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Recent studies in human genetics and in silico analyses have revealed that a number of genes are head-head orientated with other genes or non-coding RNAs. The expression of regulatory element-containing 5’-upstream regions of gene pairs are referred to as bi-directional promoters and are thought to have a key role in biological regulatory mechanisms. For example, tumor suppressor protein-encoding TP53 and BRCA1 genes are head-head bound with WRAP53 and NBR2, respectively. DNA-repair factor-encoding ATM and PRKDC (DNA-PKcs) genes have bidirectional partner NPAT and MCM4, respectively. Surveillance of the human DNA database has revealed that the numbers of DNA repair/mitochondrial function/immune response-associated genes are bound with other genes that are transcribed to opposite direction. The observations may encourage us to investigate in the molecular mechanisms how DNA repair/mitochondrial function/immune response-associated genes are regulated by bidirectional promoters. Not only protein-coding genes, but also quite a few ncRNAs, which play important roles in various cellular events, are transcribed under the regulation of the bidirectional promoters. More importantly, we know that dysregulation in the promoter activity and transcription initiation of genes might cause human diseases. Provides an overview of the process of transcription Explains why there so many bidirectional promoters present in human genomes Covers how the diverse biological functions of (non-coding RNAs) ncRNAs are controlled
"A Subject Collection from Cold Spring Harbor Perspectives in Biology."
This Open Access volume provides comprehensive reviews and describes the latest techniques to study eukaryotic ribosome biogenesis. For more than 50 years ribosomes are a major research topic. Our knowledge about ribosome biogenesis and function such as transcription, mRNA modification, and translation was the sine qua non for developing the powerful RNA-based vaccines against RNA-viruses causing the world-threatening Covid-19 pandemia. The chapters in this book are organized into six parts. Part One discusses a comparative survey about the unity and diversity of ribosome biogenesis in pro- and eukaryotic cells. Part Two deals with the genomic organization of eukaryotic rDNA and the role of RNA polymerase I in ribosomal RNA transcription. Part Three explores in vitro methods to study RNA polymerase I structure and its function, and Part Four analyzes the nucleo-cytoplasmic transport of assembled ribosomes and RNP complexes. Part Five covers modifications that increase the complexity of rRNAs, and Part Six provides readers with a review of eukaryotic translation and - for the first time - describes a new method to analyze translation in vitro. 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. Cutting-edge and comprehensive, Ribosome Biogenesis: Methods and Protocols is a valuable resource for scientists and researchers interested in learning more about the increasing importance of in vitro RNA-technologies.
This laboratory guide represents a growing collection of tried, tested and optimized laboratory protocols for the isolation and characterization of eukaryotic RNA, with lesser emphasis on the characterization of prokaryotic transcripts. Collectively the chapters work together to embellish the RNA story, each presenting clear take-home lessons, liberally incorporating flow charts, tables and graphs to facilitate learning and assist in the planning and implementation phases of a project. RNA Methodologies, 3rd edition includes approximately 30% new material, including chapters on the more recent technologies of RNA interference including: RNAi; Microarrays; Bioinformatics. It also includes new sections on: new and improved RT-PCR techniques; innovative 5’ and 3’ RACE techniques; subtractive PCR methods; methods for improving cDNA synthesis. * Author is a well-recognized expert in the field of RNA experimentation and founded Exon-Intron, a well-known biotechnology educational workshop center * Includes classic and contemporary techniques * Incorporates flow charts, tables, and graphs to facilitate learning and assist in the planning phases of projects
Molecular Biology: Principles of Genome Function offers a fresh, distinctive approach to the teaching of molecular biology. It is an approach that reflects the challenge of teaching a subject that is in many ways unrecognizable from the molecular biology of the 20th century - a discipline in which our understanding has advanced immeasurably, but about which many intriguing questions remain to be answered. It is written with severalguiding themes in mind: - A focus on key principles provides a robust conceptual framework on which students can build a solid understanding of the discipline; - An emphasis on thecommonalities that exist between the three kingdoms of life, and the discussion of differences between the three kingdoms where such differences offer instructive insights into molecular processes and components, gives students an accurate depiction of our current understanding of the conserved nature of molecular biology, and the differences that underpin biological diversity; - An integrated approach demonstrates how certain molecular phenomena have diverse impacts on genomefunction by presenting them as themes that recur throughout the book, rather than as artificially separated topics At heart, molecular biology is an experimental science, and a centralelement to the understanding of molecular biology is an appreciation of the approaches taken to yield the information from which concepts and principles are deduced. Yet there is also the challenge of introducing the experimental evidence in a way that students can readily comprehend. Molecular Biology responds to this challenge with Experimental Approach panels, which branch off from the text in a clearly-signposted way. These panels describe pieces ofresearch that have been undertaken, and which have been particularly valuable in elucidating difference aspects of molecular biology. Each panel is carefully cross-referenced to the discussion of key molecular biologytools and techniques, which are presented in a dedicated chapter at the end of the book. Beyond this, Molecular Biology further enriches the learning experience with full-colour, custom-drawn artwork; end-of-chapter questions and summaries; relevant suggested further readings grouped by topic; and an extensive glossary of key terms. Among the students being taught today are the molecular biologists of tomorrow; these individuals will be ina position to ask fascinating questions about fields whose complexity and sophistication become more apparent with each year that passes. Molecular Biology: Principles of Genome Function is the perfectintroduction to this challenging, dynamic, but ultimately fascinating discipline.
Discoveries from the past decades revealed that RNA molecules are much more than inert intermediates between the coding DNA sequences and their functional products, proteins. Today, RNAs are recognized as active regulatory molecules influencing gene expression, chromatin organization and genome stability, thus impacting all aspects of plant life including development, growth, reproduction and stress tolerance. Innovations in methodologies, the expanding application of next-generation sequencing technologies, and the creation of public datasets and databases have exposed a new universe of RNA-based mechanisms and led to the discovery of new families of non-coding RNAs, uncovered the large extent of alternative splicing events, and highlighted the potential roles of RNA modifications and RNA secondary structures. Furthermore, considerable advances have been made in identifying RNA-binding and processing factors involved in the synthesis and maturation of different forms of RNA molecules as well as in RNA processing, biochemical modifications or degradation. This Research Topic showcases the broad biological significance of RNAs in plant systems and contains eight original research articles, one review and four mini-reviews, covering various RNA-based mechanisms in higher plants. Emerging new technologies and novel multidisciplinary approaches are empowering the scientific community and will expectedly bring novel insights into our understanding of the mechanisms through which RNA is regulated and regulates biological processes in plant cells.
Behavior and Culture in One Dimension adopts a broad interdisciplinary approach, presenting a unified theory of sequences and their functions and an overview of how they underpin the evolution of complexity. Sequences of DNA guide the functioning of the living world, sequences of speech and writing choreograph the intricacies of human culture, and sequences of code oversee the operation of our literate technological civilization. These linear patterns function under their own rules, which have never been fully explored. It is time for them to get their due. This book explores the one-dimensional sequences that orchestrate the structure and behavior of our three-dimensional habitat. Using Gibsonian concepts of perception, action, and affordances, as well as the works of Howard Pattee, the book examines the role of sequences in the human behavioral and cultural world of speech, writing, and mathematics. The book offers a Darwinian framework for understanding human cultural evolution and locates the two major informational transitions in the origins of life and civilization. It will be of interest to students and researchers in ecological psychology, linguistics, cognitive science, and the social and biological sciences.