Post-Transcriptional Gene Regulation

This volume strives to present current technical approaches to most aspects of post-transcriptional control and provide the reader with 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.

Step-by-step instructions that ensure successful results Tricks of the trade and notes on troubleshooting and avoiding known pitfalls

Klappentext

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 convinently 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 useful and versatile laboratory bench resource that will become an essential reference in the field.

Inhalt
Preface.- Contributors.- I: Bioinformatics.- Bioinformatics Approaches for Studying Untranslated Regions of mRNAsParamjeet S. Bagga.- Identification of mRNA Polyadenylation Sites in Genomes Using cDNA Sequences, Expressed Sequence Tags, and TraceJu Youn Lee, Ji Yeon Park, and Bin Tian.- Bioinformatic Tools for Studying Post-Transcriptional Gene Regulation: The UAlbany TUTR Collection and Other Informatic ResourcesFrancis Doyle, Christopher Zaleski, Ajish D. George, Erin K. Stenson, Adele Ricciardi, and Scott A. Tenenbaum.- II: Fundamental Aspects of the Study of RNA Biology.- In-Line Probing Analysis of RiboswitchesElizabeth E. Regulski and Ronald R. Breaker.- Ribotrap: Targeted Purification of RNA-Specific RNPs from Cell Lysates Through Immunoaffinity Precipitation to Identify Regulatory Proteins and RNAsDale L. Beach and Jack D. Keene.- Advances in RIP-Chip Analysis: RNA-Binding Protein Immunoprecipitation-Microarray ProfilingTimothy E. Baroni, Sridar V. Chittur, Ajish D. George, and Scott A. Tenenbaum.- Biosensors for RNA AptamersProtein InteractionSara Tombelli, Maria Minunni, and Marco Mascini.- A Tethering Approach to Study Proteins that Activate mRNA Turnover in Human CellsSandra L. Clement and Jens Lykke-Andersen.- RNA Analysis by Biosynthetic Tagging Using 4-Thiouracil and Uracil PhosphoribosyltransferaseGusti M. Zeiner, Michael D. Cleary, Ashley E. Fouts, Christopher D. Meiring, Edward S. Mocarski, and John C. Boothroyd.- Efficient 5? Cap-Dependent RNA Purification: Use in Identifying and Studying Subsets of RNAEdyta Z. Bajak and Curt H. Hagedorn.- III: Techniques for Specific Aspects of RNA Biology.- Enrichment of Alternatively Spliced IsoformsJulian P. Venables.- In Vivo Methods to Assess Polyadenylation EfficiencyLisa K. Hague, Tyra Hall-Pogar, andCarol S. Lutz.- Monitoring the Temporal and Spatial Distribution of RNA in Living Yeast CellsRoy M. Long and Carl R. Urbinati.- Analysis of mRNA Partitioning Between the Cytosol and Endoplasmic Reticulum Compartments of Mammalian CellsSamuel B. Stephens, Rebecca D. Dodd, Rachel S. Lerner, Brook M. Pyhtila, and Christopher V. Nicchitta.- In Vivo and In Vitro Analysis of Poly(A) Length Effects on mRNA TranslationJing Peng, Elizabeth L. Murray, and Daniel R. Schoenberg.- A Ribosomal Density-Mapping Procedure to Explore Ribosome Positions Along Translating mRNAsNaama Eldad and Yoav Arava.- Identification of Changes in Gene Expression by Quantitation of mRNA LevelsWendy M. Olivas.- Application of the Invader® RNA Assay to the Polarity of Vertebrate mRNA DecayElizabeth L. Murray and Daniel R. Schoenberg.- Development of an In Vitro mRNA Decay System in Insect CellsKevin Sokoloski, John R. Anderson, and Jeffrey Wilusz.- Using Synthetic Precursor and Inhibitor miRNAs to Understand miRNA FunctionLance P. Ford and Angie Cheng.- A Step-by-Step Procedure to Analyze the Efficacy of siRNA Using Real-Time PCRAngie Cheng, Charles L. Johnson, and Lance P. Ford.