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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

Due December 2018 • 500 pages (approx.), illustrated, index
Hardcover • $162 129.60
ISBN  978-1-621822-24-0
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  •     Contents    


Once thought to be just a messenger that allows genetic information encoded in DNA to direct the formation of proteins, RNA (ribonucleic acid) is now known to be a highly versatile molecule that has multiple roles in cells. It can function as an enzyme, scaffold various subcellular structures, and regulate gene expression through a variety of mechanisms, as well as act as a key component of the protein synthesis and splicing machinery. Perhaps most interestingly, increasing evidence indicates that RNA preceded DNA as the hereditary material and played a crucial role in the early evolution of life on Earth. This new edition of the classic reviews our understanding of the field, highlighting in particular techniques used to study and apply RNA biology.


A. Imaging RNA Biology in cells
Quantifying Single mRNA Translation Kinetics in Living Cells
Tatsuya Morisaki and Timothy J. Stasevich
Imaging the Life and Death of mRNAs in Single Cells
Jeffrey A. Chao and Timothée Lionnet
Illuminating Genomic Dark Matter with RNA Imaging
Arjun Raj and John Rinn
Principles of Stress Granules Revealed by Imaging Approaches
Briana Van Treeck and Roy Parker
B. Computing RNA Biology: Transciptome-wide analyses
Approaches for Understanding the Mechanisms of lncRNAs Regulation of Gene Expression
Patrick McDonel and Mitchell Guttman
Mapping the dsRNA World
Daniel P. Reich and Brenda L. Bass
Discovering and Mapping the Modified Nucleotides that Comprise the Epitranscriptome of mRNA
Bastian Linder and Samie R. Jaffrey
What are 3' UTRs Doing?
Christine Mayr
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
C. Massively parallel RNA structure and interactions
The Future of CLIP
Jernej Ule, Hun-Way Hwang, and Robert B. Darnell
Technique Development for Probing RNA Structure In Vivo and Genome-Wide
Philip C. Bevilacqua and Saah M. Assmann
The RNA Base-Pairing Problem and Base-Pairing Solutions
Zhipeng Lu and Howard Y. Chang
Principles and Practices of Hybridization Capture Experiments to Study lncRNAs that Act on Chromatin
Matthew D. Simon and Martin Machyna
Detecting RNA G-quadruplexes in the Transcriptome
Shun 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
D. 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
E. Structural Biology
Combining Mass Spectrometry and NMR Spectroscopy for Integrative Structural Biology of Protein-RNA Complexes
Alexander Leitner, Georg Dorn, and Frédéric H.-T. Allain
Extensions, Extra Factors and Extreme Complexity: Ribosomal Structures Provide Insights into Eukaryotic Translation
Melanie Weisser and Nenad Ban
Group II Introns RNPs and Reverse Transcriptases: From Retroelements to Research Tools
Marlene Belfort and Alan M. Lambowitz
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
Molecular Mechanisms of pre-mRNA Splicing through Structural Biology of the Spliceosome
Chuangye Yan, Ruixue Wan, and Yigong Shi
Structural Insights into Nuclear Pre-mRNA Splicing in Higher Eukaryotes
Berthold Kastner, Cindy L. Will, Holger Stark, and Reinhard Lührmann
Alternate RNA Structures
Marie Teng-Pei Wu and Victoria D’Souza
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
Single-molecule Analysis of Reverse Transcriptase Enzymes
Linnea I. Jansson and Michael D. Stone
Relating Structure and Dynamics in RNA Biology
Kevin P. Larsen, Junhong Choi, Arjun Prabhakar, Elisabetta Viani Puglisi, and Joseph D. Puglisi
F. Exploring the primordial RNA World
The Origin of Biological Homochirality
Donna G. Blackmond
Protocells and RNA Self-Replication
Gerald F. Joyce and Jack W. Szostak
Beyond DNA and RNA: The Expanding Toolbox of Synthetic Genetics
Alexander I. Taylor, Gillian Houlihan, and Philipp Holliger