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Spliceosomal Pre-mRNA Splicing [electronic resource]: Methods and Protocols

edited by Klemens J. Hertel, Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, USA
Format
EBook; Book; Online
Published
New York : Humana Press ; Springer, c2014.
Language
English
Series
Methods in Molecular Biology
Methods in Molecular Biology (Clifton, N.J.)
ISBN
9781627039796 (alk. paper), 1627039791 (alk. paper), 9781627039802 (eBook)
Summary
"Providing a guide to classical experimental approaches to decipher splicing mechanisms and experimental strategies that rely on novel multi-disciplinary approaches, Spliceosomal Pre-mRNA Splicing: Methods and Protocols describes the theory of alternative pre-mRNA splicing in seven introductory chapters and then introduces protocols and their theoretical background relevant for a variety of experimental research. These protocol chapters cover basic methods to detect splicing events, analyses of alternative pre-mRNA splicing in vitro and in vivo, manipulation of splicing events, and high-throughput and bioinformatic analyses of alternative splicing. 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 protocols, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and practical, Spliceosomal Pre-mRNA Splicing: Methods and Protocols will aid newcomers and seasoned molecular biologists in understanding the fascinating world of alternative splicing with the ultimate goal of paving the way for many new discoveries to come."--
Contents
  • Pre-mRNA splicing reaction / Somsakul Pop Wongpalee and Shalini Sharma
  • Diversity and evolution of spliceosomal systems / Scott William Roy and Manuel Irimia
  • Mechanisms of Spliceosomal Assembly / Ni-ting Chiou and Kristen W. Lynch
  • Alternative pre-mRNA splicing / Stacey D. Wagner and J. Andrew Berglund
  • Regulation of alternative pre-mRNA splicing / Miguel B. Coelho and Christopher W.J. Smith
  • Introduction to cotranscriptional RNA splicing / Evan C. Merkhofer, Peter Hu, and Tracy L. Johnson
  • Chromatin and splicing / Nazmul Haque and Shalini Oberdoerffer
  • Preparation of splicing competent nuclear extracts / Chiu-Ho T. Webb and Klemens J. Hertel
  • Preparation of yeast whole cell splicing extract / Elizabeth A. Dunn and Stephen D. Rader
  • Efficient splinted ligation of synthetic RNA using RNA ligase / Martha R. Stark and Stephen D. Rader
  • In vitro assay of pre-mRNA splicing in mammalian nuclear extract / Maliheh Movassat, William F. Mueller, and Klemens J. Hertel
  • Kinetic analysis of in vitro pre-mRNA splicing in HeLa nuclear extract / William F. Mueller and Klemens J. Hertel
  • In vitro systems for coupling RNAP II transcription to splicing and polyadenylation / Eric G. Folco and Robin Reed
  • Isolation and accumulation of spliceosomal assembly intermediates / Janine O. Ilagan and Melissa S. Jurica
  • Complementation of U4 snRNA in S. cerevisiae splicing extracts for biochemical studies of snRNP assembly and function / Martha R. Stark and Stephen D. Rader
  • Expression and purification of splicing proteins from mammalian cells / Eric Allemand and Michelle L. Hastings
  • Single molecule approaches for studying spliceosome assembly and catalysis / Eric G. Anderson and Aaron A. Hoskins
  • Cell-based splicing of minigenes / Sarah A. Smith and Kristen W. Lynch
  • Quantifying the ratio of spliceosome components assembled on pre-mRNA / Noa Neufeld, Yehuda Brody, and Yaron Shav-Tal
  • Antisense methods to modulate pre-mRNA splicing / Joonbae Seo, Eric W. Ottesen, and Ravindra N. Singh
  • Using yeast genetics to study splicing mechanisms / Munshi Azad Hossain and Tracy L. Johnson
  • Medium throughput analysis of alternative splicing by fluorescently labeled RT-PCR / Ryan Percifield, Daniel Murphy, and Peter Stoilov
  • Chromatin immunoprecipitation approaches to determine co-transcriptional nature of splicing / Nicole I. Bieberstein, Korinna Straube, and Karla M. Neugebauer
  • Computational approaches to mine publicly available databases / Rodger B. Voelker, William A. Cresko, and J. Andrew Berglund
  • Approaches to link RNA secondary structures with splicing regulation / Mireya Plass and Eduardo Eyras
  • Methods to study splicing from high-throughput RNA sequencing data / Gael P. Alamancos, Eneritz Agirre, and Eduardo Eyras-- Global protein-RNA interaction mapping at single nucleotide resolution by iCLIP-seq / Chengguo Yao, Lingjie Weng, and Yongsheng Shi
  • Predicting alternative splicing / Yoseph Barash and Jorge Vaquero Garcia.
Description
Mode of access: World wide Web.
Notes
Includes bibliographical references and index.
Series Statement
Methods in molecular biology ; 1126
Methods in molecular biology (Clifton, N.J.) ; v. 1126
Copyright Not EvaluatedCopyright Not Evaluated
Technical Details
  • Access in Virgo Classic
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    a| Spliceosomal pre-mRNA splicing h| [electronic resource] : b| methods and protocols / c| edited by Klemens J. Hertel, Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, USA.
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    a| New York : b| Humana Press ; b| Springer, c| c2014.
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    a| Methods in molecular biology ; v| 1126
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    a| Includes bibliographical references and index.
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    t| Pre-mRNA splicing reaction / r| Somsakul Pop Wongpalee and Shalini Sharma -- t| Diversity and evolution of spliceosomal systems / r| Scott William Roy and Manuel Irimia -- t| Mechanisms of Spliceosomal Assembly / r| Ni-ting Chiou and Kristen W. Lynch -- t| Alternative pre-mRNA splicing / r| Stacey D. Wagner and J. Andrew Berglund -- t| Regulation of alternative pre-mRNA splicing / r| Miguel B. Coelho and Christopher W.J. Smith -- t| Introduction to cotranscriptional RNA splicing / r| Evan C. Merkhofer, Peter Hu, and Tracy L. Johnson -- t| Chromatin and splicing / r| Nazmul Haque and Shalini Oberdoerffer -- t| Preparation of splicing competent nuclear extracts / r| Chiu-Ho T. Webb and Klemens J. Hertel -- t| Preparation of yeast whole cell splicing extract / r| Elizabeth A. Dunn and Stephen D. Rader -- t| Efficient splinted ligation of synthetic RNA using RNA ligase / r| Martha R. Stark and Stephen D. Rader -- t| In vitro assay of pre-mRNA splicing in mammalian nuclear extract / r| Maliheh Movassat, William F. Mueller, and Klemens J. Hertel -- t| Kinetic analysis of in vitro pre-mRNA splicing in HeLa nuclear extract / r| William F. Mueller and Klemens J. Hertel -- t| In vitro systems for coupling RNAP II transcription to splicing and polyadenylation / r| Eric G. Folco and Robin Reed -- t| Isolation and accumulation of spliceosomal assembly intermediates / r| Janine O. Ilagan and Melissa S. Jurica -- t| Complementation of U4 snRNA in S. cerevisiae splicing extracts for biochemical studies of snRNP assembly and function / r| Martha R. Stark and Stephen D. Rader -- t| Expression and purification of splicing proteins from mammalian cells / r| Eric Allemand and Michelle L. Hastings -- t| Single molecule approaches for studying spliceosome assembly and catalysis / r| Eric G. Anderson and Aaron A. Hoskins -- t| Cell-based splicing of minigenes / r| Sarah A. Smith and Kristen W. Lynch -- t| Quantifying the ratio of spliceosome components assembled on pre-mRNA / r| Noa Neufeld, Yehuda Brody, and Yaron Shav-Tal -- t| Antisense methods to modulate pre-mRNA splicing / r| Joonbae Seo, Eric W. Ottesen, and Ravindra N. Singh -- t| Using yeast genetics to study splicing mechanisms / r| Munshi Azad Hossain and Tracy L. Johnson -- t| Medium throughput analysis of alternative splicing by fluorescently labeled RT-PCR / r| Ryan Percifield, Daniel Murphy, and Peter Stoilov -- t| Chromatin immunoprecipitation approaches to determine co-transcriptional nature of splicing / r| Nicole I. Bieberstein, Korinna Straube, and Karla M. Neugebauer -- t| Computational approaches to mine publicly available databases / r| Rodger B. Voelker, William A. Cresko, and J. Andrew Berglund -- t| Approaches to link RNA secondary structures with splicing regulation / r| Mireya Plass and Eduardo Eyras -- t| Methods to study splicing from high-throughput RNA sequencing data / r| Gael P. Alamancos, Eneritz Agirre, and Eduardo Eyras-- t| Global protein-RNA interaction mapping at single nucleotide resolution by iCLIP-seq / r| Chengguo Yao, Lingjie Weng, and Yongsheng Shi -- t| Predicting alternative splicing / r| Yoseph Barash and Jorge Vaquero Garcia.
    520
      
      
    a| "Providing a guide to classical experimental approaches to decipher splicing mechanisms and experimental strategies that rely on novel multi-disciplinary approaches, Spliceosomal Pre-mRNA Splicing: Methods and Protocols describes the theory of alternative pre-mRNA splicing in seven introductory chapters and then introduces protocols and their theoretical background relevant for a variety of experimental research. These protocol chapters cover basic methods to detect splicing events, analyses of alternative pre-mRNA splicing in vitro and in vivo, manipulation of splicing events, and high-throughput and bioinformatic analyses of alternative splicing. 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 protocols, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and practical, Spliceosomal Pre-mRNA Splicing: Methods and Protocols will aid newcomers and seasoned molecular biologists in understanding the fascinating world of alternative splicing with the ultimate goal of paving the way for many new discoveries to come."-- c| P. [4] of cover.
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    a| Mode of access: World wide Web.
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