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RNA: A Laboratory Manual

By Donald C. Rio, University of California, Berkeley; Manuel Ares, Jr., University of California, Santa Cruz; Gregory J. Hannon, Cold Spring Harbor Laboratory; Timothy W. Nilsen, Case Western Reserve University School of Medicine

© 2011 • 586 pp., illus., appendices, index
Paperback • $169.00 $118.30 • ISBN 978-0-879698-91-1

RNA molecules participate in and regulate a vast array of cellular processes, and the scientific community is now entering a new era in which some aspect of RNA biology—as a tool, a therapeutic, a diagnostic, or part of a fundamental process—is becoming increasingly important. But initiating RNA research can be intimidating, and without a thorough understanding of the challenges and complexities inherent in handling this fragile nucleic acid, forays into the RNA world can be quite frustrating. RNA: A Laboratory Manual provides a broad range of up-to-date techniques so that any investigator can confidently handle RNA and carry out meaningful experiments, from the most basic to the most sophisticated. Originating in four of the field’s most prominent laboratories and written with novices as well as more advanced researchers in mind, this manual provides the necessary background and strategies for approaching any RNA investigation in addition to detailed step-by-step protocols and extensive tips and troubleshooting information. RNA: A Laboratory Manual will enable any researcher to approach a wide variety of RNA-related problems with confidence and a high expectation of success.

About the Authors

Donald C. Rio is Professor of Molecular and Cell Biology at the University of California, Berkeley. His research has focused on nucleic acid biochemistry, nucleic acid–protein interactions, nucleic acid rearrangements, and genome-wide approaches to the role of RNA binding proteins in controlling alternative pre-mRNA splicing. Dr. Rio obtained his Ph.D. with Robert Tjian at the University of California, Berkeley and did postdoctoral work with Gerald Rubin. He was Assistant and Associate Professor at MIT and Associate Member of the Whitehead Institute for Biomedical Research, prior to moving to his current position.

Manuel Ares, Jr. is Professor of Molecular, Cell & Developmental Biology at the University of California, Santa Cruz. He received a Ph.D. with Stephen H. Howell on the cell cycle of Chlamydomonas at UC San Diego (1982) and did postdoctoral work with Alan M. Weiner on snRNA transcription in HeLa cells at Yale. He joined the faculty at UC Santa Cruz in 1987 and has focused on snRNA processing, structure, and function in yeast and mammalian cells. He is currently President of the RNA Society.

Gregory J. Hannon is Professor and Howard Hughes Medical Institute Investigator at Cold Spring Harbor Laboratory. He received his Ph.D. at Case Western Reserve University working with Tim Nilsen (1992) and then moved to Cold Spring Harbor Laboratory for postdoctoral studies with David Beach. A pioneering investigator in the field of RNA interference, his laboratory has characterized many of the major complexes for small interfering RNAs and microRNAs. His lab also investigates the role of small RNAs as oncogenes and tumor suppressors and the use of RNAi libraries to identify therapeutic targets for specific disease subtypes.

Timothy W. Nilsen is Professor and Director of the Center for RNA Molecular Biology at Case Western Reserve University School of Medicine. He is also Professor of Biochemistry and of Medicine. After receiving a Ph.D. from the State University of New York at Albany working with Corrado Baglioni, he joined the faculty at CWRU (1982). His research has focused on RNA biology including the mechanism of action of interferon, the mechanism of SL-addition trans-splicing and mechanisms of regulation of alternative splicing. Currently, his laboratory is investigating the mechanism(s) of microRNA mediated gene regulation in animal cells and the structure and function of messenger ribonucleoprotiens. Dr. Nilsen became Editor in Chief of the journal RNA when it was founded in 1995 and still serves in that capacity. He is on the Editorial Board of Molecular and Cellular Biology and the Board of Reviewing Editors for Science.

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RNA: A Laboratory Manual

By Donald C. Rio, University of California, Berkeley; Manuel Ares, Jr., University of California, Santa Cruz; Gregory J. Hannon, Cold Spring Harbor Laboratory; Timothy W. Nilsen, Case Western Reserve University School of Medicine

© 2011 • 586 pp., illus., appendices, index
Hardcover • $246.00 $172.20 • ISBN 978-0-879698-90-4

So much has been learned about RNA in the past 10 years that the ability to purify, analyze, and manipulate RNA molecules is now essential in all kinds of bioscience. Initiating RNA research can be intimidating, but the new book RNA: A Laboratory Manual provides a broad range of up-to-date techniques presented in a functional framework, so that any investigator can confidently handle RNA and carry out meaningful experiments, from the most basic to the highly sophisticated. Originating in four of the field's most prominent laboratories, this manual provides the necessary background and strategies for approaching any RNA investigation, as well as detailed protocols and extensive tips and troubleshooting information. It is required reading for every research laboratory in the life sciences.

About the Authors

Donald C. Rio is Professor of Molecular and Cell Biology at the University of California, Berkeley. His research has focused on nucleic acid biochemistry, nucleic acid–protein interactions, nucleic acid rearrangements, and genome-wide approaches to the role of RNA binding proteins in controlling alternative pre-mRNA splicing. Dr. Rio obtained his Ph.D. with Robert Tjian at the University of California, Berkeley and did postdoctoral work with Gerald Rubin. He was Assistant and Associate Professor at MIT and Associate Member of the Whitehead Institute for Biomedical Research, prior to moving to his current position.

Manuel Ares, Jr. is Professor of Molecular, Cell & Developmental Biology at the University of California, Santa Cruz. He received a Ph.D. with Stephen H. Howell on the cell cycle of Chlamydomonas at UC San Diego (1982) and did postdoctoral work with Alan M. Weiner on snRNA transcription in HeLa cells at Yale. He joined the faculty at UC Santa Cruz in 1987 and has focused on snRNA processing, structure, and function in yeast and mammalian cells. He is currently President of the RNA Society.

Gregory J. Hannon is Professor and Howard Hughes Medical Institute Investigator at Cold Spring Harbor Laboratory. He received his Ph.D. at Case Western Reserve University working with Tim Nilsen (1992) and then moved to Cold Spring Harbor Laboratory for postdoctoral studies with David Beach. A pioneering investigator in the field of RNA interference, his laboratory has characterized many of the major complexes for small interfering RNAs and microRNAs. His lab also investigates the role of small RNAs as oncogenes and tumor suppressors and the use of RNAi libraries to identify therapeutic targets for specific disease subtypes.

Timothy W. Nilsen is Professor and Director of the Center for RNA Molecular Biology at Case Western Reserve University School of Medicine. He is also Professor of Biochemistry and of Medicine. After receiving a Ph.D. from the State University of New York at Albany working with Corrado Baglioni, he joined the faculty at CWRU (1982). His research has focused on RNA biology including the mechanism of action of interferon, the mechanism of SL-addition trans-splicing and mechanisms of regulation of alternative splicing. Currently, his laboratory is investigating the mechanism(s) of microRNA mediated gene regulation in animal cells and the structure and function of messenger ribonucleoprotiens. Dr. Nilsen became Editor in Chief of the journal RNA when it was founded in 1995 and still serves in that capacity. He is on the Editorial Board of Molecular and Cellular Biology and the Board of Reviewing Editors for Science.

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Nuclear Organization and Function
(Cold Spring Harbor Symposia on Quantitative Biology LXXV)

Edited By Terri Grodzicker, Cold Spring Harbor Laboratory; David Spector, Cold Spring Harbor Laboratory; David Stewart, Cold Spring Harbor Laboratory; Bruce Stillman, Cold Spring Harbor Laboratory

© 2010 • 630 pp., illus. (202 color, 74 b&w)
(Paperback edition does not include online access)
Paperback • $129.00 • ISBN 978-1-936113-08-8

This volume is based on presentations by the world-renowned investigators who gathered at the 75th annual Cold Spring Harbor Symposium on Quantitative Biology to discuss the organization and function of the cell nucleus. It reviews the latest advances in research into nuclear structure, the organization of the genome within the nucleus, and spatiotemporal coordination of nuclear processes. The topics examined include nuclear domains, chromatin organization, transcription and RNA processing, DNA replication, nuclear reprogramming, and epigenetics. Cancer, premature aging syndromes, and other diseases that may be associated with altered nuclear organization are also covered.

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Nuclear Organization and Function
(Cold Spring Harbor Symposia on Quantitative Biology LXXV)

Edited By Terri Grodzicker, Cold Spring Harbor Laboratory; David Spector, Cold Spring Harbor Laboratory; David Stewart, Cold Spring Harbor Laboratory; Bruce Stillman, Cold Spring Harbor Laboratory

© 2010 • 630 pp., illus. (202 color, 74 b&w), indexes
(Hardcover edition includes online access; call for information and registration)
Hardcover • $318.00 • ISBN 978-1-936113-07-1

This volume is based on presentations by the world-renowned investigators who gathered at the 75th annual Cold Spring Harbor Symposium on Quantitative Biology to discuss the organization and function of the cell nucleus. It reviews the latest advances in research into nuclear structure, the organization of the genome within the nucleus, and spatiotemporal coordination of nuclear processes. The topics examined include nuclear domains, chromatin organization, transcription and RNA processing, DNA replication, nuclear reprogramming, and epigenetics. Cancer, premature aging syndromes, and other diseases that may be associated with altered nuclear organization are also covered.

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Emerging Model Organisms: A Laboratory Manual, Volume 2

© 2010 • 624 pp., illus. (102 b/w), appendices, index
Trim size: 8-1/2” x 10-7/8”
Paperback • $91.00 • ISBN 978-0-879698-65-2

This second volume of the groundbreaking Emerging Model Organisms series expands the collection of species presented in the first volume. Leading experts provide 18 new chapters on emerging model systems, ranging from honeybee, ant, and beetle to Ciona and amphioxus; squid and salamander to yam, Paramecium, and wallaby. Like the first volume, each chapter presents a new organism and provides a detailed explanation of why it is useful for laboratory research, along with information on husbandry, genetics and genomics, pointers toward further resources, and a set of basic laboratory protocols for working with that organism. Emerging Model Organisms serves as a practical guidebook for finding just the right organism to address specific research needs.

Review of Volume 1:
“The first volume of Emerging Model Organisms illustrates the bewildering variety of natural histories and rapidly advancing techniques that have been developed to work with a wide spectrum of organisms. If Darwin were around now, he would have been the first to happily make use of this manual—and would be impatiently awaiting the forthcoming tome, describing the emergence of honeybees, squids, ascidians, rabbits, ants...and many more.” —Nature Cell Biology

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Emerging Model Organisms: A Laboratory Manual, Volume 2

© 2010 • 624 pp., illus. (102 b/w), appendices, index
Trim size: 8-1/2” x 10-7/8”
Hardcover • $162.00 • ISBN 978-0-879699-45-1

This second volume of the groundbreaking Emerging Model Organisms series expands the collection of species presented in the first volume. Leading experts provide 18 new chapters on emerging model systems, ranging from honeybee, ant, and beetle to Ciona and amphioxus; squid and salamander to yam, Paramecium, and wallaby. Like the first volume, each chapter presents a new organism and provides a detailed explanation of why it is useful for laboratory research, along with information on husbandry, genetics and genomics, pointers toward further resources, and a set of basic laboratory protocols for working with that organism. Emerging Model Organisms serves as a practical guidebook for finding just the right organism to address specific research needs.

Review of Volume 1:
“The first volume of Emerging Model Organisms illustrates the bewildering variety of natural histories and rapidly advancing techniques that have been developed to work with a wide spectrum of organisms. If Darwin were around now, he would have been the first to happily make use of this manual—and would be impatiently awaiting the forthcoming tome, describing the emergence of honeybees, squids, ascidians, rabbits, ants...and many more.” —Nature Cell Biology

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Genetics of Complex Human Diseases: A Laboratory Manual

Edited By Ammar Al-Chalabi, MRC Centre for Neurodegeneration Research, King’s College London; Laura Almasy, Southwest Foundation for Biomedical Research, San Antonio, Texas

© 2009 • 220 pp., illus., index
Paperback • $97.00 • ISBN 978-087969883-6

Many human diseases—including Alzheimer’s disease, schizophrenia, cancer, and cardiovascular disease—show complex inheritance that requires sophisticated analysis. Genetics of Complex Human Diseases: A Laboratory Manual brings together the tools that geneticists use to find disease genes with the genetic concepts and statistical theories that underpin these research approaches. Topics covered include basic genetics and Mendelian inheritance, statistical methods, genetic epidemiology, linkage studies, transmission disequilibrium test analysis, variance components analysis, genome-wide association studies, copy-number variation, methods for high-throughput genotyping, the complexity of RNA editing, and genetic computer programs. The book’s chapters, written by leading investigators in the field, blend practical information and reviews of each topic, providing both the how and the why of complex disease analysis. Genetics of Complex Human Diseases is an important guide for anyone with an interest in human genetics or who uses genetic techniques in the study of diseases with complex inheritance.

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Genetics of Complex Human Diseases: A Laboratory Manual

Edited By Ammar Al-Chalabi, MRC Centre for Neurodegeneration Research, King’s College London; Laura Almasy, Southwest Foundation for Biomedical Research, San Antonio, Texas

© 2009 • 220 pp., illus., index
Hardcover • $162.00 • ISBN 978-087969882-9

Many human diseases—including Alzheimer’s disease, schizophrenia, cancer, and cardiovascular disease—show complex inheritance that requires sophisticated analysis. Genetics of Complex Human Diseases: A Laboratory Manual brings together the tools that geneticists use to find disease genes with the genetic concepts and statistical theories that underpin these research approaches. Topics covered include basic genetics and Mendelian inheritance, statistical methods, genetic epidemiology, linkage studies, transmission disequilibrium test analysis, variance components analysis, genome-wide association studies, copy-number variation, methods for high-throughput genotyping, the complexity of RNA editing, and genetic computer programs. The book’s chapters, written by leading investigators in the field, blend practical information and reviews of each topic, providing both the how and the why of complex disease analysis. Genetics of Complex Human Diseases is an important guide for anyone with an interest in human genetics or who uses genetic techniques in the study of diseases with complex inheritance.

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Transcriptional Regulation in Eukaryotes: Concepts, Strategies, and Techniques, Second Edition

By Michael F. Carey, University of California, Los Angeles; Craig L. Peterson, University of Massachusetts Medical School, Worcester; Stephen T. Smale, University of California, Los Angeles

© 2009 • 620 pp., appendix, index
Paperback • $169.00 • ISBN 978-087969762-4

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Transcriptional Regulation in Eukaryotes: Concepts, Strategies, and Techniques, Second Edition

By Michael F. Carey, University of California, Los Angeles; Craig L. Peterson, University of Massachusetts Medical School, Worcester; Stephen T. Smale, University of California, Los Angeles

© 2009 • 620 pp., appendix, index
Hardcover • $246.00 • ISBN 978-087969777-8