RNA Turnover in Bacteria, Archaea and Organelles

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