Identification of Regulatory RNA Elements Based on Structural Conservation PDF Download
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Author: Johannes Braun
Publisher:
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Category :
Languages : en
Pages :
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Author: Johannes Braun
Publisher:
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Category :
Languages : en
Pages :
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Author: Thomas Dandekar
Publisher: Springer Science & Business Media
ISBN: 3642979939
Category : Science
Languages : en
Pages : 270
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Book Description
This book provides an introduction to and an overview of the field of regulatory RNA, focusing on the identification of regulatory elements and motifs in such RNA molecules. Central to the book is the use of appropriate techniques to identify regulatory RNA and regulatory motifs. The prospects for this new and expanding research field - understanding regulatory RNA elements and motifs - are also explored, including new developments, medical applications, and applications in other fields.
Author: Thomas Dandekar
Publisher: Springer Science & Business Media
ISBN: 3642562981
Category : Science
Languages : en
Pages : 234
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Book Description
RNA Motifs and Regulatory Elements is the new edition of the successful book, "Regulatory RNA". It alerts the reader to the importance of regulatory RNA elements for the many different areas of cellular life. The computational and experimental methods and tools to search for new interesting regulatory RNA structures are explained and compared. The knowledge on regulatory RNA structures and elements already available is concisely summarized as well as catalogued. In addition, interesting RNA elements are analyzed in detail regarding their dynamics, regulation, and as a dominant topic of current resarch in molecular biology, including areas such as RNA mediated regulation of gene-expression, DNA/RNA chip data, and ribozymes, splicing, or telomerases in aging. Medical implications are also covered. Future progress and research are finally outlined.
Author: Bibekanand Mallick
Publisher: Springer Science & Business Media
ISBN: 3642225179
Category : Science
Languages : en
Pages : 549
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Recent progress in high-throughput technologies and genome wide transcriptome studies have lead to a significant scientific milestone of discovering non-coding RNAs (ncRNAs) which spans through a major portion of the genome. These RNAs most often act as riboregulators, and actively participate in the regulation of important cellular functions at the transcriptional and/or post-transcriptional levels rather than simply being an intermediated messenger between DNA and proteins. As the appreciation for the importance of ncRNAs continues to emerge, it is also increasingly clear that these play critical roles in gene regulatory processes during development and differentiation. Further, regulatory RNAs are useful biomarkers for diagnosis of diseases. Hence these RNA regulators are essential to the development of therapeutics. This book on “Regulatory RNAs” offers a comprehensive view on our current understanding of these regulatory RNAs viz. siRNA, miRNA, piRNA, snoRNA, long non-coding RNA, small RNA etc. It addresses both the biogenesis and mechanism of action of regulatory RNAs with a primary focus on their annotation, experimental methodologies (microarray, next-gen sequencing etc.) for their discovery, computational tools for their prediction, and above all, applications of these revolutionary regulatory molecules in understanding biological systems and diseases, including therapeutics. This comprehensive volume is intended for readers with research or teaching interests in ncRNA biology and will provide a major information resource on current research in the fast-moving fields of RNA and gene expression regulation. Cutting-edge and concise, “Regulatory RNAs: Basics, Methods and Applications” promises to support vital research in the field of regulatory RNAs, ever-continuing to grow rapidly and gain increasing importance in basic and translational biology.
Author: Bibekanand Mallick
Publisher: Springer Science & Business Media
ISBN: 3642225160
Category : Science
Languages : en
Pages : 549
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Book Description
Recent progress in high-throughput technologies and genome wide transcriptome studies have lead to a significant scientific milestone of discovering non-coding RNAs (ncRNAs) which spans through a major portion of the genome. These RNAs most often act as riboregulators, and actively participate in the regulation of important cellular functions at the transcriptional and/or post-transcriptional levels rather than simply being an intermediated messenger between DNA and proteins. As the appreciation for the importance of ncRNAs continues to emerge, it is also increasingly clear that these play critical roles in gene regulatory processes during development and differentiation. Further, regulatory RNAs are useful biomarkers for diagnosis of diseases. Hence these RNA regulators are essential to the development of therapeutics. This book on “Regulatory RNAs” offers a comprehensive view on our current understanding of these regulatory RNAs viz. siRNA, miRNA, piRNA, snoRNA, long non-coding RNA, small RNA etc. It addresses both the biogenesis and mechanism of action of regulatory RNAs with a primary focus on their annotation, experimental methodologies (microarray, next-gen sequencing etc.) for their discovery, computational tools for their prediction, and above all, applications of these revolutionary regulatory molecules in understanding biological systems and diseases, including therapeutics. This comprehensive volume is intended for readers with research or teaching interests in ncRNA biology and will provide a major information resource on current research in the fast-moving fields of RNA and gene expression regulation. Cutting-edge and concise, “Regulatory RNAs: Basics, Methods and Applications” promises to support vital research in the field of regulatory RNAs, ever-continuing to grow rapidly and gain increasing importance in basic and translational biology.
Author: Gun Woo Byeon
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Translation can be critically and pervasively regulated in a transcript-specific manner to modulate protein synthesis. However, it is poorly understood which and how cis-regulatory features of the messenger ribonucleic acid (mRNA) encode variable transcript-specific translation rates to impact spatiotemporal gene expression patterns. Here, I address the role of 5' untranslated (5' UTR) in regulating mRNA translation in vertebrate species. In the first part of the dissertation, I explore the phenomenon of extreme non-coding sequence conservation in vertebrate genomes at the level of RNA function in 5' UTRs. Extreme conservation is a fascinating mystery in comparative genomics in which sequence conservation, at levels often greater than coding regions with invariant polypeptide sequences, stretches on for hundreds of nucleotides in the non-coding regions of the genome. While extreme conservation has been extensively studied for its role in transcriptional regulation, its RNA-level function in translational regulation remains largely unknown. This work reveals the role of extremely conserved 5' UTRs in translational regulation of genes linked to the emergence of essential developmental features in vertebrate species. Extremely conserved 5' UTRs are found to contain cis-elements that promote cell-type specific non-canonical translation initiation. As these elements function as RNA molecules, an understanding of their structures is essential. To this end, I develop in-cell mutate-and-map (icM2), a methodology that maps RNA structure using high-throughput mutational analysis inside cells. icM2 maps the ensemble of multiple conformations in an extremely conserved 5' UTR which is found to be important for its translational regulatory function. I find that active RNA structural remodeling inside cells by RNA helicase activity maintains the relative balance of the conformations. Furthermore, cellular structural remodeling occurs frequently in the most conserved regions of the 5' UTRs. I propose a structural explanation for extreme conservation at the level of RNA and highlight the importance of comparative genomics and of RNA structure in understanding 5' UTR function and evolution. In the second part of the dissertation, I explore the genome-wide role of mammalian ribosome expansion segments (ES) in interacting with 5' UTRs to regulate mRNA translation. ESs are eukaryote-specific insertions to the ribosomal ribonucleic acid (rRNA). They are positioned mostly at the exterior surface of the ribosome structure, extending from the core of the ribosome like flexible tentacles. It has been recently shown that the mammalian ES9S in 18S rRNA directly interacts with a Hox gene 5' UTR element to promote its translation. Direct rRNA-mRNA interaction is not a widely recognized paradigm for translation initiation in eukaryotes. However, addressing the potential genome-wide significance of such a mechanism mediated by ribosome ESs and mRNA 5' UTRs is challenging. Since rRNAs are transcribed from tandem repeats of ribosomal DNA units that can range up to hundreds of thousands of copies, it has not been possible to directly manipulate ESs in most species. To solve this problem, I develop VELCRO-IP RNA-seq: variable expansion segment-ligand chimeric ribosome immunoprecipitation RNA sequencing. VELCRO-IP RNA-seq interrogates the interaction of a ribosome ES with mRNA elements genome-wide by combining yeast genetics, in vitro biochemical pull-down and high-throughput sequencing. By applying VELCRO-IP RNA-seq on mammalian ES9S, hundreds of mRNA regions that interact with the ribosome via specific interaction with the ES are identified. Furthermore, the 5' UTR targets of ES9S are found to promote non-canonical translation. A number of short k-mers that have Watson-Crick complementary to ES9S subsequences are overrepresented in its targets, suggesting potential importance of canonical base-pairing. These results provide evidence for the usage of direct mRNA-rRNA interaction as a mechanism of translation initiation on a wider scale than previously imagined for vertebrate species. Finally, in the last chapter, I discuss how my findings can shape future investigations into the remaining unanswered questions on 5' UTR regulation of translation. Altogether, this dissertation takes us a step closer to the ultimate goal of deciphering the code for translational regulation.
Author: Veronica van Heyningen
Publisher: Academic Press
ISBN: 0080877818
Category : Science
Languages : en
Pages : 415
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Long-Range Control of Gene Expression covers the current progress in understanding the mechanisms for genomic control of gene expression, which has grown considerably in the last few years as insight into genome organization and chromatin regulation has advanced. Discusses the evolution of cis-regulatory sequences in drosophila Includes information on genomic imprinting and imprinting defects in humans Includes a chapter on epigenetic gene regulation in cancer
Author: Dalia Ghoneim
Publisher:
ISBN:
Category :
Languages : en
Pages : 147
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The central dogma of molecular biology describes RNA as a passive intermediate in protein synthesis. RNAs have since been shown to be play active roles as catalysts, as directors of posttranscriptional modification and as regulators of gene expression. The many roles of RNA are still being characterized. We used studies of conservation across multiple species to elucidate novel roles of RNA. Nonrandom usage of synonymous codon pairs has been observed in all domains of life and can be a mechanism for translational regulation. We calculated codon pair conservation across orthologous mRNAs in Saccharomyces yeasts. Nine codon pairs associated with significantly reduced expression and translation rate in vivo (Gamble et al. 2016) are more conserved than expected based on the conservation of their constituent codons. These nine inhibitory codon pairs are the most conserved ways of encoding their dipeptides even compared to synonymous optimal codon pairs. Furthermore, highly conserved pairs tended to correlate with slow translation. We similarly observed a subset of codon pairs in Candida that has high conservation and is enriched for wobble interactions. The selection for inhibitory codon pairs suggests a role for suboptimal codon pairs in translation. Human cytomegalovirus (HCMV) infects over half the human population and has co-evolved with humans to evade the immune system. The virus' mechanisms of regulating gene expression and mechanisms of controlling human immune response are not fully understood. We investigated codon pair conservation and translation rates in cytomegalovirus across primates at different timepoints of infection. Exploring the roles of synonymous codon pair usage in regulation can contribute to identification of potential mechanisms to control viral infection. Long non-coding RNAs (lncRNAs) are untranslated stretches of RNA that can play important roles in regulation of gene expression. The majority of lncRNAs have yet to be characterized. Rapid evolution and lack of sequence conservation in lncRNAs makes de novo prediction of lncRNAs challenging. Structure and function of lncRNAs are often maintained across species even when sequences diverge, and structural conservation is an alternative criterion for comparative genomic analysis of lncRNAs. We predicted conserved and stable structures in lncRNAs from mouse sperm and testis using the tool Multifind.
Author: Veronica Juan
Publisher:
ISBN:
Category : Molecular biology
Languages : en
Pages : 334
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Author:
Publisher:
ISBN:
Category :
Languages : en
Pages : 181
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