RNA Turnover in Bacteria, Archaea and Organelles

<p>Part I Bacteria <br>Analysis of RNA decay, including polyadenylation, in mutant E. coli<br>Analyzing the decay of stable RNAs in E. coli <br>Genomic analyses of mRNA decay in E. coli using microarrays <br>Methods to co-immunopurify degradative activities in E. coli<br>Proteomics approach (affinity purification) for analyzing degradosome composition in E. coli <br>Characterizing decay in vitro, including structural studies <br>Defining RNA degradative activities in pathogenic bacteria (e.g., Studying tm-mediated surveillance and nonstop mRNA decay<br>Defining small RNA function in RNA decay <br>Characterizing mRNA destabilization mediated by Hfq-binding noncoding RNAs</p> <p>Part II Archaea<br>Methods for the global analysis of mRNA stability in Archaea <br>In vivo and in vitro studies of degradative activities in Archaea<br>Structural studies of degradative activities using Archaea</p> <p>Part III Eukaryotes <br>Dcp2/Dcp1 single-step kinetics <br>Dcp2/Dcp1 and DCPS activity assays<br>Purification and analyses of decapping activtors in Saccharomyces Reconstitution and analyses of the human Lsm complex<br>Analyses of deadenylation in S. cerevisiae in vitro<br>Deadenylation in mammalian-cell extracts <br>Cell-free deadenylation assays using Drosophila embryos <br>Cytoplasmic deadenylation assays using Xenopus oocytes<br>Activity and structural analyses of the reconstituted eukaryotic RNA exosome <br>Biochemical studies of the eukaryotic exosome<br>Assays of 5?-3? exonucleases in Saccharomyces cerevisiae<br>mRNA half-life measurements in Saccharomyces cerevisiae (all methods, including ts RNA polymerase) <br>Genome-wide analyses of mRNA stability in Saccharomyces cerevisiae using transcription inhibitors and microarrays (discuss different growth/stress conditions and relative half-lives)<br>Microscope-based cytometry to measure mRNA decay rates in large numbers of individual living Saccharomyces cerevisiae<br>Genome-wide analyses of mRNA stability in Trypanosomes using transcription inhibitors and microarrays (discuss different growth/stress conditions and relative half-lives)<br>mRNA half-life measurements in Drosophila melanogaster (all methods)<br>Measuring maternal transcript destabilization in Drosophila melanogaster; also mRNA destabilization during oocyte maturation and egg activation<br>mRNA half-life measurements in mammalian cells <br>Mammalian-cell mRNA decay using microarrays after block in transcription <br>In vivo labeling of RNA with 2,4-dithiouracil for cell-specific microarray analyses of mRNA synthesis and decay<br>Tracking the decay of single RNA molecules<br>Downregulating a decay factor and using microarrays to identify targets<br>Microarrays or other analyses of RNA after affinity purification or immunopurification to study RNA decay<br>Three-hybrid analysis to study RNA decay</p>