Post-transcriptional gene regulation / edited by Jeffrey Wilusz.

Format:

Book

Contributor:

Wilusz, Jeffrey.

Series:

Methods in molecular biology (Clifton, N.J.) ; 419.

Methods in molecular biology ; 419

Language:

English

Subjects (All):

Genetic regulation--Laboratory manuals.

Genetic regulation.

Messenger RNA--Laboratory manuals.

Messenger RNA.

Cellular control mechanisms--Laboratory manuals.

Cellular control mechanisms.

Bioinformatics.

Gene Expression Regulation--methods.

RNA, Messenger.

Transcription Factors--methods.

Computational Biology--methods.

Medical Subjects:

Gene Expression Regulation--methods.

RNA, Messenger.

Transcription Factors--methods.

Computational Biology--methods.

Genre:

Laboratory manuals.

Physical Description:

xviii, 318 pages : illustrations ; 24 cm.

Place of Publication:

Totowa, N.J. : Humana Press, [2008]

Summary:

In Post-Transcriptional Gene Regulation, renowned authors present current technical approaches to most aspects of post-transcriptional control and provide a useful and versatile laboratory bench resource. With chapters split into sections covering bioinformatics, fundamental aspects of the study of RNA biology, and techniques for specific aspects of RNA biology, the expert authors have filled the book with invaluable tricks of the trade, perfected in their state-of-the-art laboratories.

This new volume from the Methods in Molecular Biology series is conveniently divided into three sections. The first section presents a series of bioinformatic approaches to address the use of RNA databases and algorithms to the study of post-transcriptional regulation involving untranslated regions of transcripts. In the second section, a series of methods applicable to fundamental issues in mRNA biology are presented. These include RNA structure/function, mRNP analysis and novel methods for mRNA labeling and isolation. The third section of this volume presents methodologies to study Particular aspects of post-transcriptional control. This section includes methods for the study of alternative splicing and 3' end processing, mRNA localization, mRNA translation, mRNA stability and si/miRNA regulation. Collectively, Post-Transcriptional Gene Regulation provides the reader with a broad array of laboratory protocols that will become an essential reference in the field.

Features

Step-by-step instructions that ensure successful results

Tricks of the trade and notes on troubleshooting and avoiding known pitfalls

Contents:

Part I Bioinformatics

1 Bioinformatics Approaches for Studying Untranslated Regions of mRNAs / Paramjeet S. Bagga 1

2 Identification of mRNA Polyadenylation Sites in Genomes Using cDNA Sequences, Expressed Sequence Tags, and Trace / Ju Youn Lee, Ji Yeon Park, Bin Tian 23

3 Bioinformatic Tools for Studying Post-Transcriptional Gene Regulation: The UAlbany TUTR Collection and Other Informatic Resources / Francis Doyle, Christopher Zaleski, Ajish D. George, Erin K. Stenson, Adele Ricciardi, Scott A. Tenenbaum 39

Part II Fundamental Aspects of the Study of RNA Biology

4 In-Line Probing Analysis of Riboswitches / Elizabeth E. Regulski, Ronald R. Breaker 53

5 Ribotrap: Targeted Purification of RNA-Specific RNPs from Cell Lysates Through Immunoaffinity Precipitation to Identify Regulatory Proteins and RNAs / Dale L. Beach, Jack D. Keene 69

6 Advances in RIP-Chip Analysis: RNA-Binding Protein Immunoprecipitation-Microarray Profiling / Timothy E. Baroni, Sridar V. Chittur, Ajish D. George, Scott A. Tenenbaum 93

7 Biosensors for RNA Aptamers-Protein Interaction / Sara Tombelli, Maria Minunni, Marco Mascini 109

8 A Tethering Approach to Study Proteins that Activate mRNA Turnover in Human Cells / Sandra L. Clement, Jens Lykke-Andersen 121

9 RNA Analysis by Biosynthetic Tagging Using 4-Thiouracil and Uracil Phosphoribosyltransferase / Gusti M. Zeiner, Michael D. Cleary, Ashley E. Fouts, Christopher D. Meiring, Edward S. Mocarski, John C. Boothroyd 135

10 Efficient 5' Cap-Dependent RNA Purification: Use in Identifying and Studying Subsets of RNA / Edyta Z. Bajak, Curt H. Hagedorn 147

Part III Techniques for Specific Aspects of RNA Biology

11 Enrichment of Alternatively Spliced Isoforms / Julian P. Venables 161

12 In Vivo Methods to Assess Polyadenylation Efficiency / Lisa K. Hague, Tyra Hall-Pogar, Carol S. Lutz 171

13 Monitoring the Temporal and Spatial Distribution of RNA in Living Yeast Cells / Roy M. Long, Carl R. Urbinati 187

14 Analysis of mRNA Partitioning Between the Cytosol and Endoplasmic Reticulum ComPartments of Mammalian Cells / Samuel B. Stephens, Rebecca D. Dodd, Rachel S. Lerner, Brook M. Pyhtila, Christopher V. Nicchitta 197

15 In Vivo and In Vitro Analysis of Poly(A) Length Effects on mRNA Translation / Jing Peng, Elizabeth L. Murray, Daniel R. Schoenberg 215

16 A Ribosomal Density-Mapping Procedure to Explore Ribosome Positions Along Translating mRNAs / Naama Eldad, Yoav Arava 231

17 Identification of Changes in Gene Expression by Quantitation of mRNA Levels / Wendy M. Olivas 243

18 Application of the Invader RNA Assay to the Polarity of Vertebrate mRNA Decay / Elizabeth L. Murray, Daniel R. Schoenberg 259

19 Development of an In Vitro mRNA Decay System in Insect Cells / Kevin Sokoloski, John R. Anderson, Jeffrey Wilusz 277

20 Using Synthetic Precursor and Inhibitor miRNAs to Understand miRNA Function / Lance P. Ford, Angie Cheng 289

21 A Step-by-Step Procedure to Analyze the Efficacy of siRNA Using Real-Time PCR / Angie Cheng, Charles L. Johnson, Lance P. Ford 303.

Notes:

Includes bibliographical references and index.

ISBN:

9781588297839

1588297837

OCLC:

166358115