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RNA Worlds: New Tools for Deep Exploration


Subject Area(s):  Molecular Biology

Edited by Thomas R. Cech, Howard Hughes Medical Institute; University of Colorado Boulder; Joan A. Steitz, Howard Hughes Medical Institute; Yale University; John F. Atkins, The University of Utah

Download a Free Excerpt from RNA Worlds, New Tools for Deep Exploration:

Preface
Structural Insights into Nuclear pre-mRNA Splicing in Higher Eukaryotes
Index


© 2018 • 559 pages, illustrated (153 color and 13 B&W), index
Hardcover • $162 129.60
ISBN  978-1-621822-24-0
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  •     Description    
  •     Contents    

Description

RNA (ribonucleic acid) molecules drive much of cellular action. Messenger RNA (mRNA) relays genetic information from DNA to ribosomes to direct the formation of proteins. At the same time, noncoding RNAs act as enzymes, scaffolds, and regulatory molecules, contributing greatly to the regulation of gene activity, RNA splicing, protein synthesis, and even DNA replication.

This new edition of the highly successful RNA Worlds series focuses on emerging tools for analysis of RNA biology and how these tools are driving our understanding of RNA structure and function. The contributors review new approaches for imaging RNA molecules in cells, techniques for analyzing the behavior of single RNA molecules in vitro and in vivo, transcriptome-wide analyses, and novel methods for determining the structure of RNA and RNP (ribonucleoprotein) complexes. They discuss the insights these provide into the transcription and splicing machinery, ribosomes, reverse transcriptases, and subcellular structures such as stress granules.

Also included are chapters exploring CRISPR editing, RNA switches for use in synthetic biology, and development of novel drugs targeting pathogenic RNA structures. In addition, the book covers recent insights into the primordial RNA World, including protocells and homochirality. It will therefore be of interest not only to biochemists and molecular biologists but to evolutionary biologists pondering the emergence of life on Earth.

Contents

Preface
Foreword to the First Edition of The RNA World
Francis Crick
Prologue to the First Edition of The RNA World
James D. Watson
IMAGING RNA BIOLOGY
Imaging the Life and Death of mRNAs in Single Cells
Jeffrey A. Chao and Timothée Lionnet
Quantifying Single mRNATranslation Kinetics in Living Cells
Tatsuya Morisaki and Timothy J. Stasevich
Illuminating Genomic Dark Matter with RNA Imaging
Arjun Raj and John L. Rinn
Principles of Stress Granules Revealed by Imaging Approaches
Briana Van Treeck and Roy Parker
COMPUTING RNA BIOLOGY: TRANSCRIPTOME-WIDE ANALYSES
Nascent RNA and the Coordination of Splicing with Transcription
Karla M. Neugebauer
U1 snRNP Telescripting: Suppression of Premature Transcription Termination in Introns as a New Layer of Gene Regulation
Christopher C. Venters, Jung-Min Oh, Chao Di, Byung Ran So, and Gideon Dreyfuss
Approaches for Understanding the Mechanisms of Long Noncoding RNA Regulation of Gene Expression
Patrick McDonel and Mitchell Guttman
What Are 3´ UTRs Doing?
Christine Mayr
Discovering and Mapping the Modified Nucleotides That Comprise the Epitranscriptome of mRNA
Bastian Linder and Samie R. Jaffrey
Mapping the dsRNA World
Daniel P. Reich and Brenda L. Bass
PROBING RNA STRUCTURE AND PROTEIN INTERACTIONS
Technique Development for Probing RNA Structure In Vivo and Genome-Wide
Philip C. Bevilacqua and Sarah M. Assmann
The RNA Base-Pairing Problem and Base-Pairing Solutions
Zhipeng Lu and Howard Y. Chang
Detecting RNA G-Quadruplexes (rG4s) in the Transcriptome
Chun Kit Kwok, Giovanni Marsico, and Shankar Balasubramanian
Linking RNA Sequence, Structure, and Function on Massively Parallel High-Throughput Sequencers
Sarah K. Denny and William J. Greenleaf
The Future of Cross-Linking and Immunoprecipitation (CLIP)
Jernej Ule, Hun-Way Hwang, and Robert B. Darnell
Principles and Practices of Hybridization Capture Experiments to Study Long Noncoding RNAs That Act on Chromatin
Matthew D. Simon and Martin Machyna
ENGINEERING RNA BIOLOGY
CRISPR Tools for Systematic Studies of RNA Regulation
Jesse Engreitz, Omar Abudayyeh, Jonathan Gootenberg, and Feng Zhang
Drugging the RNA World
Matthew D. Disney, Brendan G. Dwyer, and Jessica L. Childs-Disney
RNA Switches for Synthetic Biology
Calvin M. Schmidt and Christina D. Smolke
SOLVING RNP STRUCTURES
Extensions, Extra Factors, and Extreme Complexity: Ribosomal Structures Provide Insights into Eukaryotic Translation
Melanie Weisser and Nenad Ban
Structural Biology of Telomerase
Yaqiang Wang, Lukas Sušac, and Juli Feigon
Structural Basis of Nuclear pre-mRNA Splicing: Lessons from Yeast
Clemens Plaschka, Andrew J. Newman, and Kiyoshi Nagai
Structural Insights into Nuclear pre-mRNA Splicing in Higher Eukaryotes
Berthold Kastner, Cindy L. Will, Holger Stark, and Reinhard Lührmann
Molecular Mechanisms of pre-mRNA Splicing through Structural Biology of the Spliceosome
Chuangye Yan, Ruixue Wan, and Yigong Shi
Combining Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) Spectroscopy for Integrative Structural Biology of Protein-RNA Complexes
Alexander Leitner, Georg Dorn, and Frédéric H.-T. Allain
Group II Intron RNPs and Reverse Transcriptases: From Retroelements to Research Tools
Marlene Belfort and Alan M. Lambowitz
Alternate RNA Structures
Marie Teng-Pei Wu and Victoria D’Souza
EXAMINING SINGLE RNA MOLECULES IN VITRO
The Story of RNA Folding, as Told in Epochs
Daniel Herschlag, Steve Bonilla, and Namita Bisaria
Coming Together: RNAs and Proteins Assemble under the Single-Molecule Fluorescence Microscope
Ameya P. Jalihal, Paul E. Lund, and Nils G. Walter
Relating Structure and Dynamics in RNA Biology
Kevin P. Larsen, Junhong Choi, Arjun Prabhakar, Elisabetta Viani Puglisi, and Joseph D. Puglisi
Single-Molecule Analysis of Reverse Transcriptase Enzymes
Linnea I. Jansson and Michael D. Stone
EXPLORING THE PRIMORDIAL RNA WORLD
Protocells and RNA Self-Replication
Gerald F. Joyce and Jack W. Szostak
The Origin of Biological Homochirality
Donna G. Blackmond
Beyond DNA and RNA: The Expanding Toolbox of Synthetic Genetics
Alexander I. Taylor, Gillian Houlihan, and Philipp Holliger
Index