You searched for subject:(Non Coding RNA).
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University of New South Wales
1.
Hughes, Rachel.
P53 and Sp1 Associated RNAs Act As Non-coding Transcriptional Regulators at Homologous Loci.
Degree: Biotechnology & Biomolecular Sciences, 2016, University of New South Wales
URL: http://handle.unsw.edu.au/1959.4/56903 
;
https://unsworks.unsw.edu.au/fapi/datastream/unsworks:41920/SOURCE02?view=true
► RNA functionality has been proven to extend far beyond the outdated protein coding divide, as transcripts not bound for translation are instead found to act…
(more)
▼ RNA functionality has been proven to extend far beyond the outdated protein
coding divide, as transcripts not bound for translation are instead found to act as endogenous messengers and moderators, utilising inherent sequence homology to interact with DNA or protein targets. A RIP-Seq of six major transcription factors including p53 and Sp1 uncovered multiple bound RNAs, some of which were interestingly protein
coding. Of these, the HIST1H1D and SF3B5 mRNAs were knocked down in order to investigate the ability of their affiliated transcription factors to localise to the target genes. Both RNAs demonstrated an inherent ability to modulate transcription factor localisation to homology containing loci in cis by acting as protein guides in the case of SF3B5, and as decoys in HIST1H1D. Expression of other linker histone H1 proteins was also observed to be under HIST1H1D
RNA regulation, suggesting a network involving the p53 tumour suppressive cascade which induces senescence in damaged cells. Together, the data confirms an innate complexity of
RNA that is only beginning to be unveiled, with major ties to tumour preventative pathways and therefore therapeutic possibilities.
Advisors/Committee Members: Morris, Kevin, Biotechnology & Biomolecular Sciences, Faculty of Science, UNSW.
Subjects/Keywords: RNA; Non-Coding RNA; mRNA
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APA (6th Edition):
Hughes, R. (2016). P53 and Sp1 Associated RNAs Act As Non-coding Transcriptional Regulators at Homologous Loci. (Masters Thesis). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/56903 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:41920/SOURCE02?view=true
Chicago Manual of Style (16th Edition):
Hughes, Rachel. “P53 and Sp1 Associated RNAs Act As Non-coding Transcriptional Regulators at Homologous Loci.” 2016. Masters Thesis, University of New South Wales. Accessed January 19, 2021.
http://handle.unsw.edu.au/1959.4/56903 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:41920/SOURCE02?view=true.
MLA Handbook (7th Edition):
Hughes, Rachel. “P53 and Sp1 Associated RNAs Act As Non-coding Transcriptional Regulators at Homologous Loci.” 2016. Web. 19 Jan 2021.
Vancouver:
Hughes R. P53 and Sp1 Associated RNAs Act As Non-coding Transcriptional Regulators at Homologous Loci. [Internet] [Masters thesis]. University of New South Wales; 2016. [cited 2021 Jan 19].
Available from: http://handle.unsw.edu.au/1959.4/56903 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:41920/SOURCE02?view=true.
Council of Science Editors:
Hughes R. P53 and Sp1 Associated RNAs Act As Non-coding Transcriptional Regulators at Homologous Loci. [Masters Thesis]. University of New South Wales; 2016. Available from: http://handle.unsw.edu.au/1959.4/56903 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:41920/SOURCE02?view=true
University of North Carolina – Greensboro
2.
Boyd, Patricia Shaqirah.
Computational modeling of small non-coding RNA
intramolecular structures and the determination of their
collisional cross sections.
Degree: 2018, University of North Carolina – Greensboro
URL: http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=23124
► Ribonucleic acid (RNA) plays important and fundamental roles in different biological activities which include transmission of genetic information, regulation of gene expression, catalysis for biochemical…
(more)
▼ Ribonucleic acid (
RNA) plays important and fundamental
roles in different biological activities which include transmission
of genetic information, regulation of gene expression, catalysis
for biochemical reactions and biomarkers for different diseases.
The roles they play, as well as the interactions they perform
within the body, are made possible by the stable secondary
RNA
structures that exist in the cell. The problem however, is that
even through years of experimental work to determine the structures
of
RNA, little is known, and the majority of
RNA structures remain
structurally uncharacterized.
RNA may undergo different types of
modifications in the cell that can potentially impact its secondary
structure. In addition to having limited knowledge on the actual
RNA structures, none of current analytical methods can be
universally used to detect all types of
RNA modifications and its
corresponding position that exist within a biological system. To
address these issues for
RNA research work as well as improving the
accuracy on identifying specific
RNA biomarkers, this study aims to
investigate some of the intrinsic properties of
RNA biomarkers that
may affect the ion mobility mass spectrometric measurements of
RNA
samples. The long-term goal of this study is to develop an
analytical method for differentiating and identifying isomeric
RNA
with or without any modification. Particularly, we are interested
in the identification of specific isomeric
RNA biomarkers which
have identical nucleotide composition and high sequence similarity.
MicroRNA (miRNA) are selected as an initial model in this study.;
Collisional Cross Section, miRNA,
Non-
coding RNA
Advisors/Committee Members: Norman Chiu (advisor).
Subjects/Keywords: MicroRNA; Non-coding RNA
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Boyd, P. S. (2018). Computational modeling of small non-coding RNA
intramolecular structures and the determination of their
collisional cross sections. (Masters Thesis). University of North Carolina – Greensboro. Retrieved from http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=23124
Chicago Manual of Style (16th Edition):
Boyd, Patricia Shaqirah. “Computational modeling of small non-coding RNA
intramolecular structures and the determination of their
collisional cross sections.” 2018. Masters Thesis, University of North Carolina – Greensboro. Accessed January 19, 2021.
http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=23124.
MLA Handbook (7th Edition):
Boyd, Patricia Shaqirah. “Computational modeling of small non-coding RNA
intramolecular structures and the determination of their
collisional cross sections.” 2018. Web. 19 Jan 2021.
Vancouver:
Boyd PS. Computational modeling of small non-coding RNA
intramolecular structures and the determination of their
collisional cross sections. [Internet] [Masters thesis]. University of North Carolina – Greensboro; 2018. [cited 2021 Jan 19].
Available from: http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=23124.
Council of Science Editors:
Boyd PS. Computational modeling of small non-coding RNA
intramolecular structures and the determination of their
collisional cross sections. [Masters Thesis]. University of North Carolina – Greensboro; 2018. Available from: http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=23124
3.
Boyd, Patricia Shaqirah.
Computational modeling of small non-coding RNA intramolecular structures and the determination of their collisional cross sections.
Degree: 2018, NC Docks
URL: http://libres.uncg.edu/ir/uncg/f/Boyd_uncg_0154M_12485.pdf
► Ribonucleic acid (RNA) plays important and fundamental roles in different biological activities which include transmission of genetic information, regulation of gene expression, catalysis for biochemical…
(more)
▼ Ribonucleic acid (RNA) plays important and fundamental roles in different biological activities which include transmission of genetic information, regulation of gene expression, catalysis for biochemical reactions and biomarkers for different diseases. The roles they play, as well as the interactions they perform within the body, are made possible by the stable secondary RNA structures that exist in the cell. The problem however, is that even through years of experimental work to determine the structures of RNA, little is known, and the majority of RNA structures remain structurally uncharacterized. RNA may undergo different types of modifications in the cell that can potentially impact its secondary structure. In addition to having limited knowledge on the actual RNA structures, none of current analytical methods can be universally used to detect all types of RNA modifications and its corresponding position that exist within a biological system. To address these issues for RNA research work as well as improving the accuracy on identifying specific RNA biomarkers, this study aims to investigate some of the intrinsic properties of RNA biomarkers that may affect the ion mobility mass spectrometric measurements of RNA samples. The long-term goal of this study is to develop an analytical method for differentiating and identifying isomeric RNA with or without any modification. Particularly, we are interested in the identification of specific isomeric RNA biomarkers which have identical nucleotide composition and high sequence similarity. MicroRNA (miRNA) are selected as an initial model in this study.
Subjects/Keywords: MicroRNA; Non-coding RNA
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Boyd, P. S. (2018). Computational modeling of small non-coding RNA intramolecular structures and the determination of their collisional cross sections. (Thesis). NC Docks. Retrieved from http://libres.uncg.edu/ir/uncg/f/Boyd_uncg_0154M_12485.pdf
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):
Boyd, Patricia Shaqirah. “Computational modeling of small non-coding RNA intramolecular structures and the determination of their collisional cross sections.” 2018. Thesis, NC Docks. Accessed January 19, 2021.
http://libres.uncg.edu/ir/uncg/f/Boyd_uncg_0154M_12485.pdf.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Boyd, Patricia Shaqirah. “Computational modeling of small non-coding RNA intramolecular structures and the determination of their collisional cross sections.” 2018. Web. 19 Jan 2021.
Vancouver:
Boyd PS. Computational modeling of small non-coding RNA intramolecular structures and the determination of their collisional cross sections. [Internet] [Thesis]. NC Docks; 2018. [cited 2021 Jan 19].
Available from: http://libres.uncg.edu/ir/uncg/f/Boyd_uncg_0154M_12485.pdf.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Boyd PS. Computational modeling of small non-coding RNA intramolecular structures and the determination of their collisional cross sections. [Thesis]. NC Docks; 2018. Available from: http://libres.uncg.edu/ir/uncg/f/Boyd_uncg_0154M_12485.pdf
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
4.
Coley, Brian D.
Detection of Argonaute (Ago) protein associated MiRNA by combining anti-ago antibody recognition with real-time PCR.
Degree: 2014, NC Docks
URL: http://libres.uncg.edu/ir/uncg/f/Coley_uncg_0154M_11565.pdf
► MicroRNAs (miRNAs) are small molecules of noncoding RNA that range between ~19-22 nucleotides in length. In recent years, scientists have observed that these small RNA…
(more)
▼ MicroRNAs (miRNAs) are small molecules of noncoding RNA that range between ~19-22 nucleotides in length. In recent years, scientists have observed that these small RNA molecules exist in the extracellular environment within eukaryotic organisms. Furthermore, these microRNA molecules are known to associate with a family of proteins named Argonaute proteins. These microRNA/Argonaute protein complexes are the core of a larger assembly of proteins that compose the RNA Induced Silencing Complex (RISC). The RISC has exhibited the ability to inhibit the translation of, or cleave, its target messenger RNA (mRNA), the latter of which being exclusive only to Argonaute 2 protein (Ago2). It has also been observed in the literature that these Argonaute/miRNA complexes often target genomic regions associated with various cancers in humans and, currently, more than 2000 miRNAs have been discovered and published in the literature. Current methods for analyzing miRNA expression involve total RNA extraction using methods such as ethanol precipitation. However, total RNA extraction does not take into consideration that the major functional component of post-transcriptional inhibition is indeed that Argonaute protein/miRNA complex and not the miRNA alone. In this study, we investigate a novel method to capture and detect the active Ago2/miRNA (miRNP) complex and quantitate associated miRNAs by utilizing an antibody against Ago2 and subsequent application of real-time PCR to successfully capture the active miRNP complex and quantitate the associated miRNAs.
Subjects/Keywords: Non-coding RNA; Gene silencing
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APA ·
Chicago ·
MLA ·
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CSE |
Export
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Manager
APA (6th Edition):
Coley, B. D. (2014). Detection of Argonaute (Ago) protein associated MiRNA by combining anti-ago antibody recognition with real-time PCR. (Thesis). NC Docks. Retrieved from http://libres.uncg.edu/ir/uncg/f/Coley_uncg_0154M_11565.pdf
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):
Coley, Brian D. “Detection of Argonaute (Ago) protein associated MiRNA by combining anti-ago antibody recognition with real-time PCR.” 2014. Thesis, NC Docks. Accessed January 19, 2021.
http://libres.uncg.edu/ir/uncg/f/Coley_uncg_0154M_11565.pdf.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Coley, Brian D. “Detection of Argonaute (Ago) protein associated MiRNA by combining anti-ago antibody recognition with real-time PCR.” 2014. Web. 19 Jan 2021.
Vancouver:
Coley BD. Detection of Argonaute (Ago) protein associated MiRNA by combining anti-ago antibody recognition with real-time PCR. [Internet] [Thesis]. NC Docks; 2014. [cited 2021 Jan 19].
Available from: http://libres.uncg.edu/ir/uncg/f/Coley_uncg_0154M_11565.pdf.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Coley BD. Detection of Argonaute (Ago) protein associated MiRNA by combining anti-ago antibody recognition with real-time PCR. [Thesis]. NC Docks; 2014. Available from: http://libres.uncg.edu/ir/uncg/f/Coley_uncg_0154M_11565.pdf
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Drexel University
5.
Owens, Michael Carl.
Structural Characterization of the lncRNA WSPAR.
Degree: 2018, Drexel University
URL: https://idea.library.drexel.edu/islandora/object/idea%3A8858
► Long non-coding RNAs (lncRNAs) are RNA molecules of at least 200 nucleotides in length with no protein coding potential. While there is growing information about…
(more)
▼ Long non-coding RNAs (lncRNAs) are RNA molecules of at least 200 nucleotides in length with no protein coding potential. While there is growing information about how lncRNAs function in a variety of biological processes, little structural information is known about these molecules. The first step of forming a structure-function relationship for RNA is the development of a secondary structure model. Such information about secondary structure is gathered via chemical structure probing and in silico folding. However, few secondary structures for lncRNAs have been published. Herein, we report a secondary structure model for the lncRNA WSPAR (Wnt Signaling Pathway Activating RNA), generated via SHAPE (Selective 2' Hydroxyl Acylation analyzed by Primer Extension) probing and validated with DMS. This model allowed us to identify structural elements which are highly conserved across mammals. These findings indicate a functional importance for these elements of WSPAR in its role of upregulating wnt signaling in the context of several cancers.
M.S., Biochemistry – Drexel University, 2018
Advisors/Committee Members: Noguchi, Eishi, College of Medicine.
Subjects/Keywords: Biochemistry; Chromatin; Non-coding RNA; RNA – Structure
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APA ·
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to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Owens, M. C. (2018). Structural Characterization of the lncRNA WSPAR. (Thesis). Drexel University. Retrieved from https://idea.library.drexel.edu/islandora/object/idea%3A8858
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):
Owens, Michael Carl. “Structural Characterization of the lncRNA WSPAR.” 2018. Thesis, Drexel University. Accessed January 19, 2021.
https://idea.library.drexel.edu/islandora/object/idea%3A8858.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Owens, Michael Carl. “Structural Characterization of the lncRNA WSPAR.” 2018. Web. 19 Jan 2021.
Vancouver:
Owens MC. Structural Characterization of the lncRNA WSPAR. [Internet] [Thesis]. Drexel University; 2018. [cited 2021 Jan 19].
Available from: https://idea.library.drexel.edu/islandora/object/idea%3A8858.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Owens MC. Structural Characterization of the lncRNA WSPAR. [Thesis]. Drexel University; 2018. Available from: https://idea.library.drexel.edu/islandora/object/idea%3A8858
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of New South Wales
6.
Mills, James.
Human brain transcriptomic: towards understanding multiple system atrophy.
Degree: Biotechnology & Biomolecular Sciences, 2015, University of New South Wales
URL: http://handle.unsw.edu.au/1959.4/55473
;
https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true
► The human brain is a remarkably complex organ. It is a heterogeneous collection of billions of neurons and glial cells that are interconnected to form…
(more)
▼ The human brain is a remarkably complex organ. It is a heterogeneous collection of billions of neurons and glial cells that are interconnected to form a finely tuned network capable of higher cognition. It is thought that the transcriptome may hold the key to understanding the complexity seen in the human brain. Next-generation sequencing allows the brain’s transcriptome to be probed at an unmatched resolution. This has uncovered a myriad of
RNA elements, including
RNA that does not code for protein, known as
non-
coding RNA (ncRNA). Originally, thought to be transcriptional noise, it is now appreciated that ncRNAs have numerous functional properties, with the ability to interact with DNA, other
RNA molecules and proteins in different cellular compartments. It is thought that an increase in the number of ncRNAs being expressed throughout the brain, is a major driver of the increased intellectual capacity seen in humans and primates. The increase in the complexity of the human brain, also makes it prone to a number of different neurodegenerative and psychiatric diseases. These diseases are set to have dramatic economic and social impacts by the middle of the 21st century. To avert this looming epidemic an adequate understanding of the human brain is needed, so diagnostic tools and treatment targets can be developed. One such disorder is multiple system atrophy(MSA). MSA is a sporadic, rapidly progressing neurodegenerative disease. Currently no treatment exists and very little is known about the molecular basis of MSA. Before an understanding of the diseased brain can be reached an understanding of the healthy brain is necessary.Here, the transcriptome of grey matter (GM) and white matter (WM) from the superior frontal gyrus (SFG) of the healthy prefrontal cortex (PFC) was analysed. This revealed pervasive transcription and highlighted the differences in the transcriptome profiles of distinct cortical structures throughout the brain. A number of protein-
coding genes were expressed exclusively in GM or WM, including gamma-aminobutyric acid A receptor, beta 2 (GABRB2) and P21 Protein (Cdc42/Rac)-Activated Kinase 2 (PAK2), respectively. Further, an interesting phenomenon known as isoform switching was detected in genes such as the G protein-coupled receptor 123 (GPR123). It was also revealed that in the healthy frontal cortex long intervening
non-
coding RNAs (lincRNAs), a subclass of long
non-
coding RNAs (lncRNAs), appear to be important drivers of tissue differentiation.To further establish the role of lincRNAs in the healthy human brain a comprehensive analysis of the oligodendrocyte maturation-associated lincRNA (OLMALINC) was carried out. It was found that OLMALINC is a recently evolved lincRNA with its highest expression levels in the human brain. OLMALINC was knocked down in human neurons and oligodendrocytes. Depletion of OLMALINC transcription revealed that it plays a role oligodendrocyte maturation. This study was one of the first functional characterisations of a lincRNA expressed in the human brain, and thus…
Advisors/Committee Members: Janitz, Michael, Faculty of Science, UNSW.
Subjects/Keywords: Neurodegeneration; RNA-Seq; Long non-coding RNA
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APA ·
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Manager
APA (6th Edition):
Mills, J. (2015). Human brain transcriptomic: towards understanding multiple system atrophy. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true
Chicago Manual of Style (16th Edition):
Mills, James. “Human brain transcriptomic: towards understanding multiple system atrophy.” 2015. Doctoral Dissertation, University of New South Wales. Accessed January 19, 2021.
http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true.
MLA Handbook (7th Edition):
Mills, James. “Human brain transcriptomic: towards understanding multiple system atrophy.” 2015. Web. 19 Jan 2021.
Vancouver:
Mills J. Human brain transcriptomic: towards understanding multiple system atrophy. [Internet] [Doctoral dissertation]. University of New South Wales; 2015. [cited 2021 Jan 19].
Available from: http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true.
Council of Science Editors:
Mills J. Human brain transcriptomic: towards understanding multiple system atrophy. [Doctoral Dissertation]. University of New South Wales; 2015. Available from: http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true
Rutgers University
7.
Naqvi, Ammar S., 1984-.
Temporal patterns of short non-coding RNA modifications and expression.
Degree: PhD, Computational and Integrative Biology, 2015, Rutgers University
URL: https://rucore.libraries.rutgers.edu/rutgers-lib/47155/
► We investigated the function and properties of small RNAs, particularly microRNAs and tRNA-derived fragments (tRFs) with age. We report the characterization of a novel 3'-to-…
(more)
▼ We investigated the function and properties of small RNAs, particularly microRNAs and tRNA-derived fragments (tRFs) with age. We report the characterization of a novel 3'-to- 5' exonuclease, Nibbler (Nbr), that generates differing isoforms of miRNAs in Drosophila.. We developed a robust approach to help identify and characterize 3' heterogeneity in microRNAs controlled by Nbr, which assisted in identifying age- associated traits, including neurodegeneration and lifespan. Subsequently, given the fact Nbr interacts with Ago1 and not Ago2, we observed an accumulation of certain isoforms, which lead us to ask if there were particular patterns and trends that were Ago-specific. Interestingly, we report a novel age-associated change of select isoforms with age that is Ago2 specific. RNA deep-sequencing analysis coupled with experimental evidence reflected an increased loading of miRNA isoforms into Ago2 with age. Essentially, the loss of methylated miRNAs led to accelerated brain degeneration and shortened lifespan. Intriguingly, we also observed and identified Ago-loaded tRFs, which appear to have properties similar to those of miRNAs. We found this class of small RNAs to also display age-associated changes. For the first time, we found that differentially loaded Drosophila tRFs mapping to both nuclear and mitochondrial tRNA genes associating with all 20 amino acids. These tRFs show a number of similarities with miRNAs, including seed sequences, suggesting a similar role and function. Moreover, we further characterized and predicted targets for these tRFs and show a significant enrichment in development and neuronal function, suggesting a role in brain-related processes with age. In sum, we discovered a novel component of the canonical microRNA biogenesis pathway, responsible for the generation of multiple isoforms. We also connected specific age- associated patterns and trends of select microRNA isoforms, which were found to impact proper brain development and lifespan. Moreover, we identified differentially loaded tRFs and elucidated their structures, loading, and expression patterns, which corresponded closely with microRNAs. Finally, we were able to identify tRF seed regions that potentially play a role in brain activity or brain changes with age.
Advisors/Committee Members: Grigoriev, Andrey (chair), Nam, Jongmin (internal member), Bonini, Nancy (outside member).
Subjects/Keywords: Non-coding RNA; Small interfering RNA
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APA ·
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MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Naqvi, Ammar S., 1. (2015). Temporal patterns of short non-coding RNA modifications and expression. (Doctoral Dissertation). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/47155/
Chicago Manual of Style (16th Edition):
Naqvi, Ammar S., 1984-. “Temporal patterns of short non-coding RNA modifications and expression.” 2015. Doctoral Dissertation, Rutgers University. Accessed January 19, 2021.
https://rucore.libraries.rutgers.edu/rutgers-lib/47155/.
MLA Handbook (7th Edition):
Naqvi, Ammar S., 1984-. “Temporal patterns of short non-coding RNA modifications and expression.” 2015. Web. 19 Jan 2021.
Vancouver:
Naqvi, Ammar S. 1. Temporal patterns of short non-coding RNA modifications and expression. [Internet] [Doctoral dissertation]. Rutgers University; 2015. [cited 2021 Jan 19].
Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/47155/.
Council of Science Editors:
Naqvi, Ammar S. 1. Temporal patterns of short non-coding RNA modifications and expression. [Doctoral Dissertation]. Rutgers University; 2015. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/47155/
8.
Furlan, Giulia.
Investigating the contribution of the non-coding gene Ftx to X-chromosome inactivation in mammals : Étude de la contribution du gène non-codant Ftx dans l'inactivation du chromosome X chez les mammifères.
Degree: Docteur es, Physiologie et biologie des organismes, populations, interactions. Génomes, épigénomes, destin cellulaire, 2016, Sorbonne Paris Cité
URL: http://www.theses.fr/2016USPCC191
► L’inactivation du chromosome X (XCI) est un mécanisme qui permet l’extinction transcriptionelle d’un des deux chromosomes X chez la femelle. XCI est régulé par une…
(more)
▼ L’inactivation du chromosome X (XCI) est un mécanisme qui permet l’extinction transcriptionelle d’un des deux chromosomes X chez la femelle. XCI est régulé par une région spécifique nommée centre de l’inactivation du chromosome (Xic), contenant plusieurs gènes produisant de longs ARNs non codants (lncRNAs). Parmi ces lncRNAs, le transcrit Xist est l’effecteur principal pour l’XCI. Xist peut s’accumuler en cis sur le chromosome et recruter la machinerie qui permettra l’initiation et la propagation de l’extinction transcriptionnelle à l’échelle du chromosome.Le laboratoire d’accueil a identifié un nouveau gène du Xic qui produit le lncRNA Ftx. Dans cette étude, on a pu montrer que l’inactivation du chromosome X est fortement perturbée dans les cellules Ftx-/- et s’accompagne par une forte baisse du niveau d’expression et d’accumulation de Xist. Dans ce contexte, certaines cellules parviennent à maintenir l’expression de Xist mais le profil de couverture du chromosome X par Xist est anormal, présentant un profil diffus ; ceci est associé à une extinction transcriptionnelle déficiente des gènes liés à l’X. Dans les lignées hétérozygotes Ftx+/-, l’expression et l’accumulation de Xist est aussi affectée mais dans une moindre mesure, si bien qu’il apparaît que le nombre de copies de Ftx soit important pour sa fonction. Par ailleurs, l’inactivation du chromosome X dans les cellules Ftx+/- est biaisée de telle sorte que le chromosome X portant une copie fonctionnelle de Ftx est préférentiellement inactivé, suggérant un rôle en cis de Ftx. Ces résultats montrent que Ftx est un activateur de Xist et qu’il est essentiel pour la mise en place de l’inactivation
X-chromosome inactivation (XCI) is a female-specific, chromosome-wide regulatory process that, in eutherians, ensures dosage compensation for X-linked genes between sexes. XCI is controlled by a cis-acting locus on the X-chromosome, the X-inactivation center (Xic), enriched in genes producing long non-coding RNAs (lncRNAs). The Xic-linked gene Xist is the master player of XCI, and produces a lncRNA that accumulates in cis on the X-chromosome and recruits the machinery responsible for initiation and propagation of silencing.The laboratory has identified an additional Xic-linked non-coding gene, Ftx. In this study, we could find that, in female Ftx-/- lines, XCI is strongly impaired, with a significant decrease in the levels of Xist expression and in the percentage of cells showing normal Xist accumulation patterns. Importantly, a high proportion of the cells that still retain Xist expression show abnormal X-chromosome coating and a decreased ability to silence X-linked genes. These data reveal that Ftx is a positive Xist regulator and it is required for proper XCI establishment. In female Ftx+/- lines, the levels of Xist expression and the percentage of cells showing normal Xist accumulation patterns are also decreased, albeit to a lower extent compared to Ftx-/- lines, suggesting that Ftx works in a copy-dependent manner. In addition, a high proportion of Ftx+/- cells…
Advisors/Committee Members: Rougeulle, Claire (thesis director).
Subjects/Keywords: Ftx; XIST non-coding RNA; Ftx; XIST non-coding RNA
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APA (6th Edition):
Furlan, G. (2016). Investigating the contribution of the non-coding gene Ftx to X-chromosome inactivation in mammals : Étude de la contribution du gène non-codant Ftx dans l'inactivation du chromosome X chez les mammifères. (Doctoral Dissertation). Sorbonne Paris Cité. Retrieved from http://www.theses.fr/2016USPCC191
Chicago Manual of Style (16th Edition):
Furlan, Giulia. “Investigating the contribution of the non-coding gene Ftx to X-chromosome inactivation in mammals : Étude de la contribution du gène non-codant Ftx dans l'inactivation du chromosome X chez les mammifères.” 2016. Doctoral Dissertation, Sorbonne Paris Cité. Accessed January 19, 2021.
http://www.theses.fr/2016USPCC191.
MLA Handbook (7th Edition):
Furlan, Giulia. “Investigating the contribution of the non-coding gene Ftx to X-chromosome inactivation in mammals : Étude de la contribution du gène non-codant Ftx dans l'inactivation du chromosome X chez les mammifères.” 2016. Web. 19 Jan 2021.
Vancouver:
Furlan G. Investigating the contribution of the non-coding gene Ftx to X-chromosome inactivation in mammals : Étude de la contribution du gène non-codant Ftx dans l'inactivation du chromosome X chez les mammifères. [Internet] [Doctoral dissertation]. Sorbonne Paris Cité; 2016. [cited 2021 Jan 19].
Available from: http://www.theses.fr/2016USPCC191.
Council of Science Editors:
Furlan G. Investigating the contribution of the non-coding gene Ftx to X-chromosome inactivation in mammals : Étude de la contribution du gène non-codant Ftx dans l'inactivation du chromosome X chez les mammifères. [Doctoral Dissertation]. Sorbonne Paris Cité; 2016. Available from: http://www.theses.fr/2016USPCC191
NSYSU
9.
Tu, Ya-Ting.
Identify Metastasis-related LncRNA in Breast Cancer by Microarray Approach.
Degree: Master, Biological Sciences, 2017, NSYSU
URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0611117-145225
► Breast cancer occurs in mammary gland epithelial tissue and is the most commonly diagnosed cancer in women throughout the world. Previous studies indicated that invasion…
(more)
▼ Breast cancer occurs in mammary gland epithelial tissue and is the most commonly diagnosed cancer in women throughout the world. Previous studies indicated that invasion of cancer cells was the major cause of the death, which had been a major challenge in the treatment of breast cancer. In human genome, recent studies reveal that there is < 2 % of the total genome sequence as protein-
coding genes, however, at least 98 % of genome are transcribed into
non-
coding RNA (ncRNA). So far, the study of ncRNA is mainly concentrated on the microRNA (miRNA) and long
non-
coding RNA (lncRNA). An increasing number of researches reveal that ncRNAs have been shown to play an important role in gene regulation, normal cellular functions and disease processes. However, the detail biological function of lncRNA involving in breast metastasis is still unclear. In this study, we performed the expression profiles of two breast cancer cell lines, MB-231-P and MB-231-IV2-1, by microarray approach (Agilent SurePrint G3 Human V2 GE; including 34092 protein-
coding genes and 8715 lncRNAs). After finishing the microarray profiling, we identified about 213 lncRNAs upregulated and 301 lncRNAs downregulated in MB-231-IV2-1 cell line compared to MB-231-P, respectively. Finally, we successfully identified several metastasis-related lncRNA candidates according microarray data and The Cancer Genome Atlas (TCGA). Among them, LINC01420 was selected for further study in this study. We assessed the expression levels of LINC01420 in breast cancer tissues by real-time PCR approach. Our data revealed that the expression levels of LINC01420 were significantly increased in breast cancer compared with adjacent normal tissues. We further identified the full length of LINC01420 by 5â and 3â rapid amplification of cDNA ends (RACE) in breast cancer cell. Our results revealed that LINC01420 could generate three splicing transcripts (V1, V2 and V3) via alternative splicing. Furthermore, knockdown of LINC01420 could suppress breast cancer cell growth by inducing cell cycle arrest at S phase. Interesting, the cell growth and the invasion ability of MB-231-IV2-1 cell significantly decreased after LINC01420-V1 and -V3 knockdown. These results implied that LINC01420-V1 and -V3 might be critical isoforms and exon 2 might be a functional oncogene region involving in modulating biological function in breast cancer. Our results suggest that LINC01420 might be a functional oncogene in breast tumorigenesis.
Advisors/Committee Members: Kuo-Wang Tsai (committee member), Sung-Chou Li (chair), Huey-Wen Shyu (chair), Ming-Hong Tai (committee member).
Subjects/Keywords: Non-coding RNA; Metastasis; LINC01420; Long non-coding RNA; Breast cancer
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APA ·
Chicago ·
MLA ·
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CSE |
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to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Tu, Y. (2017). Identify Metastasis-related LncRNA in Breast Cancer by Microarray Approach. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0611117-145225
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Tu, Ya-Ting. “Identify Metastasis-related LncRNA in Breast Cancer by Microarray Approach.” 2017. Thesis, NSYSU. Accessed January 19, 2021.
http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0611117-145225.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Tu, Ya-Ting. “Identify Metastasis-related LncRNA in Breast Cancer by Microarray Approach.” 2017. Web. 19 Jan 2021.
Vancouver:
Tu Y. Identify Metastasis-related LncRNA in Breast Cancer by Microarray Approach. [Internet] [Thesis]. NSYSU; 2017. [cited 2021 Jan 19].
Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0611117-145225.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Tu Y. Identify Metastasis-related LncRNA in Breast Cancer by Microarray Approach. [Thesis]. NSYSU; 2017. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0611117-145225
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Michigan State University
10.
Takyar, Seyedeh Shohreh.
Fast NCRNA identification techniques.
Degree: 2012, Michigan State University
URL: http://etd.lib.msu.edu/islandora/object/etd:809
► Thesis M.S. Michigan State University. Computer Science 2012.
Many noncoding RNAs (ncRNAs) function through both their sequences and secondary structures. Thus, secondary structure derivation is…
(more)
▼ Thesis M.S. Michigan State University. Computer Science 2012.
Many noncoding RNAs (ncRNAs) function through both their sequences and secondary structures. Thus, secondary structure derivation is an important issue in today's RNA research. The state-of-the-art structure annotation tools are based on comparative analysis, which derives consensus structure of homologous ncRNAs. Despite promising results from existing ncRNA aligning and consensus structure derivation tools, there is a need for more efficient and accurate ncRNA secondary structure modeling and alignment methods.In this thesis, we introduce grammar string, a novel ncRNA secondary structure representation that encodes an ncRNA's sequence and secondary structure in the parameter space of a context-free grammar (CFG). Being a string defined on a special alphabet constructed from a CFG, it converts ncRNA alignment into sequence alignment with n square complexity. We explain how this representation is used in derivation of consensus secondary structure through multiple ncRNA alignment and also how existing clustering methods could be applied to ncRNAs represented by this model.
Description based on online resource; title from PDF t.p. (ProQuest, viewed Sept. 17, 2013)
Advisors/Committee Members: Sun, Yanni, Brown, Titus, Cole, James.
Subjects/Keywords: Non-coding RNA – Identification; Non-coding RNA; Bioinformatics
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APA ·
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CSE |
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to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Takyar, S. S. (2012). Fast NCRNA identification techniques. (Thesis). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:809
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):
Takyar, Seyedeh Shohreh. “Fast NCRNA identification techniques.” 2012. Thesis, Michigan State University. Accessed January 19, 2021.
http://etd.lib.msu.edu/islandora/object/etd:809.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Takyar, Seyedeh Shohreh. “Fast NCRNA identification techniques.” 2012. Web. 19 Jan 2021.
Vancouver:
Takyar SS. Fast NCRNA identification techniques. [Internet] [Thesis]. Michigan State University; 2012. [cited 2021 Jan 19].
Available from: http://etd.lib.msu.edu/islandora/object/etd:809.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Takyar SS. Fast NCRNA identification techniques. [Thesis]. Michigan State University; 2012. Available from: http://etd.lib.msu.edu/islandora/object/etd:809
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Ruhr Universität Bochum
11.
Zöllner, Hannah.
Charakterisierung nicht-kodierender RNAs im
Pankreaskarzinom.
Degree: 2014, Ruhr Universität Bochum
URL: http://nbn-resolving.de/urn/resolver.pl?urn=urn:nbn:de:hbz:294-42519
► Um die Prognose von Pankreaskarzinom-Patienten zu verbessern, ist ein besseres molekulares Verständnis dieser Krebserkrankung nötig, um neue diagnostische und therapeutische Ansätze generieren zu können. In…
(more)
▼ Um die Prognose von Pankreaskarzinom-Patienten zu
verbessern, ist ein besseres molekulares Verständnis dieser
Krebserkrankung nötig, um neue diagnostische und therapeutische
Ansätze generieren zu können. In dieser Arbeit wurde eine
Wachstumsinhibition von Pankreaskarzinomzellen durch die
Reexpression von miR-199b in vitro und in vivo nachgewiesen. Im
Falle von miR-199-3p konnte diese auf einen G1-Zellzyklusarrest
zurückgeführt werden. Eine erhöhte Apoptoserate konnte dagegen als
Ursache ausgeschlossen werden. Als Zielgene von miR-199-3p im
Pankreaskarzinom wurden TSPAN5, EMP1 und ACTA2 identifiziert. Des
Weiteren wurde in der vorliegenden Arbeit die als Biomarker für
verschiedene Krebsarten nachgewiesene miR-1246 als Pseudo-miRNA
identifiziert. Es handelt sich bei den Biomarker-Molekülen vielmehr
um Fragmente der am Vorgang des splicings von
RNA beteiligten
RNU2-1.
Advisors/Committee Members: Chemie.
Subjects/Keywords: non-coding RNA; miRNS; Bauchspeicheldrüsenkrebs;
Biomarker; Serum
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Zöllner, H. (2014). Charakterisierung nicht-kodierender RNAs im
Pankreaskarzinom. (Thesis). Ruhr Universität Bochum. Retrieved from http://nbn-resolving.de/urn/resolver.pl?urn=urn:nbn:de:hbz:294-42519
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):
Zöllner, Hannah. “Charakterisierung nicht-kodierender RNAs im
Pankreaskarzinom.” 2014. Thesis, Ruhr Universität Bochum. Accessed January 19, 2021.
http://nbn-resolving.de/urn/resolver.pl?urn=urn:nbn:de:hbz:294-42519.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Zöllner, Hannah. “Charakterisierung nicht-kodierender RNAs im
Pankreaskarzinom.” 2014. Web. 19 Jan 2021.
Vancouver:
Zöllner H. Charakterisierung nicht-kodierender RNAs im
Pankreaskarzinom. [Internet] [Thesis]. Ruhr Universität Bochum; 2014. [cited 2021 Jan 19].
Available from: http://nbn-resolving.de/urn/resolver.pl?urn=urn:nbn:de:hbz:294-42519.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Zöllner H. Charakterisierung nicht-kodierender RNAs im
Pankreaskarzinom. [Thesis]. Ruhr Universität Bochum; 2014. Available from: http://nbn-resolving.de/urn/resolver.pl?urn=urn:nbn:de:hbz:294-42519
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
12.
稲垣, 幸.
ショウジョウバエにおける新規mRNA-like non-coding RNAの同定及びその解析 : Identification and functional analysis of mRNA-like non-coding RNAs in Drosophila; ショウジョウバエ ニオケル シンキ mRNA-like non-coding RNA ノ ドウテイ オヨビ ソノ カイセキ.
Degree: Nara Institute of Science and Technology / 奈良先端科学技術大学院大学
URL: http://hdl.handle.net/10061/4070
Subjects/Keywords: non-coding RNA
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Chicago ·
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to Zotero / EndNote / Reference
Manager
APA (6th Edition):
稲垣, . (n.d.). ショウジョウバエにおける新規mRNA-like non-coding RNAの同定及びその解析 : Identification and functional analysis of mRNA-like non-coding RNAs in Drosophila; ショウジョウバエ ニオケル シンキ mRNA-like non-coding RNA ノ ドウテイ オヨビ ソノ カイセキ. (Thesis). Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Retrieved from http://hdl.handle.net/10061/4070
Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
稲垣, 幸. “ショウジョウバエにおける新規mRNA-like non-coding RNAの同定及びその解析 : Identification and functional analysis of mRNA-like non-coding RNAs in Drosophila; ショウジョウバエ ニオケル シンキ mRNA-like non-coding RNA ノ ドウテイ オヨビ ソノ カイセキ.” Thesis, Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Accessed January 19, 2021.
http://hdl.handle.net/10061/4070.
Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
稲垣, 幸. “ショウジョウバエにおける新規mRNA-like non-coding RNAの同定及びその解析 : Identification and functional analysis of mRNA-like non-coding RNAs in Drosophila; ショウジョウバエ ニオケル シンキ mRNA-like non-coding RNA ノ ドウテイ オヨビ ソノ カイセキ.” Web. 19 Jan 2021.
Note: this citation may be lacking information needed for this citation format:
No year of publication.
Vancouver:
稲垣 . ショウジョウバエにおける新規mRNA-like non-coding RNAの同定及びその解析 : Identification and functional analysis of mRNA-like non-coding RNAs in Drosophila; ショウジョウバエ ニオケル シンキ mRNA-like non-coding RNA ノ ドウテイ オヨビ ソノ カイセキ. [Internet] [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; [cited 2021 Jan 19].
Available from: http://hdl.handle.net/10061/4070.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.
Council of Science Editors:
稲垣 . ショウジョウバエにおける新規mRNA-like non-coding RNAの同定及びその解析 : Identification and functional analysis of mRNA-like non-coding RNAs in Drosophila; ショウジョウバエ ニオケル シンキ mRNA-like non-coding RNA ノ ドウテイ オヨビ ソノ カイセキ. [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; Available from: http://hdl.handle.net/10061/4070
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.
University of Manchester
13.
Pettini, Tom.
The role of novel long non-coding RNAs in Hox gene
regulation.
Degree: 2013, University of Manchester
URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:190102
► Whole genome transcriptome analysis has revealed that a large proportion of the genome in higher metazoa is transcribed, yet only a small proportion of this…
(more)
▼ Whole genome transcriptome analysis has revealed
that a large proportion of the genome in higher metazoa is
transcribed, yet only a small proportion of this transcription is
protein-
coding. One possible function of
non-
coding transcription
is that it enables complex and diverse body plans to evolve through
variation in deployment of a relatively common set of
protein-
coding genes. Functional studies suggest that long
non-
coding RNAs (lncRNAs) regulate gene expression via diverse
mechanisms, operating in both cis and trans to activate or repress
target genes. An emerging theme common to lncRNA function is
interaction with proteins that modify chromatin and mediate
epigenetic regulation. The Hox gene complexes are particularly rich
in lncRNAs and require precise and fine-tuned expression to deploy
Hox transcription factors throughout development. Here we identify
and functionally characterize two novel lncRNAs within the D.
melanogaster Hox complex, in the interval between Scr and Antp. We
use nascent transcript fluorescent in-situ hybridization (ntFISH)
to characterize the embryonic expression patterns of each lncRNA
with respect to flanking Hox genes, and to analyze co-transcription
within individual nuclei. We find that the transcription of one
lncRNA, ncX, is an initial response to early transcription factors
and may activate Scr expression, while transcription of the other
lncRNA, ncPRE is consistent with activation and/or maintenance of
Scr expression. ntFISH performed in D.virilis embryos revealed the
presence of a lncRNA ortholog with highly similar expression to
ncX, indicating functional conservation of lncRNA transcription
across ~60 million years of evolution. We identify the ncPRE lncRNA
locus as a binding site for multiple proteins associated with
Polycomb/Trithorax response elements (PREs/TREs) and show that DNA
encoding the ncPRE lncRNA functions as a bona fide PRE, mediating
trans-interactions between chromosomes and silencing of nearby
genes. We find that transcription through the ncPRE DNA relieves
silencing, suggesting a role for endogenous transcription of the
ncPRE lncRNA in relieving Polycomb-silencing and enabling Scr
activation. We demonstrate that both lncRNA transcripts are
required for proper Scr expression, and over-expression of either
lncRNAs from ectopic genomic loci has no effect on Scr expression,
but ectopic expression at the endogenous locus is associated with
ectopic Scr activation, indicating that the lncRNA-mediated
regulation functions locally at the site of transcription on the
chromosome. ncX may mediate transvection effects previously
observed at the Scr locus, independent of the protein Zeste.
Together our results support a model of competing mechanisms in the
regulation of Scr expression - a background of Polycomb repression
acting from the ncPRE locus, which in the first thoracic segment is
counteracted by lncRNA transcription and Trithorax binding to
ncPRE, enabling activation and maintenance of Scr expression. This
work provides a functional insight into the complex…
Advisors/Committee Members: PAPALOPULU, NANCY A, Papalopulu, Nancy, Ronshaugen, Matthew.
Subjects/Keywords: long non-coding RNA; Hox genes
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Pettini, T. (2013). The role of novel long non-coding RNAs in Hox gene
regulation. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:190102
Chicago Manual of Style (16th Edition):
Pettini, Tom. “The role of novel long non-coding RNAs in Hox gene
regulation.” 2013. Doctoral Dissertation, University of Manchester. Accessed January 19, 2021.
http://www.manchester.ac.uk/escholar/uk-ac-man-scw:190102.
MLA Handbook (7th Edition):
Pettini, Tom. “The role of novel long non-coding RNAs in Hox gene
regulation.” 2013. Web. 19 Jan 2021.
Vancouver:
Pettini T. The role of novel long non-coding RNAs in Hox gene
regulation. [Internet] [Doctoral dissertation]. University of Manchester; 2013. [cited 2021 Jan 19].
Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:190102.
Council of Science Editors:
Pettini T. The role of novel long non-coding RNAs in Hox gene
regulation. [Doctoral Dissertation]. University of Manchester; 2013. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:190102
14.
Coyne, Victoria Lee.
Characterization of long non-coding RNAs in the Hox
Complex of Drosophila.
Degree: 2016, University of Manchester
URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:305935
► Long non-coding RNAs (lncRNAs) are often defined as transcripts >200nts that have no discernable protein-coding ability (Quinn and Chang, 2016). Although relatively little is understood…
(more)
▼ Long
non-
coding RNAs (lncRNAs) are often defined as
transcripts >200nts that have no discernable protein-
coding
ability (Quinn and Chang, 2016). Although relatively little is
understood about the molecular mechanisms of lncRNA function, they
have established roles in regulation of gene expression during
development, cell differentiation and pluripotency (Fatica and
Bozzoni, 2014; Luo et al., 2016; Quinn and Chang, 2016; Rinn and
Chang, 2012) across vastly diverse organisms ranging from plants to
humans (Ulitsky and Bartel, 2013). LncRNAs have also been
associated with numerous pathological conditions, such as cancers
(Brunner et al., 2012), cardiovascular disease and
neurodegeneration (Chen et al., 2013). Investigations into lncRNAs
in wide ranging organisms, have revealed that many influence gene
activity by forming ribonucleoprotein complexes that affect the
conformational state of chromatin (Rinn and Chang, 2012). A genomic
region that has revealed several functional lncRNAs in diverse
organisms is the Hox complex (Pauli et al., 2011; Pettini, 2012;
Rinn et al., 2007). The Hox complex encodes a set of transcription
factors (TFs), physically clustered in the genome, which provide
morphological identity along the anterior to posterior axis of
developing embryos (Mallo and Alonso, 2013), throughout the
majority of bilatarian animals (Moreno et al., 2011). Misexpression
or mutation of Hox genes causes morphological and
pathophysiological defects (Quinonez and Innis, 2014). We
investigated clustering of lncRNAs throughout the D. melanogaster
genome using available annotations and carried out
RNA-seq in D.
virilis to expand the repertoire of lncRNAs and identify clusters
of lncRNAs. We found the Hox complex to be heavily enriched with
lncRNAs in both organisms, and syntenic transcripts from D.
melanogaster could be identified in D. pseudoobscura and D.
virilis. Several lncRNAs aligned with polycomb response elements
(PREs); transcription of PREs has previously been linked to a
switch in their activity (Herzog et al., 2014). However, we found
that transcribed PREs in D. melanogaster move positions relative to
the protein-
coding genes in other drosophilids, whilst the
transcriptional units remain in the same syntenic region.
Conservation of syntenic transcripts without evidence of remaining
a PRE suggest that the transcription is not linked to PRE function,
agreeing with recent findings that transcription of PREs does not
affect their function (Kassis and Muller, 2015). We investigated
functions of a novel lncRNA and adjacent PRE in the Hox complex by
ectopic expression and utilization of other genetic manipulation
tools. Overexpression of either the lncRNA or PRE and partial
duplication of the lncRNA caused phenotypes such as missing
halteres and/or T3 legs, misshaped T3 legs or malformed abdominal
segments. The observations that ectopic expression of this lncRNA
and an adjacent regulatory element from the Hox complex causes
phenotypes that can be linked to adjacent Hox gene misregulation,
Antp and Ubx, suggest that they…
Advisors/Committee Members: O'KEEFE, RAYMOND RT, GRIFFITHS-JONES, SAMUEL SR, O'Keefe, Raymond, Griffiths-Jones, Samuel, Ronshaugen, Matthew.
Subjects/Keywords: long non-coding RNA evolution development
Hox
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APA (6th Edition):
Coyne, V. L. (2016). Characterization of long non-coding RNAs in the Hox
Complex of Drosophila. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:305935
Chicago Manual of Style (16th Edition):
Coyne, Victoria Lee. “Characterization of long non-coding RNAs in the Hox
Complex of Drosophila.” 2016. Doctoral Dissertation, University of Manchester. Accessed January 19, 2021.
http://www.manchester.ac.uk/escholar/uk-ac-man-scw:305935.
MLA Handbook (7th Edition):
Coyne, Victoria Lee. “Characterization of long non-coding RNAs in the Hox
Complex of Drosophila.” 2016. Web. 19 Jan 2021.
Vancouver:
Coyne VL. Characterization of long non-coding RNAs in the Hox
Complex of Drosophila. [Internet] [Doctoral dissertation]. University of Manchester; 2016. [cited 2021 Jan 19].
Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:305935.
Council of Science Editors:
Coyne VL. Characterization of long non-coding RNAs in the Hox
Complex of Drosophila. [Doctoral Dissertation]. University of Manchester; 2016. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:305935
McMaster University
15.
Jahanshahi, Shahrzad.
DEVELOPMENT OF DNA CONSTRUCTS, BACTERIAL STRAINS AND METHODOLOGIES TO CHARACTERIZE THE IBS/SIB FAMILY OF TYPE I TOXIN-ANTITOXINS IN ESCHERICHIA COLI.
Degree: PhD, 2019, McMaster University
URL: http://hdl.handle.net/11375/24983
► Almost all bacteria contain genes that may lead to their growth stasis and death.Normally, these toxins are believed to be neutralized with their cognate antitoxinsfrom…
(more)
▼ Almost all bacteria contain genes that may lead to their growth stasis and death.Normally, these toxins are believed to be neutralized with their cognate antitoxinsfrom a toxin-antitoxin (TA) operon. These modules are also abundant in pathogenic bacteria suggesting a role for them both in normal bacterial physiology and pathogenicity. Their functions have been subject to intense debates. Due to the cell killing capability of the toxin and the gene silencing capability of the antitoxin, they have been utilized for basic research, biotechnology and medical applications. However, further advancements of these applications have been impeded by our limited knowledge of the biology of TAs. Among these TA systems is the Ibs/Sib (A-E) family. Here, we discuss our efforts in characterizing these systems, with a focus on the IbsC/SibC member. Studying them has shown to not be straightforward due to the complexity of their underlying mechanisms and the current approaches being laborious and lacking sensitivity to be applied to these low abundant molecules. We have developed fluorescence-based platforms to take advantage of sensitive and high throughput and resolution techniques such as Fluorescence Assisted Cell Sorting (FACS) to study these molecules instead of
relying on traditional culturing methods. While developing these platforms, we gained insights about the biology and regulation of these molecules. To expand this knowledge, we actively pursued investigating the regulation of these molecules at the transcriptional and post-transcriptional levels, both in their native context and in artificial systems. The rest of this thesis summarizes our efforts in solving one of the biggest pieces of the Ibs/Sib puzzle, namely their physiological expressions. With the strategies we have optimized for specific detection of these low abundance molecules, and the knowledge of their biology and regulation presented, we are now at an exciting phase to interrupt the long pause in the study of functions by these molecules and advancement of TA-based applications.
Thesis
Doctor of Philosophy (PhD)
Almost all bacteria contain genes that may lead to their growth stasis or death. Normally, these toxins are believed to be neutralized with their cognate antitoxins. In spite of the efforts to understand these toxin-antitoxin (TA) systems, their physiological roles are subject to intense debate. These systems are hard to study mainly because 1) they are only activated under specific conditions and 2) they are low in abundance. Current approaches are not high throughput and sensitive enough. In this thesis, we developed DNA constructs, bacterial strains and methodologies to facilitate the study of these molecules, particularly the Ibs-Sib family. We next employed these tools to gain a fundamental knowledge of their
expression under different conditions, which revealed surprising information about the function of these molecules. We believe that future studies can greatly benefit from the tools offered here to tremendously enhance our…
Advisors/Committee Members: Li, Yingfu, Biomedical Engineering.
Subjects/Keywords: small non-coding RNA; Toxin-Antitoxin
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Jahanshahi, S. (2019). DEVELOPMENT OF DNA CONSTRUCTS, BACTERIAL STRAINS AND METHODOLOGIES TO CHARACTERIZE THE IBS/SIB FAMILY OF TYPE I TOXIN-ANTITOXINS IN ESCHERICHIA COLI. (Doctoral Dissertation). McMaster University. Retrieved from http://hdl.handle.net/11375/24983
Chicago Manual of Style (16th Edition):
Jahanshahi, Shahrzad. “DEVELOPMENT OF DNA CONSTRUCTS, BACTERIAL STRAINS AND METHODOLOGIES TO CHARACTERIZE THE IBS/SIB FAMILY OF TYPE I TOXIN-ANTITOXINS IN ESCHERICHIA COLI.” 2019. Doctoral Dissertation, McMaster University. Accessed January 19, 2021.
http://hdl.handle.net/11375/24983.
MLA Handbook (7th Edition):
Jahanshahi, Shahrzad. “DEVELOPMENT OF DNA CONSTRUCTS, BACTERIAL STRAINS AND METHODOLOGIES TO CHARACTERIZE THE IBS/SIB FAMILY OF TYPE I TOXIN-ANTITOXINS IN ESCHERICHIA COLI.” 2019. Web. 19 Jan 2021.
Vancouver:
Jahanshahi S. DEVELOPMENT OF DNA CONSTRUCTS, BACTERIAL STRAINS AND METHODOLOGIES TO CHARACTERIZE THE IBS/SIB FAMILY OF TYPE I TOXIN-ANTITOXINS IN ESCHERICHIA COLI. [Internet] [Doctoral dissertation]. McMaster University; 2019. [cited 2021 Jan 19].
Available from: http://hdl.handle.net/11375/24983.
Council of Science Editors:
Jahanshahi S. DEVELOPMENT OF DNA CONSTRUCTS, BACTERIAL STRAINS AND METHODOLOGIES TO CHARACTERIZE THE IBS/SIB FAMILY OF TYPE I TOXIN-ANTITOXINS IN ESCHERICHIA COLI. [Doctoral Dissertation]. McMaster University; 2019. Available from: http://hdl.handle.net/11375/24983
Oregon State University
16.
Fahlgren, Noah.
Origins and evolution of plant microRNA genes.
Degree: PhD, Molecular and Cellular Biology, 2010, Oregon State University
URL: http://hdl.handle.net/1957/19627
► Eukaryotic small RNA (~20-30 nucleotides) are diverse regulatory molecules that repress gene expression at the transcriptional and post-transcriptional levels, defend hosts against invading viruses and…
(more)
▼ Eukaryotic small
RNA (~20-30 nucleotides) are diverse regulatory molecules that repress gene expression at the transcriptional and post-transcriptional levels, defend hosts against invading viruses and defend genomes against selfish DNA elements. Small
RNA populations are studied by high-throughput sequencing of the total small
RNA fraction isolated from cells, however, the sequencing depth achieved by next-generation platforms makes genome mapping and analysis computationally intensive with standard methods. Here, methods to generate, parse, map, quantify, standardize and analyze large small
RNA data sets are presented. This work demonstrates that small
RNA profiling is quantitative and reproducible and that statistical methods can be adapted to facilitate objective comparisons between small
RNA and small
RNA populations.
Plants
RNA silencing systems, including microRNA (miRNA), are important components of complex regulatory networks. Several plant MIRNA gene families and their target gene families are ancient, but over two-thirds of Arabidopsis MIRNA families are species-specific or restricted to the Brassicaceae lineage. In this work, the repertoires of MIRNA in the closely related species A. thaliana, A. lyrata and Capsella rubella were studied. Despite the relatively recent speciation of A. thaliana and A. lyrata ~10 million years ago, at least 13% of the MIRNA from each is species-specific. Additionally, 24–46 Arabidopsis MIRNA families arose after the Arabidopsis–Capsella split ~20 million years ago, supporting a net birth-death rate of 1.2–2.3 MIRNA per million years. These data, and data from other species, suggest that MIRNA are born and lost frequently throughout the evolution of plants. Further, evidence for the recent origin of 32 MIRNA families by duplication events, mostly of protein-
coding loci, was demonstrated, but only ~50% of these loci are predicted miRNA targets. Despite the link between MIRNA formation and potential target loci, only 25 young A. thaliana miRNA have verified targets. As a group, young miRNA tend to be expressed weakly, processed imprecisely and lack biologically relevant targets. Additionally, variation between young Arabidopsis miRNA was significantly higher than for ancient miRNA, suggesting that most of the young MIRNA are more likely evolving neutrally. Together, the data presented argue that most young MIRNA are evolutionarily transient.
Advisors/Committee Members: Carrington, James C. (advisor), Mockler, Todd C. (committee member).
Subjects/Keywords: microRNA evolution; Non-coding RNA – Evolution
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APA ·
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CSE |
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to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Fahlgren, N. (2010). Origins and evolution of plant microRNA genes. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/19627
Chicago Manual of Style (16th Edition):
Fahlgren, Noah. “Origins and evolution of plant microRNA genes.” 2010. Doctoral Dissertation, Oregon State University. Accessed January 19, 2021.
http://hdl.handle.net/1957/19627.
MLA Handbook (7th Edition):
Fahlgren, Noah. “Origins and evolution of plant microRNA genes.” 2010. Web. 19 Jan 2021.
Vancouver:
Fahlgren N. Origins and evolution of plant microRNA genes. [Internet] [Doctoral dissertation]. Oregon State University; 2010. [cited 2021 Jan 19].
Available from: http://hdl.handle.net/1957/19627.
Council of Science Editors:
Fahlgren N. Origins and evolution of plant microRNA genes. [Doctoral Dissertation]. Oregon State University; 2010. Available from: http://hdl.handle.net/1957/19627
University of North Carolina – Greensboro
17.
Wambua, Dickson M.
Mass spectrometric methods and bioinformatics tools for
accurate identification of MicroRNA biomarkers.
Degree: 2012, University of North Carolina – Greensboro
URL: http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=9464
► MicroRNA (miRNA) are a class of endogenous non-protein-coding RNA of ~19-25 nucleotides long that post-transcriptionally regulate protein expression by targeting messenger RNAs for cleavage or…
(more)
▼ MicroRNA (miRNA) are a class of endogenous
non-protein-
coding RNA of ~19-25 nucleotides long that
post-transcriptionally regulate protein expression by targeting
messenger RNAs for cleavage or translational repression. MiRNAs
have been implicated in the initiation and progression of 160+
human diseases. Unique miRNA differential expression signatures can
be used as a basis of discriminating against the presence or
absence of human diseases. MiRNAs are therefore a promising and
emerging class of disease biomarkers and therapeutic targets;
however, the accurate detection of a specific miRNA has continued
to be a challenging issue. Recently, mass spectrometry (MS) has
seen remarkable technological advancements making it an attractive
alternative to the conventional molecular biology miRNA
characterization techniques. This study consistently documents the
development of various analytical techniques aimed at
characterization of miRNAs. The current literature in the field of
miRNA is covered in chapter one. In chapter two, two new MS based
concepts for detection of miRNA are introduced; a) the miRNA is
captured using a specific complementary DNA probe, eluted and
digested with specific endonuclease. The digested miRNA fragments
are measured by MS resulting in a peak pattern that is dependent on
the miRNA sequence i.e. an intrinsic mass signature and b) a unique
mass signature is created by incorporating extra nucleotide(s) to
the 3' end of miRNA and the extended miRNA is measured by using MS.
The molecular mass of the extended miRNA, which is defined as
extended mass signature, is expected to be different from the other
miRNA within the same sample. These two approaches can improve the
accuracy on qualitative MS identification of specific miRNA. To
better understand miRNA function however, it is important to
elucidate the nucleotide sequence of the miRNA. Chapter three of
this study introduces a novel MS based assay for the sequencing of
miRNA through chemical hydrolysis. In this study, by taking
advantage of the mixing between a miRNA sample and an acidic MALDI
matrix prior to the MALDI-TOF MS measurements, a unique yet simple
and relatively cost-effective approach to generate miRNA sequencing
ladders was developed. By using this method, 100% sequence coverage
and accuracy in the sequencing of selected miRNAs were achieved.
When many samples are involved, the data generated from miRNA
measurements can be complex and manual data processing is tedious
and challenging, as such, the spectral interpretation of mass
spectrometric data can quickly turn out to be the bottleneck in
miRNA analysis. The success of MS as a tool for analysis of miRNA
will therefore strongly depend on the development of relevant
computational software with the ability to properly interpret and
analyze the large data. To meet this need, chapter four of this
work explains the development of MicroRNA MultiTool, a
computational software for the rapid interpretation of MS data
containing human miRNA. Users can directly enter data obtained from
mass…
Advisors/Committee Members: Norman Chiu (advisor).
Subjects/Keywords: Non-coding RNA; Mass spectrometry; Biochemical markers
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Wambua, D. M. (2012). Mass spectrometric methods and bioinformatics tools for
accurate identification of MicroRNA biomarkers. (Doctoral Dissertation). University of North Carolina – Greensboro. Retrieved from http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=9464
Chicago Manual of Style (16th Edition):
Wambua, Dickson M. “Mass spectrometric methods and bioinformatics tools for
accurate identification of MicroRNA biomarkers.” 2012. Doctoral Dissertation, University of North Carolina – Greensboro. Accessed January 19, 2021.
http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=9464.
MLA Handbook (7th Edition):
Wambua, Dickson M. “Mass spectrometric methods and bioinformatics tools for
accurate identification of MicroRNA biomarkers.” 2012. Web. 19 Jan 2021.
Vancouver:
Wambua DM. Mass spectrometric methods and bioinformatics tools for
accurate identification of MicroRNA biomarkers. [Internet] [Doctoral dissertation]. University of North Carolina – Greensboro; 2012. [cited 2021 Jan 19].
Available from: http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=9464.
Council of Science Editors:
Wambua DM. Mass spectrometric methods and bioinformatics tools for
accurate identification of MicroRNA biomarkers. [Doctoral Dissertation]. University of North Carolina – Greensboro; 2012. Available from: http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=9464
Michigan State University
18.
Achawanantakun, Rujira.
Identification and analysis of non-coding RNAs in large scale genomic data.
Degree: 2014, Michigan State University
URL: http://etd.lib.msu.edu/islandora/object/etd:2757
► Thesis Ph. D. Michigan State University. Computer Science 2014.
The high-throughput sequencing technologies have created the opportunity of large-scale transcriptome analyses and intensify attention on…
(more)
▼ Thesis Ph. D. Michigan State University. Computer Science 2014.
The high-throughput sequencing technologies have created the opportunity of large-scale transcriptome analyses and intensify attention on the study of non-coding RNAs (ncRNAs). NcRNAs pay important roles in many cellular processes. For example, transfer RNAs and ribosomal RNAs are involved in protein translation process; micro RNAs regulate gene expression; long ncRNAs are found to associate with many human diseases ranging from autism to cancer.Many ncRNAs function through both their sequences and secondary structures. Thus, accurate secondary structure prediction provides important information to understand the tertiary structures and thus the functions of ncRNAs.The state-of-the-art ncRNA identification tools are mainly based on two approaches. The first approach is a comparative structure analysis, which determines the consensus structure from homologous ncRNAs. Structure prediction is a costly process, because the size of the putative structures increases exponentially with the sequence length. Thus it is not practical for very long ncRNAs such as lncRNAs. The accuracy of current structure prediction tools is still not satisfactory, especially on sequences containing pseudoknots. An alternative identification approach that has been increasingly popular is sequence based expression analysis, which relies on next generation sequencing (NGS) technologies for quantifying gene expression on a genome-wide scale. The specific expression patterns are used to identify the type of ncRNAs. This method therefore is limited to ncRNAs that have medium to high expression levels and have the unique expression patterns that are different from other ncRNAs. In this work, we address the challenges presented in ncRNA identification using different approaches. To be specific, we have proposed four tools, grammar-string based alignment, KnotShape, KnotStructure, and lncRNA-ID. Grammar-string is a novel ncRNA secondary structure representation that encodes an ncRNA's sequence and secondary structure in the parameter space of a context-free grammar and a full RNA grammar including pseudoknots. It simplifies a complicated structure alignment to a simple grammar string-based alignment. Also, grammar-string-based alignment incorporates both sequence and structure into multiple sequence alignment. Thus, we can then enhance the speed of alignment and achieve an accurate consensus structure. KnotShape and KnotStructure focus on reducing the size of the structure search space to enhance the speed of a structure prediction process. KnotShape predicts the best shape by grouping similar structures together and applying SVM classification to select the best representative shape. KnotStructure improve the performance of structure prediction by using grammar-string based-alignment and the predicted shape output by KnotShape.lncRNA-ID is specially designed for lncRNA identification. It incorporates balanced random forest learning to construct a classification model to distinguish…
Advisors/Committee Members: Sun, Yanni, Brown, Titus, Tan, Pang-Ning, Cole, James.
Subjects/Keywords: Non-coding RNA – Identification; Non-coding RNA – Analysis; Genomics; Support vector machines; Non-coding RNA; Computer science; Biology; Random forest; Long non-coding RNA
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APA ·
Chicago ·
MLA ·
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to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Achawanantakun, R. (2014). Identification and analysis of non-coding RNAs in large scale genomic data. (Thesis). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:2757
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Achawanantakun, Rujira. “Identification and analysis of non-coding RNAs in large scale genomic data.” 2014. Thesis, Michigan State University. Accessed January 19, 2021.
http://etd.lib.msu.edu/islandora/object/etd:2757.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Achawanantakun, Rujira. “Identification and analysis of non-coding RNAs in large scale genomic data.” 2014. Web. 19 Jan 2021.
Vancouver:
Achawanantakun R. Identification and analysis of non-coding RNAs in large scale genomic data. [Internet] [Thesis]. Michigan State University; 2014. [cited 2021 Jan 19].
Available from: http://etd.lib.msu.edu/islandora/object/etd:2757.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Achawanantakun R. Identification and analysis of non-coding RNAs in large scale genomic data. [Thesis]. Michigan State University; 2014. Available from: http://etd.lib.msu.edu/islandora/object/etd:2757
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Manchester
19.
Pettini, Tom.
The role of novel long non-coding RNAs in Hox gene regulation.
Degree: PhD, 2013, University of Manchester
URL: https://www.research.manchester.ac.uk/portal/en/theses/the-role-of-novel-long-noncoding-rnas-in-hox-gene-regulation(c8e44900-3ac0-40be-8ec6-b50179381d17).html
;
http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.647365
► Whole genome transcriptome analysis has revealed that a large proportion of the genome in higher metazoa is transcribed, yet only a small proportion of this…
(more)
▼ Whole genome transcriptome analysis has revealed that a large proportion of the genome in higher metazoa is transcribed, yet only a small proportion of this transcription is protein-coding. One possible function of non-coding transcription is that it enables complex and diverse body plans to evolve through variation in deployment of a relatively common set of protein-coding genes. Functional studies suggest that long non-coding RNAs (lncRNAs) regulate gene expression via diverse mechanisms, operating in both cis and trans to activate or repress target genes. An emerging theme common to lncRNA function is interaction with proteins that modify chromatin and mediate epigenetic regulation. The Hox gene complexes are particularly rich in lncRNAs and require precise and fine-tuned expression to deploy Hox transcription factors throughout development. Here we identify and functionally characterize two novel lncRNAs within the D. melanogaster Hox complex, in the interval between Scr and Antp. We use nascent transcript fluorescent in-situ hybridization (ntFISH) to characterize the embryonic expression patterns of each lncRNA with respect to flanking Hox genes, and to analyze co-transcription within individual nuclei. We find that the transcription of one lncRNA, ncX, is an initial response to early transcription factors and may activate Scr expression, while transcription of the other lncRNA, ncPRE is consistent with activation and/or maintenance of Scr expression. ntFISH performed in D.virilis embryos revealed the presence of a lncRNA ortholog with highly similar expression to ncX, indicating functional conservation of lncRNA transcription across ~60 million years of evolution. We identify the ncPRE lncRNA locus as a binding site for multiple proteins associated with Polycomb/Trithorax response elements (PREs/TREs) and show that DNA encoding the ncPRE lncRNA functions as a bona fide PRE, mediating trans-interactions between chromosomes and silencing of nearby genes. We find that transcription through the ncPRE DNA relieves silencing, suggesting a role for endogenous transcription of the ncPRE lncRNA in relieving Polycomb-silencing and enabling Scr activation. We demonstrate that both lncRNA transcripts are required for proper Scr expression, and over-expression of either lncRNAs from ectopic genomic loci has no effect on Scr expression, but ectopic expression at the endogenous locus is associated with ectopic Scr activation, indicating that the lncRNA-mediated regulation functions locally at the site of transcription on the chromosome. ncX may mediate transvection effects previously observed at the Scr locus, independent of the protein Zeste. Together our results support a model of competing mechanisms in the regulation of Scr expression - a background of Polycomb repression acting from the ncPRE locus, which in the first thoracic segment is counteracted by lncRNA transcription and Trithorax binding to ncPRE, enabling activation and maintenance of Scr expression. This work provides a functional insight into the complex…
Subjects/Keywords: 572.8; long non-coding RNA; Hox genes
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Pettini, T. (2013). The role of novel long non-coding RNAs in Hox gene regulation. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/the-role-of-novel-long-noncoding-rnas-in-hox-gene-regulation(c8e44900-3ac0-40be-8ec6-b50179381d17).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.647365
Chicago Manual of Style (16th Edition):
Pettini, Tom. “The role of novel long non-coding RNAs in Hox gene regulation.” 2013. Doctoral Dissertation, University of Manchester. Accessed January 19, 2021.
https://www.research.manchester.ac.uk/portal/en/theses/the-role-of-novel-long-noncoding-rnas-in-hox-gene-regulation(c8e44900-3ac0-40be-8ec6-b50179381d17).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.647365.
MLA Handbook (7th Edition):
Pettini, Tom. “The role of novel long non-coding RNAs in Hox gene regulation.” 2013. Web. 19 Jan 2021.
Vancouver:
Pettini T. The role of novel long non-coding RNAs in Hox gene regulation. [Internet] [Doctoral dissertation]. University of Manchester; 2013. [cited 2021 Jan 19].
Available from: https://www.research.manchester.ac.uk/portal/en/theses/the-role-of-novel-long-noncoding-rnas-in-hox-gene-regulation(c8e44900-3ac0-40be-8ec6-b50179381d17).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.647365.
Council of Science Editors:
Pettini T. The role of novel long non-coding RNAs in Hox gene regulation. [Doctoral Dissertation]. University of Manchester; 2013. Available from: https://www.research.manchester.ac.uk/portal/en/theses/the-role-of-novel-long-noncoding-rnas-in-hox-gene-regulation(c8e44900-3ac0-40be-8ec6-b50179381d17).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.647365
Rutgers University
20.
Swanson, Karl, 1990-.
Microrna discovery in Belgica Antarctica: microrna loci relocation across taxa from duplication.
Degree: MS, Biology, 2015, Rutgers University
URL: https://rucore.libraries.rutgers.edu/rutgers-lib/47160/
► Small non-coding RNAs are a diverse class of molecules with wide biological importance, including regulatory roles, implications for evolution and possible medical therapeutics. The advent…
(more)
▼ Small
non-
coding RNAs are a diverse class of molecules with wide biological importance, including regulatory roles, implications for evolution and possible medical therapeutics. The advent of next generation sequencing technology and various computational tools has aided in increasing the throughput and methods of discovery for these molecules. In this thesis we utilize and expand upon the most current methodologies of computational discovery, sequencing analysis and visualization for
non-
coding RNA, particularly microRNA (miRNA), in the Antarctic midge, Belgica antarctica and Drosophila melanogaster. These methods and the unique properties of B. antarctica’s genome lead to discoveries of evolutionary and functional importance, especially for a class of miRNA called mirtrons. We show that mirtrons within the B. antarctica can relocate to an alternative gene loci, or are lost from their host gene. This relocation and loss of mirtrons is based on computational discovery and predictions, but is supported and validated by other examples in literature covering a wide range of taxa. The data and results suggest a re-examination of the mechanisms that birth miRNA, specifically in terms of evolutionary duplication events. Additionally we describe and expand upon a tool for the in silico visualization of small
non-
coding RNA sequencing data, Genome Navigator. This tool can be used interactively to visualize concepts generated from high-throughput DNA and
RNA sequencing data. We applied the new functionalities of Genome Navigator to elucidate biogenesis properties of another class of small
non-
coding RNA, called tRNA-derived fragments (tRFs). These properties strikingly resemble the canonical biogenesis cleavage patterns of miRNA.
Advisors/Committee Members: Grigoriev, Andrey (chair), Yakoby, Nir (internal member), Klein, Eric (internal member).
Subjects/Keywords: Non-coding RNA; Belgica antarctica; Gene mapping
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Swanson, Karl, 1. (2015). Microrna discovery in Belgica Antarctica: microrna loci relocation across taxa from duplication. (Masters Thesis). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/47160/
Chicago Manual of Style (16th Edition):
Swanson, Karl, 1990-. “Microrna discovery in Belgica Antarctica: microrna loci relocation across taxa from duplication.” 2015. Masters Thesis, Rutgers University. Accessed January 19, 2021.
https://rucore.libraries.rutgers.edu/rutgers-lib/47160/.
MLA Handbook (7th Edition):
Swanson, Karl, 1990-. “Microrna discovery in Belgica Antarctica: microrna loci relocation across taxa from duplication.” 2015. Web. 19 Jan 2021.
Vancouver:
Swanson, Karl 1. Microrna discovery in Belgica Antarctica: microrna loci relocation across taxa from duplication. [Internet] [Masters thesis]. Rutgers University; 2015. [cited 2021 Jan 19].
Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/47160/.
Council of Science Editors:
Swanson, Karl 1. Microrna discovery in Belgica Antarctica: microrna loci relocation across taxa from duplication. [Masters Thesis]. Rutgers University; 2015. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/47160/
21.
NC DOCKS at The University of North Carolina at Greensboro; Wambua, Dickson M.
Mass spectrometric methods and bioinformatics tools for accurate identification of MicroRNA biomarkers.
Degree: 2012, NC Docks
URL: http://libres.uncg.edu/ir/uncg/f/Wambua_uncg_0154D_11054.pdf
► MicroRNA (miRNA) are a class of endogenous non-protein-coding RNA of ~19-25 nucleotides long that post-transcriptionally regulate protein expression by targeting messenger RNAs for cleavage or…
(more)
▼ MicroRNA (miRNA) are a class of endogenous non-protein-coding RNA of ~19-25 nucleotides long that post-transcriptionally regulate protein expression by targeting messenger RNAs for cleavage or translational repression. MiRNAs have been implicated in the initiation and progression of 160+ human diseases. Unique miRNA differential expression signatures can be used as a basis of discriminating against the presence or absence of human diseases. MiRNAs are therefore a promising and emerging class of disease biomarkers and therapeutic targets; however, the accurate detection of a specific miRNA has continued to be a challenging issue. Recently, mass spectrometry (MS) has seen remarkable technological advancements making it an attractive alternative to the conventional molecular biology miRNA characterization techniques. This study consistently documents the development of various analytical techniques aimed at characterization of miRNAs. The current literature in the field of miRNA is covered in chapter one. In chapter two, two new MS based concepts for detection of miRNA are introduced; a) the miRNA is captured using a specific complementary DNA probe, eluted and digested with specific endonuclease. The digested miRNA fragments are measured by MS resulting in a peak pattern that is dependent on the miRNA sequence i.e. an intrinsic mass signature and b) a unique mass signature is created by incorporating extra nucleotide(s) to the 3' end of miRNA and the extended miRNA is measured by using MS. The molecular mass of the extended miRNA, which is defined as extended mass signature, is expected to be different from the other miRNA within the same sample. These two approaches can improve the accuracy on qualitative MS identification of specific miRNA. To better understand miRNA function however, it is important to elucidate the nucleotide sequence of the miRNA. Chapter three of this study introduces a novel MS based assay for the sequencing of miRNA through chemical hydrolysis. In this study, by taking advantage of the mixing between a miRNA sample and an acidic MALDI matrix prior to the MALDI-TOF MS measurements, a unique yet simple and relatively cost-effective approach to generate miRNA sequencing ladders was developed. By using this method, 100% sequence coverage and accuracy in the sequencing of selected miRNAs were achieved. When many samples are involved, the data generated from miRNA measurements can be complex and manual data processing is tedious and challenging, as such, the spectral interpretation of mass spectrometric data can quickly turn out to be the bottleneck in miRNA analysis. The success of MS as a tool for analysis of miRNA will therefore strongly depend on the development of relevant computational software with the ability to properly interpret and analyze the large data. To meet this need, chapter four of this work explains the development of MicroRNA MultiTool, a computational software for the rapid interpretation of MS data containing human miRNA. Users can directly enter data obtained from mass…
Subjects/Keywords: Non-coding RNA; Mass spectrometry; Biochemical markers
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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):
NC DOCKS at The University of North Carolina at Greensboro; Wambua, D. M. (2012). Mass spectrometric methods and bioinformatics tools for accurate identification of MicroRNA biomarkers. (Thesis). NC Docks. Retrieved from http://libres.uncg.edu/ir/uncg/f/Wambua_uncg_0154D_11054.pdf
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):
NC DOCKS at The University of North Carolina at Greensboro; Wambua, Dickson M. “Mass spectrometric methods and bioinformatics tools for accurate identification of MicroRNA biomarkers.” 2012. Thesis, NC Docks. Accessed January 19, 2021.
http://libres.uncg.edu/ir/uncg/f/Wambua_uncg_0154D_11054.pdf.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
NC DOCKS at The University of North Carolina at Greensboro; Wambua, Dickson M. “Mass spectrometric methods and bioinformatics tools for accurate identification of MicroRNA biomarkers.” 2012. Web. 19 Jan 2021.
Vancouver:
NC DOCKS at The University of North Carolina at Greensboro; Wambua DM. Mass spectrometric methods and bioinformatics tools for accurate identification of MicroRNA biomarkers. [Internet] [Thesis]. NC Docks; 2012. [cited 2021 Jan 19].
Available from: http://libres.uncg.edu/ir/uncg/f/Wambua_uncg_0154D_11054.pdf.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
NC DOCKS at The University of North Carolina at Greensboro; Wambua DM. Mass spectrometric methods and bioinformatics tools for accurate identification of MicroRNA biomarkers. [Thesis]. NC Docks; 2012. Available from: http://libres.uncg.edu/ir/uncg/f/Wambua_uncg_0154D_11054.pdf
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Rochester
22.
Mathews, David H. (1971 - ).
RNA Secondary Structure Comparative Analysis: Method
Development and Application to Genomics.
Degree: PhD, 2016, University of Rochester
URL: http://hdl.handle.net/1802/31383
► RNA not only codes protein sequences, it also functions by having specific structures. Because RNA secondary structure is more stable than tertiary structure, it is…
(more)
▼ RNA not only codes protein sequences, it also
functions by having specific structures.
Because RNA secondary
structure is more stable than tertiary structure, it is feasible
to
study secondary structure independently. To improve secondary
structure prediction
accuracy, comparative analysis can be used.
It assumes RNAs that conserve function
usually evolve under
structural constraints.
Previous computational methods that use
comparative analysis did not accommodate
domain insertions, where
structural motifs are inserted in a sequence with respect to its
homologs. For this work, domain insertion was introduced into the
program Dynalign,
which takes two sequences as input and outputs
their conserved structures. This update,
Dynalign II,
significantly improves prediction accuracy upon Dynalign,
especially over
base pairs in inserted domains.
Computational
comparative analysis methods for RNA structure prediction require
parameters that quantify evolutionary constraints on RNA secondary
structure and
sequence alignment, e.g., parameters for base pairs
and nucleotides deletion, insertion
and mutation. A machine
learning method called a log linear model was used to
quantify
these parameters using structural alignments of homologous RNAs as
the
training set. It was found that evolution favors structural
conservation and disfavors
structural mutation between homologous
RNAs.
Comparative analysis also helps identify functional
non-coding RNAs (ncRNA). Since
homologous ncRNAs evolve under
structural constraints, predicted structural conservation of
homologous genomic sequences can be utilized to identify ncRNAs. A
new program, Multifind, was developed. It takes multiple sequences
as input and
assesses the probability that they are homologous
ncRNAs using a support vector
machine (SVM). One input to SVM is
based on the conservation of the input sequence
structures
predicted by Multilign, a multiple sequence conserved structure
prediction
program based on Dynalign. Multifind performs better
than competing programs on
testing sets constructed from a RNA
database Rfam and detects unique ncRNAs on
genomic data
sets.
Subjects/Keywords: Comparative sequence analysis; Non-coding RNA; RNA; RNA secondary structure
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APA ·
Chicago ·
MLA ·
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Manager
APA (6th Edition):
Mathews, D. H. (. -. ). (2016). RNA Secondary Structure Comparative Analysis: Method
Development and Application to Genomics. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/31383
Chicago Manual of Style (16th Edition):
Mathews, David H (1971 - ). “RNA Secondary Structure Comparative Analysis: Method
Development and Application to Genomics.” 2016. Doctoral Dissertation, University of Rochester. Accessed January 19, 2021.
http://hdl.handle.net/1802/31383.
MLA Handbook (7th Edition):
Mathews, David H (1971 - ). “RNA Secondary Structure Comparative Analysis: Method
Development and Application to Genomics.” 2016. Web. 19 Jan 2021.
Vancouver:
Mathews DH(-). RNA Secondary Structure Comparative Analysis: Method
Development and Application to Genomics. [Internet] [Doctoral dissertation]. University of Rochester; 2016. [cited 2021 Jan 19].
Available from: http://hdl.handle.net/1802/31383.
Council of Science Editors:
Mathews DH(-). RNA Secondary Structure Comparative Analysis: Method
Development and Application to Genomics. [Doctoral Dissertation]. University of Rochester; 2016. Available from: http://hdl.handle.net/1802/31383
Louisiana State University
23.
Korde, Asawari.
Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes.
Degree: PhD, 2014, Louisiana State University
URL: etd-05232014-193901
;
https://digitalcommons.lsu.edu/gradschool_dissertations/274
► Transcription by RNA polymerase III (Pol III) requires sequential assembly of Pol III-specific transcription factors. At the tRNA gene, the TFIIIC complex recognizes and specifically…
(more)
▼ Transcription by RNA polymerase III (Pol III) requires sequential assembly of Pol III-specific transcription factors. At the tRNA gene, the TFIIIC complex recognizes and specifically binds at intragenic promoter elements A-box and B-box and aids the assembly of TFIIIB to upstream of the transcriptional start site. Upon binding, Pol III is recruited near start sites and transcription of tRNA genes is initiated. Apart from transcription of a gene, these bound Pol III complexes influence transcription, chromatin state and genome organization of neighboring RNA polymerase II (Pol II)-transcribed genes. Such effects are known as extra-transcriptional effects of Pol III complex. Our study provides evidence of a unique “extra-transcriptional” activity of assembled Pol III transcription complexes at the tRNA gene that blocks progression of intergenic RNA polymerase II transcription. We demonstrated that the Pol III transcription complex bound to the tRNA gene upstream of the Saccharomyces cerevisiae ATG31 gene protects the ATG31 promoter against readthrough transcriptional interference from the upstream non-coding intergenic SUT467. The protection is predominately mediated by binding of the TFIIIB complex. Failure to block this readthrough resulted in compromised ATG31 translation. Given the recent discovery of widespread pervasive transcription in yeast, protection of neighboring genes from intergenic transcriptional interference may be a key extra-transcriptional function of assembled RNA polymerase III complexes. Our data from RNA-seq analysis demonstrated genome-wide effects of DNA bound Pol III complexes on neighboring chromosomal loci, by comparing expression profiles from tfc6 under-expressing mutants and wild-type S. cerevisiae strains. Reduced TFIIIC occupancy in mutant strains altered Pol II derived transcripts and displayed 5’ or 3’ extension of protein-coding genes, readthrough from non-coding transcripts and increase in the transcription of genes near the potential TFIIIC binding sites, including tRNA genes and putative ETC sites. Interestingly, not all genes in the vicinity of TFIIIC binding sites were transcriptionally mis-regulated, suggesting variable strength of influence on Pol II transcripts by TFIIIC bound sites. Finally, as observed in SUT467-ATG31 readthrough, we anticipated translation defects in 5’ or 3’ extended transcripts in mutants. Overall these genome-wide results suggest much complex regulatory role of Pol III transcription factors bound sites than previously anticipated.
Subjects/Keywords: RNA-seq; tRNA gene; barriers; non-coding RNA; insulators; RNA polymerases
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Korde, A. (2014). Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes. (Doctoral Dissertation). Louisiana State University. Retrieved from etd-05232014-193901 ; https://digitalcommons.lsu.edu/gradschool_dissertations/274
Chicago Manual of Style (16th Edition):
Korde, Asawari. “Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes.” 2014. Doctoral Dissertation, Louisiana State University. Accessed January 19, 2021.
etd-05232014-193901 ; https://digitalcommons.lsu.edu/gradschool_dissertations/274.
MLA Handbook (7th Edition):
Korde, Asawari. “Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes.” 2014. Web. 19 Jan 2021.
Vancouver:
Korde A. Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes. [Internet] [Doctoral dissertation]. Louisiana State University; 2014. [cited 2021 Jan 19].
Available from: etd-05232014-193901 ; https://digitalcommons.lsu.edu/gradschool_dissertations/274.
Council of Science Editors:
Korde A. Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes. [Doctoral Dissertation]. Louisiana State University; 2014. Available from: etd-05232014-193901 ; https://digitalcommons.lsu.edu/gradschool_dissertations/274
University of Georgia
24.
Hu, Ping.
A study of non-coding rox1 and rox2 RNAs in Drosophila species.
Degree: 2014, University of Georgia
URL: http://hdl.handle.net/10724/24167
► rox1 and rox2 are two non-coding RNAs found in male Drosophila melanogaster, which can direct the MSL complex to bind to the X-chromosome to up-regulate…
(more)
▼ rox1 and rox2 are two non-coding RNAs found in male Drosophila melanogaster, which can direct the MSL complex to bind to the X-chromosome to up-regulate all X-linked genes two-fold. rox1 and rox2 RNAs lack similarity in their primary
sequences, but they have functional redundancy; that is, in the presence either one of them, males survive. The mechanism of this redundancy is unclear. Here we have used comparative bioinformatics methods to predict an double internal-loop structure
near 3’-end of rox RNAs shared by rox1 and rox2; this structure might contribute to the rox1 and rox2 RNA functional redundancy. rox1 and rox2 RNAs in other Drosophila species have not been previously reported; we identify putative rox1 and rox2 RNAs in
Drosophila simulans, sechellia, yakuba and erecta.
Subjects/Keywords: Non-coding RNA; rox1 RNA; rox2 RNA; dosage compasation; Drosophila species
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Hu, P. (2014). A study of non-coding rox1 and rox2 RNAs in Drosophila species. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/24167
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):
Hu, Ping. “A study of non-coding rox1 and rox2 RNAs in Drosophila species.” 2014. Thesis, University of Georgia. Accessed January 19, 2021.
http://hdl.handle.net/10724/24167.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Hu, Ping. “A study of non-coding rox1 and rox2 RNAs in Drosophila species.” 2014. Web. 19 Jan 2021.
Vancouver:
Hu P. A study of non-coding rox1 and rox2 RNAs in Drosophila species. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 19].
Available from: http://hdl.handle.net/10724/24167.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Hu P. A study of non-coding rox1 and rox2 RNAs in Drosophila species. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/24167
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Texas – Austin
25.
Qin, Yidan.
Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine.
Degree: PhD, Microbiology, 2016, University of Texas – Austin
URL: http://hdl.handle.net/2152/41602
► Thermostable group II intron reverse transcriptases (TGIRTs) from thermophilic bacteria are advantageous for biotechnological applications that require cDNA synthesis, such as RT-qPCR and RNA-seq. TGIRTs…
(more)
▼ Thermostable group II intron reverse transcriptases (TGIRTs) from thermophilic bacteria are advantageous for biotechnological applications that require cDNA synthesis, such as RT-qPCR and
RNA-seq. TGIRTs have higher thermostability, processivity and fidelity than conventional retroviral RTs, along with a novel end-to-end template-switching activity that attaches
RNA-seq adapters to target RNAs without
RNA ligation. First, I optimized the TGIRT template-switching method for
RNA-seq analysis of small
non-
coding RNAs (ncRNAs). I showed that TGIRT-seq gives full-length reads of tRNAs, which are refractory to retroviral RTs, and enables identification of a variety of base modifications in tRNAs by distinctive patterns of misincorporated nucleotides. With collaborators, I developed an efficient and quantitative high-throughput tRNA sequencing method, identified RNAs bound by the human interferon-induced protein IFIT5, yielding new insights into its functions in tRNA quality control and innate immunity, and uncovered a novel mRNA-independent mechanism for elongation of nascent peptides. Second, I developed a new, streamlined TGIRT-seq method for comprehensive analysis of all
RNA size classes in a single
RNA-seq. This method enables
RNA-seq library construction from <1 ng of fragmented RNAs in <5 h. By using the method, I showed that human plasma contains large numbers of protein-
coding and long ncRNAs together with diverse classes of small ncRNAs, which are mostly present as full-length transcripts. With collaborators, I showed that TGIRT-seq analysis of circulating RNAs identified potential biomarkers at different stages of multiple myeloma and may provide a sensitive,
non-invasive diagnostic tool for a variety of human diseases. Finally, I adapted TGIRTs for use in mapping of
RNA structures and
RNA-protein interaction sites, and identification of
RNA targets of cellular
RNA-binding proteins. My research led to a series of new biological insights, which would have been difficult or impossible to obtain by current methods, and established TGIRTs as a tool for a broad range of applications in
RNA research and diagnostics.
Advisors/Committee Members: Lambowitz, Alan (advisor), Iyer, Vishwanath R (committee member), Krug, Robert M (committee member), Russell, Rick (committee member), Stevens, Scott W (committee member), Sullivan, Christopher S (committee member).
Subjects/Keywords: RNA-seq; Diagnostics; Precision medicine; Non-coding RNA; Circulating RNA
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Qin, Y. (2016). Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/41602
Chicago Manual of Style (16th Edition):
Qin, Yidan. “Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine.” 2016. Doctoral Dissertation, University of Texas – Austin. Accessed January 19, 2021.
http://hdl.handle.net/2152/41602.
MLA Handbook (7th Edition):
Qin, Yidan. “Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine.” 2016. Web. 19 Jan 2021.
Vancouver:
Qin Y. Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2016. [cited 2021 Jan 19].
Available from: http://hdl.handle.net/2152/41602.
Council of Science Editors:
Qin Y. Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine. [Doctoral Dissertation]. University of Texas – Austin; 2016. Available from: http://hdl.handle.net/2152/41602
Michigan State University
26.
Yuan, Cheng.
Non-coding RNA identification in large-scale genomic data.
Degree: 2014, Michigan State University
URL: http://etd.lib.msu.edu/islandora/object/etd:3077
► Thesis Ph. D. Michigan State University. Computer Science 2014.
Noncoding RNAs (ncRNAs), which function directly as RNAs without translating into proteins, play diverse and important…
(more)
▼ Thesis Ph. D. Michigan State University. Computer Science 2014.
Noncoding RNAs (ncRNAs), which function directly as RNAs without translating into proteins, play diverse and important biological functions. ncRNAs function not only through their primary structures, but also secondary structures, which are defined by interactions between Watson-Crick and wobble base pairs. Common types of ncRNA include microRNA, rRNA, snoRNA, tRNA. Functions of ncRNAs vary among different types. Recent studies suggest the existence of large number of ncRNA genes. Identification of novel and known ncRNAs becomes increasingly important in order to understand their functionalities and the underlying communities.Next-generation sequencing (NGS) technology sheds lights on more comprehensive and sensitive ncRNA annotation. Lowly transcribed ncRNAs or ncRNAs from rare species with low abundance may be identified via deep sequencing. However, there exist several challenges in ncRNA identification in large-scale genomic data. First, the massive volume of datasets could lead to very long computation time, making existing algorithms infeasible. Second, NGS has relatively high error rate, which could further complicate the problem. Third, high sequence similarity among related ncRNAs could make them difficult to identify, resulting in incorrect output. Fourth, while secondary structures should be adopted for accurate ncRNA identification, they usually incur high computational complexity. In particular, some ncRNAs contain pseudoknot structures, which cannot be effectively modeled by the state-of-the-art approach. As a result, ncRNAs containing pseudoknots are hard to annotate.In my PhD work, I aimed to tackle the above challenges in ncRNA identification. First, I designed a progressive search pipeline to identify ncRNAs containing pseudoknot structures. The algorithms are more efficient than the state-of-the-art approaches and can be used for large-scale data. Second, I designed a ncRNA classification tool for short reads in NGS data lacking quality reference genomes. The initial homology search phase significantly reduces size of the original input, making the tool feasible for large-scale data. Last, I focused on identifying 16S ribosomal RNAs from NGS data. 16S ribosomal RNAs are very important type of ncRNAs, which can be used for phylogenic study. A set of graph based assembly algorithms were applied to form longer or full-length 16S rRNA contigs. I utilized paired-end information in NGS data, so lowly abundant 16S genes can also be identified. To reduce the complexity of problem and make the tool practical for large-scale data, I designed a list of error correction and graph reduction techniques for graph simplification.
Description based on online resource; title from PDF t.p. (viewed on Oct. 17, 2017)
Advisors/Committee Members: Sun, Yanni, Cole, James, Shiu, Shin-Han, Chen, Jin, Chan, Christina.
Subjects/Keywords: Computer science; Bioinformatics; Genomics; Non-coding RNA – Analysis; RNA – Identification; RNA
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Yuan, C. (2014). Non-coding RNA identification in large-scale genomic data. (Thesis). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:3077
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):
Yuan, Cheng. “Non-coding RNA identification in large-scale genomic data.” 2014. Thesis, Michigan State University. Accessed January 19, 2021.
http://etd.lib.msu.edu/islandora/object/etd:3077.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Yuan, Cheng. “Non-coding RNA identification in large-scale genomic data.” 2014. Web. 19 Jan 2021.
Vancouver:
Yuan C. Non-coding RNA identification in large-scale genomic data. [Internet] [Thesis]. Michigan State University; 2014. [cited 2021 Jan 19].
Available from: http://etd.lib.msu.edu/islandora/object/etd:3077.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Yuan C. Non-coding RNA identification in large-scale genomic data. [Thesis]. Michigan State University; 2014. Available from: http://etd.lib.msu.edu/islandora/object/etd:3077
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Rochester
27.
Harmancı, Arif Özgün (1982 - ).
Probabilistic computational methods for structural
alignment of RNA sequences.
Degree: PhD, 2011, University of Rochester
URL: http://hdl.handle.net/1802/13722
► In this thesis, the problem of structural alignment of homologous RNA sequences is addressed. The structural alignment of a given set of RNA sequences is…
(more)
▼ In this thesis, the problem of structural alignment
of homologous RNA sequences is addressed.
The structural alignment
of a given set of RNA sequences is a secondary structure
for each
sequence, such that the structures are similar to each other, and a
sequence alignment
between the sequences that is conforming with
the secondary structures. A solution
to this problem was proposed
by Sankoff as a dynamic programming algorithm whose time
and
memory complexities are polynomial in the length of shortest
sequence and exponential
in the number of input sequences,
respectively. Variants of Sankoff’s method employ
constraints that
reduce the computation by restricting the allowed alignments or
structures.
In the first part of the thesis, a new methodology is
presented for the purpose of
establishing alignment constraints
based on nucleotide alignment and insertion posterior
probabilities. Using a hidden Markov model, posterior probabilities
of alignment and insertion
are computed and these probabilities
are additively combined to obtain probabilities
of co-incidence.
The constraints on alignments are computed by adaptively
thresholding
these probabilities to determine co-incidence
constraints for pruning of computations that
hold with high
probability. The proposed constraints are implemented into
Dynalign, a free
energy minimization algorithm for structural
alignment. Compared with prior non-adaptive
approaches, the
probabilistic constraints offer a significant reduction in
computation time
along with a marginal increase in base pair
prediction accuracy.
Next, a novel algorithm for structural
alignment of two RNA sequences is presented.
The similarity of the
structures is imposed by matched helical regions in the structural
alignnment.
A matched helical region represents a conserved helix
in each structure. Compared
to the structural alignment models of
previous methods, the matched helical regions extend
the
possibilities for alignment of paired nucleotides, which enables
the new structural
alignment space to better accomodate the
structural variability within a sequence family. A probability
distribution over the space of structural alignments is proposed
based on
pseudo-free energy changes, that account for both
stability of structures and plausibility of
the sequence
alignment. Three different problems are addressed for structural
alignment
prediction as inferences from the distribution: 1.
Estimation of the maximum a posteriori
(MAP) structural alignment,
i.e., the structural alignment with highest probability in
the
space, 2. Computation of base pairing probabilities of nucleotides
in each sequence,
3. Sampling the structural alignment space for
analysis of modes of the distribution over
structural alignments.
Finally, the problem of structure prediction for an arbitrary
number of homologous
sequences is addressed. To circumvent the
computational complexity, the prediction is
broken down into an
iterative computation of base pairing probabilities for each
sequence
using extrinsic…
Subjects/Keywords: Non-coding RNA; Secondary structure; RNA structural alignment
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Harmancı, A. . (. -. ). (2011). Probabilistic computational methods for structural
alignment of RNA sequences. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/13722
Chicago Manual of Style (16th Edition):
Harmancı, Arif Özgün (1982 - ). “Probabilistic computational methods for structural
alignment of RNA sequences.” 2011. Doctoral Dissertation, University of Rochester. Accessed January 19, 2021.
http://hdl.handle.net/1802/13722.
MLA Handbook (7th Edition):
Harmancı, Arif Özgün (1982 - ). “Probabilistic computational methods for structural
alignment of RNA sequences.” 2011. Web. 19 Jan 2021.
Vancouver:
Harmancı A(-). Probabilistic computational methods for structural
alignment of RNA sequences. [Internet] [Doctoral dissertation]. University of Rochester; 2011. [cited 2021 Jan 19].
Available from: http://hdl.handle.net/1802/13722.
Council of Science Editors:
Harmancı A(-). Probabilistic computational methods for structural
alignment of RNA sequences. [Doctoral Dissertation]. University of Rochester; 2011. Available from: http://hdl.handle.net/1802/13722
University of Rochester
28.
Xu, Zhenjiang.
Non-Coding RNA: From Structure Prediction to Discovery in
Genomes.
Degree: PhD, 2013, University of Rochester
URL: http://hdl.handle.net/1802/26787
► RNA plays remarkably diverse roles in organisms, such as maintaining telomeres, regulating gene expression, and catalyzing reactions. With current techniques, it is often slow and…
(more)
▼ RNA plays remarkably diverse roles in organisms,
such as maintaining telomeres,
regulating gene expression, and
catalyzing reactions. With current techniques, it is often
slow
and expensive to solve the majority of those RNA structures
experimentally. Thus
computational RNA analysis remains an
attractive tool.
RNA secondary structure, the sum of canonical
base pairs (A-U, G-U and G-C),
can be predicted by free energy
minimization using a nearest neighbor model. The
prediction
accuracy, however, is limited. Dynalign improves prediction by
finding
conserved structures of two homologous RNA sequences. A
novel algorithm, Multilign,
was developed to compute conserved
structures for more than two sequences
progressively using
multiple Dynalign calculations. It keeps base pairs in low free
energy
structures predicted by all the Dynalign calculations and
removes false competing base
pairs. The benchmark on various RNA
families showed that Multilign performs better
than Dynalign.
Traditionally, the averages of structure prediction accuracies are
tabulated to
compare the performance of different RNA secondary
prediction algorithms without
statistical testing. It was
demonstrated here that the prediction accuracies of methods
correlate with each other. The paired two-sample t-test was
introduced to rigorously
evaluate whether one method outperforms
another. A pipeline of statistical analyses was
proposed to guide
the choice of data set size and performance assessment for
benchmarks.
Functional RNA motifs tend to have stable and
conserved secondary structure and
can be identified from genomes
with algorithms derived from secondary structure
prediction. The
Streptomyces coelicolor genome was scanned using a Dynalign-based
method to search ncRNA. The prediction result was compared with the
results from
RNAz (another program finding RNA genes) and 454
sequencing data, showing the three
sets of data overlap little.
Untranslated regions of human hypoxia-related genes were also
scanned and many candidates of conserved, structural cis-regulatory
motifs were found.
Collaborating with Butler Lab, bioinformatics
analysis was performed on RNA
deep sequencing data generated from
four S. cerevisiae genotypes, BY4724, rrp6-Δ ,
air1-Δ rrp6-Δ and
air2-Δ rrp6-Δ to study the RNA exosome substrate specificity. The
differentially expressed genes were identified in these genotypes,
revealing that Air1p
and Air2p convey substrate specificities
during RNA degradation.
Subjects/Keywords: RNA; Secondary Structure; Prediction; Non-Coding RNA; Genomes
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APA (6th Edition):
Xu, Z. (2013). Non-Coding RNA: From Structure Prediction to Discovery in
Genomes. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/26787
Chicago Manual of Style (16th Edition):
Xu, Zhenjiang. “Non-Coding RNA: From Structure Prediction to Discovery in
Genomes.” 2013. Doctoral Dissertation, University of Rochester. Accessed January 19, 2021.
http://hdl.handle.net/1802/26787.
MLA Handbook (7th Edition):
Xu, Zhenjiang. “Non-Coding RNA: From Structure Prediction to Discovery in
Genomes.” 2013. Web. 19 Jan 2021.
Vancouver:
Xu Z. Non-Coding RNA: From Structure Prediction to Discovery in
Genomes. [Internet] [Doctoral dissertation]. University of Rochester; 2013. [cited 2021 Jan 19].
Available from: http://hdl.handle.net/1802/26787.
Council of Science Editors:
Xu Z. Non-Coding RNA: From Structure Prediction to Discovery in
Genomes. [Doctoral Dissertation]. University of Rochester; 2013. Available from: http://hdl.handle.net/1802/26787
McMaster University
29.
Moody, Matthew John.
NON-CODING RNAS AND MRNA SECONDARY STRUCTURE IN STREPTOMYCES.
Degree: PhD, 2017, McMaster University
URL: http://hdl.handle.net/11375/22027
► Work over the past two decades has revealed that non-coding RNAs (ncRNAs) are prevalent in all kingdoms of life. Using RNA-seq we discovered hundreds of…
(more)
▼ Work over the past two decades has revealed that non-coding RNAs (ncRNAs) are prevalent in all kingdoms of life. Using RNA-seq we discovered hundreds of ncRNAs in the antibiotic-producing genus of bacteria, Streptomyces. These included trans-encoded small RNAS (sRNAs), cis-antisense RNAs, and a new type of antisense RNA we termed cutoRNAs (convergent untranslated overlapping RNAs) that arise when transcription termination does not occur in the intergenic region between two convergently arranged genes. Many of these ncRNAs feature prominently in the specialized metabolite biosynthetic clusters (e.g. antibiotics, anticancer agents, immunosuppressants). Hence, it is likely that understanding the functions of these RNAs will be important for new molecule discovery. We found that one highly expressed antisense RNA (ScbN) was expressed opposite the -butyrolactone synthase scbA in the model streptomycete Streptomyces coelicolor. However, ScbN had no detectible impact on the expression of scbA. Instead, the transcription terminator of scbN, which also forms a hairpin within the coding sequence of scbA, was found to reduce expression of scbA more than 10-fold. This led us to bioinformatically search for similar coding-sequence hairpins throughout all bacteria, leading to the discovery of many stable RNA structures with conserved locations throughout very divergent bacteria (e.g. Streptomyces, Escherichia coli, Bacillus subtilis).
Thesis
Doctor of Philosophy (PhD)
The flow of genetic information, from DNA to RNA to proteins, often portrays RNA as a mere intermediary molecule. An alternative, and perhaps more accurate, way to view RNA is that it is central to all cellular processes. Many RNAs are not translated into proteins and instead act as regulatory molecules, impacting the expression of other genes. In this work we found many examples of these regulatory RNAs in a group of bacteria known to produce many of the world’s antibiotics. Understanding the roles these regulatory RNAs play in impacting gene expression will be important for the discovery of new molecules, such as antibiotics. In addition to distinct regulatory RNAs mentioned above, we found that RNA structures within the coding sequences of mRNAs that are translated into proteins have dramatic regulatory consequences. We describe the characterization of one such RNA structure in a gene involved in bacterial communication, and develop a bioinformatic tool to hunt for other such structures conserved throughout bacteria.
Advisors/Committee Members: Elliot, Marie A, Biology.
Subjects/Keywords: bacteria; gene regulation; non-coding rna; streptomyces; quorum sensing; RNA structure
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Moody, M. J. (2017). NON-CODING RNAS AND MRNA SECONDARY STRUCTURE IN STREPTOMYCES. (Doctoral Dissertation). McMaster University. Retrieved from http://hdl.handle.net/11375/22027
Chicago Manual of Style (16th Edition):
Moody, Matthew John. “NON-CODING RNAS AND MRNA SECONDARY STRUCTURE IN STREPTOMYCES.” 2017. Doctoral Dissertation, McMaster University. Accessed January 19, 2021.
http://hdl.handle.net/11375/22027.
MLA Handbook (7th Edition):
Moody, Matthew John. “NON-CODING RNAS AND MRNA SECONDARY STRUCTURE IN STREPTOMYCES.” 2017. Web. 19 Jan 2021.
Vancouver:
Moody MJ. NON-CODING RNAS AND MRNA SECONDARY STRUCTURE IN STREPTOMYCES. [Internet] [Doctoral dissertation]. McMaster University; 2017. [cited 2021 Jan 19].
Available from: http://hdl.handle.net/11375/22027.
Council of Science Editors:
Moody MJ. NON-CODING RNAS AND MRNA SECONDARY STRUCTURE IN STREPTOMYCES. [Doctoral Dissertation]. McMaster University; 2017. Available from: http://hdl.handle.net/11375/22027
University of Houston
30.
-9636-8146.
Long Noncoding RNAs in Cardiac and Skeletal Muscle Differentiation during Mouse Embryogenesis.
Degree: PhD, Biology, 2017, University of Houston
URL: http://hdl.handle.net/10657/4789
► Development is a multistep process that involves a close co-ordination of gene regulatory networks. Lineage specification is a crucial step involved in embryogenesis and understanding…
(more)
▼ Development is a multistep process that involves a close co-ordination of gene regulatory networks. Lineage specification is a crucial step involved in embryogenesis and understanding the significant steps involved in gene regulatory mechanisms is critical. Long
non-
coding RNAs, longer than 200 nucleotides have been identified as a new regulator of many molecular mechanisms involved in the development and pathological conditions.
From the genome-wide transcriptome analysis of Mesp1-lineage reporter mouse ESC line (UH3), we identified mesoderm specific lncRNAs, from which we selected a subset of 12 lncRNAs for functional characterization.
Of this, we identified lincRNA Platr14 to have a positive expression in vivo in cardiac plate and somites of E9.5 mouse embryos. Platr14 was seen enriched in vitro in the undifferentiated AB2.2 ES cell line, and the inhibition of Platr14 showed a decrease in the beating percentage of embryoid bodies which correlated with a deregulation of the mesoderm and cardiac-specific genes.
Since Platr14 was enriched in the region of the myotome of E9.5 Embryos, we studied its role in myogenesis. Platr14 showed enrichment in skeletal muscle and the tongue in E15.5 embryonic mouse tissues. Knockdown of Platr14 in C2C12 mesenchymal cell line showed a deregulation of myogenic markers as well as a reduction in the fusion rate for the myotube formation. Though overexpression of Platr14 showed an up-regulation of the main myogenic markers, it did not show any significant change in the myotube formation rate. Strikingly, Platr14 overexpression in the terminal stages showed a repression in the expression of terminal myogenic markers. The whole transcriptome analysis by
RNA-Sequencing of differentiating C2C12 myoblasts at day 2, showed a down-regulation of genes associated with the mesenchymal formation, somitogenesis, metabolism, cell migration, calcium transport and cell-cell signaling all related to developmental changes. In-silico analysis identified conservation of 3’ UTR of Platr14 across species as well as unique sites complementary to about 29 DNA binding sites of the mouse genome. Gene Ontology studies identified these DNA binding sites to have roles related to developmental processes.
In this dissertation, we identified lincRNA Platr14, to have a novel role in mesoderm lineage driving the cardiac and skeletal myogenic differentiation.
Advisors/Committee Members: Schwartz, Robert J. (advisor), Lin, Chin-Yo (committee member), Frigo, Daniel E. (committee member), Chen, Li (committee member), Cooney, Austin J. (committee member).
Subjects/Keywords: Long non coding RNA; RNA; Platr14; Cardiac; Skeletal myogenesis; Differentiation
Record Details
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
-9636-8146. (2017). Long Noncoding RNAs in Cardiac and Skeletal Muscle Differentiation during Mouse Embryogenesis. (Doctoral Dissertation). University of Houston. Retrieved from http://hdl.handle.net/10657/4789
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Chicago Manual of Style (16th Edition):
-9636-8146. “Long Noncoding RNAs in Cardiac and Skeletal Muscle Differentiation during Mouse Embryogenesis.” 2017. Doctoral Dissertation, University of Houston. Accessed January 19, 2021.
http://hdl.handle.net/10657/4789.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
MLA Handbook (7th Edition):
-9636-8146. “Long Noncoding RNAs in Cardiac and Skeletal Muscle Differentiation during Mouse Embryogenesis.” 2017. Web. 19 Jan 2021.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Vancouver:
-9636-8146. Long Noncoding RNAs in Cardiac and Skeletal Muscle Differentiation during Mouse Embryogenesis. [Internet] [Doctoral dissertation]. University of Houston; 2017. [cited 2021 Jan 19].
Available from: http://hdl.handle.net/10657/4789.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Council of Science Editors:
-9636-8146. Long Noncoding RNAs in Cardiac and Skeletal Muscle Differentiation during Mouse Embryogenesis. [Doctoral Dissertation]. University of Houston; 2017. Available from: http://hdl.handle.net/10657/4789
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
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Open Access Theses and Dissertations
