss of function in the IP3 receptor (ITR-1) or in PLCβ (EGL-8) results in an enhanced response to exogenous dsRNA, with a more robust silencing response than that seen in WT worms. Conversely the potentiation of IP3 signalling by the loss of function IPP-5, a phosphatase which catalyses the hydrolysis of IP3, results in resistance to RNAi. In order to better understand the context of the IP3 signalling events which are regulating the RNAi response I sought to identify the upstream activator of EGL-8 in this mechanism. EGL-8 is canonically activated by Gαq homologue ELG-30. However, by screening the RNAi responses of Gα signalling mutants using a range of assays, EGL-30 was ruled out as an activator of EGL-8 in the pathway regulating RNAi, since EGL-30 loss of function does not result in an enhanced RNAi response. The Gαo/i homologue, GOA-1, was identified as the most likely activator of EGL-8 due to the strongly enhanced RNAi response in goa-1 loss of function mutants in a number of assays. Other Gα subunits and known regulators of GOA-1 and EGL-30 signalling were also analysed. The RNAi response is a multistep process in which the exogenous RNAi pathway must compete with the closely related and interlinked endogenous small RNA pathways for resources. With the aim of better understanding how changes in IP3 signalling might be influencing the RNAi response, small RNA sequencing was performed to look for evidence of change in the endogenous small RNA pathways of itr-1 mutants, and followed up with qPCR. However, no substantial changes to the endogenous small RNA pathways were found. Downstream of the production of primary siRNAs from exogenous dsRNA, separate argonautes mediate cytoplasmic and nuclear RNAi responses. I utilised an established assay to test for effects of IP3 signalling on nuclear RNAi. The results suggest no specific alterations to the nuclear RNAi pathway in these mutants.
Subjects/Keywords: RNA intereference; RNAi; IP3 Signalling; C. elegans
Record Details
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Record Details
Similar Records
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Rees, A. (2020). Investigating the role of the IP3 signalling pathway in RNA interference in C. elegans. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.55509 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.810025
Chicago Manual of Style (16th Edition):
Rees, Alice. “Investigating the role of the IP3 signalling pathway in RNA interference in C. elegans.” 2020. Doctoral Dissertation, University of Cambridge. Accessed February 27, 2021.
https://doi.org/10.17863/CAM.55509 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.810025.
MLA Handbook (7th Edition):
Rees, Alice. “Investigating the role of the IP3 signalling pathway in RNA interference in C. elegans.” 2020. Web. 27 Feb 2021.
Vancouver:
Rees A. Investigating the role of the IP3 signalling pathway in RNA interference in C. elegans. [Internet] [Doctoral dissertation]. University of Cambridge; 2020. [cited 2021 Feb 27].
Available from: https://doi.org/10.17863/CAM.55509 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.810025.
Council of Science Editors:
Rees A. Investigating the role of the IP3 signalling pathway in RNA interference in C. elegans. [Doctoral Dissertation]. University of Cambridge; 2020. Available from: https://doi.org/10.17863/CAM.55509 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.810025
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Open Access Theses and Dissertations
