RNA Turnover in Bacteria, Archaea and Organelles

RNA Turnover in Bacteria, Archaea and Organelles

1st Edition - December 19, 2008

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  • Editors: Lynne E. Maquat, Cecilia Arraiano
  • Hardcover ISBN: 9780123743770
  • eBook ISBN: 9780080922065

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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

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

Product details

  • No. of pages: 620
  • Language: English
  • Copyright: © Academic Press 2008
  • Published: December 19, 2008
  • Imprint: Academic Press
  • Hardcover ISBN: 9780123743770
  • eBook ISBN: 9780080922065

About the Editors

Lynne E. Maquat

Affiliations and Expertise

University of Rochester, NY, USA

Cecilia Arraiano

Affiliations and Expertise

Universidade Nova de Lisboa, Portugal

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