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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: Thomas Dandekar
Publisher: Springer Science & Business Media
ISBN: 3642562981
Category : Science
Languages : en
Pages : 234
Get Book Here
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:
Publisher:
ISBN:
Category :
Languages : en
Pages : 181
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Book Description
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: Altuna Akalin
Publisher: CRC Press
ISBN: 1498781861
Category : Mathematics
Languages : en
Pages : 463
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Book Description
Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.
Author: Ryan Alexander Flynn
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Deciphering the molecular basis of pathway control inside cell remains one of the biggest challenges in basic and medical research. Recent data has demonstrated that the transcriptional complexity of the genome is significantly more complex than originally anticipated. These results and more focused studies have demonstrated that RNA molecules are critical for many cellular pathways and can be drivers of disease, but the full characterization of how RNA exerts its control over such pathways remains far from resolved. In living cells RNAs rarely act alone, frequently partnering with RNA binding proteins (RBPs) that modulate the structure, localization, and function of their RNA targets. With the advent of deep sequencing, the cellular repertoire of RNAs has become vast, while methods to study and characterize their functions have trailed the pace of discovery. Researchers have been able to describe many of the functions that protein-coding genes control, due to the decades of research devoted to tool development. This is far from the case for RNA, where its complexity and expression creates a bottleneck toward fully understanding its physical properties and how it interacts with other cellular biomolecules to control biology. Here we present novel tools to investigate fundamental principals of RNA biology and use them to uncover new roles for RNAs and RBPs inside living cells. First, Fully Automated and Standardized individual nucleotide Crosslinking and Immunoprecipitation (FAST-iCLIP) was developed to improve the speed and accuracy of the standard CLIP method. CLIP reveals where RBPs directly interact with RNAs in vivo, however it previously represented a critical bottleneck for the entire RNA biology community due lack of easy experimental and computational implantation. Second, we developed in vivo CLICK Selective 2' Hydroxyl Acylation and Profiling Experiment (icSHAPE), which provides a global measurement of RNA secondary structure at nucleobase resolution. These strategies provide the groundwork for global and direct measurements of uncharacterized RNA-protein interactions and RNA structures. Application of these methods to unanswered questions was the next critical challenge. The genome encodes 37 DEAD box RNA helicase proteins, however the rules of their RNA target specificity and mechanisms of action remain largely unknown. We found that DDX21, an RNA helicase previously know only to function in the nucleolus, operates across distinct compartments of the nucleus to control both transcriptional and post-transcriptional processed all governing the synthesis of fully functioning ribosomes. Subsequently we characterized a RNA-based mechanism that cells use to globally control the transcriptional output of the genome. We show that the 7SK small nuclear RNA (snRNA) has a regulatory role at promoters, enhancers, and newly identified super enhancer elements. Importantly, 7SK is limits enhancer RNA initiation and synthesis and does so in a novel snRNP majorly composed of the BAF chromatin remodeling complex. Overall, this thesis introduces new RNA-centric technologies and uses them to discover novel principals of gene expression networks. Insights from these studies are applicable to human disease as DDX-family members and components of the BAF complex are known to be mutated in cancer and neural disease such as autism, possibly leading to new avenues for therapeutic stratifies.
Author: Anita Marchfelder
Publisher: Springer Science & Business Media
ISBN: 3709102189
Category : Science
Languages : en
Pages : 263
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Book Description
This book provides a comprehensive and up-to-date collection of review articles focusing on RNA-mediated regulation in prokaryotes. The various modes of action include the direct interaction with proteins, direct sensing of metabolites or of physical parameters, and the interaction with RNAs to stimulate or prevent binding of ribosomes or to stimulate degradation. Written by leading experts in the field, the book covers small RNA functions, RNA thermometers, riboswitches, the diversity of small RNA-guided CRISPR-Cas defense systems and selected RNA chaperons in both prokaryotic domains, bacteria and archaea. Recent advances towards the computational identification of regulatory RNAs and their targets are included and particular attention is paid to small RNA in pathogenic bacteria. This volume is the only one exclusively covering regulatory RNAs in the prokaryotic domains to date, making it essential literature for anyone interested in RNA function and gene regulation and a valuable resource for teaching these concepts.
Author: Véronique Arluison
Publisher: Humana Press
ISBN: 9781493976331
Category : Medical
Languages : en
Pages : 395
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Book Description
This volume details the most important methods used for studying prokaryotic non-coding RNAs and their protein accomplices. Chapters present methods in sections covering different aspects of the biology of that field: identification of ncRNAs, their differential expression, characterization of their structure, abundance, intracellular location and function, their interaction with RNA binding proteins, and plausible applications of ncRNA elements in the rapidly emerging field of synthetic biology. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Bacterial Regulatory RNA: Methods and Protocols serves as a guidebook for scientists working toward the development of new tools and procedures for the vital field of sRNA biology.
Author: Gene W. Yeo
Publisher: Springer
ISBN: 1493912216
Category : Science
Languages : en
Pages : 474
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Book Description
After transcription in the nucleus, RNA binding proteins (RBPs) recognize cis-regulatory RNA elements within pre-mRNA sequence to form mRNA-protein (mRNP) complexes. Similarly to DNA binding proteins such as transcription factors that regulate gene expression by binding to DNA elements in the promoters of genes, RBPs regulate the fate of target RNAs by interacting with specific sequences or RNA secondary structural features within the transcribed RNA molecule. The set of functional RNA elements recognized by RBPs within target RNAs and which control the temporal, functional and spatial dynamics of the target RNA define a putative “mRNP code”. These cis-regulatory RNA elements can be found in the 5’ and 3’ untranslated regions (UTRs), introns, and exons of all protein-coding genes. RNA elements in 5’ and 3’ UTRs are frequently involved in targeting RNA to specific cellular compartments, affecting 3’ end formation, controlling RNA stability and regulating mRNA translation. RNA elements in introns and exons are known to function as splicing enhancers or silencers during the splicing process from pre-mRNA to mature mRNA. This book provides case studies of RNA binding proteins that regulate aspects of RNA processing that are important for fundamental understanding of diseases and development. Chapters include systems-level perspectives, mechanistic insights into RNA processing and RNA Binding proteins in genetic variation, development and disease. The content focuses on systems biology and genomics of RNA Binding proteins and their relation to human diseases.
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:
Publisher:
ISBN: 9780815332183
Category : Cells
Languages : en
Pages : 0
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Book Description
