RNA Turnover in Bacteria, Archaea and Organelles - 1st Edition - ISBN: 9780123743770, 9780080922065

RNA Turnover in Bacteria, Archaea and Organelles, Volume 447

1st Edition

Editors: Lynne E. Maquat Cecilia Arraiano
eBook ISBN: 9780080922065
Hardcover ISBN: 9780123743770
Imprint: Academic Press
Published Date: 19th December 2008
Page Count: 620
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Table of Contents

Part I Bacteria

Analysis of RNA decay, including polyadenylation, in mutant E. coli Analyzing the decay of stable RNAs in E. coli Genomic analyses of mRNA decay in E. coli using microarrays Methods to co-immunopurify degradative activities in E. coli Proteomics approach (affinity purification) for analyzing degradosome composition in E. coli Characterizing decay in vitro, including structural studies Defining RNA degradative activities in pathogenic bacteria (e.g., Studying tm-mediated surveillance and nonstop mRNA decay Defining small RNA function in RNA decay Characterizing mRNA destabilization mediated by Hfq-binding noncoding RNAs

Part II Archaea

Methods for the global analysis of mRNA stability in Archaea In vivo and in vitro studies of degradative activities in Archaea Structural studies of degradative activities using Archaea

Part III Eukaryotes

Dcp2/Dcp1 single-step kinetics Dcp2/Dcp1 and DCPS activity assays Purification and analyses of decapping activtors in Saccharomyces Reconstitution and analyses of the human Lsm complex Analyses of deadenylation in S. cerevisiae in vitro Deadenylation in mammalian-cell extracts Cell-free deadenylation assays using Drosophila embryos Cytoplasmic deadenylation assays using Xenopus oocytes Activity and structural analyses of the reconstituted eukaryotic RNA exosome Biochemical studies of the eukaryotic exosome Assays of 5?-3? exonucleases in Saccharomyces cerevisiae mRNA half-life measurements in Saccharomyces cerevisiae (all methods, including ts RNA polymerase) Genome-wide analyses of mRNA stability in Saccharomyces cerevisiae using transcription inhibitors and microarrays (discuss different growth/stress conditions and relative half-lives) Microscope-based cytometry to measure mRNA decay rates in large numbers of individual living Saccharomyces cerevisiae Genome-wide analyses of mRNA stability in Trypanosomes using transcription inhibitors and microarrays (discuss different growth/stress conditions and relative half-lives) mRNA half-life measurements in Drosophila melanogaster (all methods) Measuring maternal transcript destabilization in Drosophila melanogaster; also mRNA destabilization during oocyte maturation and egg activation mRNA half-life measurements in mammalian cells Mammalian-cell mRNA decay using microarrays after block in transcription In vivo labeling of RNA with 2,4-dithiouracil for cell-specific microarray analyses of mRNA synthesis and decay Tracking the decay of single RNA molecules Downregulating a decay factor and using microarrays to identify targets Microarrays or other analyses of RNA after affinity purification or immunopurification to study RNA decay Three-hybrid analysis to study RNA decay


Specific complexes of protein and RNA carry out many essential biological functions, including RNA processing, RNA turnover, RNA folding, as well as the translation of genetic information from mRNA into protein sequences. Messenger RNA (mRNA) decay is now emerging as an important control point and a major contributor to gene expression. Continuing identification of the protein factors and cofactors, and mRNA instability elements, responsible for mRNA decay allow researchers to build a comprehensive picture of the highly orchestrated processes involved in mRNA decay and its regulation.

Key Features

Covers the difference in processing of mRNA between eukaryotes, bacteria and archea. Benefit: Processing of mRNA differs greatly between eukaryotes, bacteria and archea and this affords researchers readily reproducible techniques to understand and study the molecular pathogenesis of disease.

Expert researchers introduce the most advanced technologies and techniques to identify mRNA processing, transport, localization and turnover which are central to the process of gene expression. Benefit: Keeps MIE buyers and online subscribers up-to-date with the latest research

Offers step by step lab instructions including necessary equipment and reagents. Benefit: Provides tried and tested techniques which eliminate searching through many different sources. Tested techniques are trustworthy and avoid pitfalls so the same mistakes are not made over and over.


Researchers in biochemistry, cell and molecular biology, genetics


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About the Editors

Lynne E. Maquat Editor

Affiliations and Expertise

University of Rochester, NY, USA

Cecilia Arraiano Editor

Affiliations and Expertise

Universidade Nova de Lisboa, Portugal