|Dataset Name||Selinger et al, Affymetrix RNA decay data|
|Short Description||Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation|
|Reference||Selinger, DW, Saxena, RM, Cheung, KJ, Church, GM, and Rosenow, C (2003) Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation . Genome Research Feb;13(2):216-23|
|Date Added to ExpressDB||May 7 2002 3:55:39:500PM|
|Number of Measures on ExpressDB||6 (here to download dataset and view measure details)|
|Long Description||Subgenic-resolution oligonucleotide microarrays were used to study global RNA degradation in wild-type Escherichia coli MG1655. RNA chemical half-lives were measured for 1036 open reading frames (ORFs) and for 329 known and predicted operons. The half-life of total mRNA was 6.8 min under the conditions tested. We also observed significant relationships between gene functional assignments and transcript stability. Unexpectedly, transcription of a single operon (tdcABCDEFG) was relatively rifampicin-insensitive and showed significant increases 2.5 min after rifampicin addition. This supports a novel mechanism of transcription for the tdc operon, whose promoter lacks any recognizable _ binding sites. Probe by probe analysis of all known and predicted operons showed that the 5_ ends of operons degrade, on average, more quickly than the rest of the transcript, with stability increasing in a 3_ direction, supporting and further generalizing the current model of a net 5_ to 3_ directionality of degradation. Hierarchical clustering analysis of operon degradation patterns revealed that this pattern predominates but is not exclusive. We found a weak but highly significant correlation between the degradation of adjacent operon regions, suggesting that stability is determined by a combination of local and operon-wide stability determinants. The 16 ORF dcw gene cluster, which has a complex promoter structure and a partially characterized degradation pattern, was studied at high resolution, allowing a detailed and integrated description of its abundance and degradation. We discuss the application of subgenic resolution DNA microarray analysis to study global mechanisms of RNA transcription and processing.|
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