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    RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast

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    Authors
    Kim, Tae Soo
    Liu, Chih Long
    Yassour, Moran
    Holik, John
    Friedman, Nir
    Buratowski, Stephen
    Rando, Oliver J.
    UMass Chan Affiliations
    Department of Biochemistry and Molecular Pharmacology
    Document Type
    Journal Article
    Publication Date
    2010-07-20
    Keywords
    RNA Polymerase II
    Gene Expression Profiling
    Schizosaccharomyces
    RNA, Messenger
    Stress, Physiological
    Genetics and Genomics
    Life Sciences
    Medicine and Health Sciences
    
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    Abstract
    BACKGROUND: The use of genome-wide RNA abundance profiling by microarrays and deep sequencing has spurred a revolution in our understanding of transcriptional control. However, changes in mRNA abundance reflect the combined effect of changes in RNA production, processing, and degradation, and thus, mRNA levels provide an occluded view of transcriptional regulation. RESULTS: To partially disentangle these issues, we carry out genome-wide RNA polymerase II (PolII) localization profiling in budding yeast in two different stress response time courses. While mRNA changes largely reflect changes in transcription, there remains a great deal of variation in mRNA levels that is not accounted for by changes in PolII abundance. We find that genes exhibiting 'excess' mRNA produced per PolII are enriched for those with overlapping cryptic transcripts, indicating a pervasive role for nonproductive or regulatory transcription in control of gene expression. Finally, we characterize changes in PolII localization when PolII is genetically inactivated using the rpb1-1 temperature-sensitive mutation. We find that PolII is lost from chromatin after roughly an hour at the restrictive temperature, and that there is a great deal of variability in the rate of PolII loss at different loci. CONCLUSIONS: Together, these results provide a global perspective on the relationship between PolII and mRNA production in budding yeast.
    Source
    Genome Biol. 2010;11(7):R75. Epub 2010 Jul 16. Link to article on publisher's site
    DOI
    10.1186/gb-2010-11-7-r75
    Permanent Link to this Item
    http://hdl.handle.net/20.500.14038/39442
    PubMed ID
    20637075
    Related Resources
    Link to Article in PubMed
    ae974a485f413a2113503eed53cd6c53
    10.1186/gb-2010-11-7-r75
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    UMass Chan Faculty and Researcher Publications

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