%0 Journal Article
%T RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast
%A Tae Soo Kim
%A Chih Long Liu
%A Moran Yassour
%A John Holik
%A Nir Friedman
%A Stephen Buratowski
%A Oliver J Rando
%J Genome Biology
%D 2010
%I BioMed Central
%R 10.1186/gb-2010-11-7-r75
%X 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.Together, these results provide a global perspective on the relationship between PolII and mRNA production in budding yeast.Gene transcription is one of the major mechanisms by which a cell responds to its environment, and the regulation of transcription has been one of the most intensively studied processes in biology over the past half century. In the past decade, the technical revolutions in whole-genome analysis have enabled unprecedented insights into the global changes in mRNA production in response to environmental cues, and into the roles for countless regulatory factors in the production of these mRNAs.The abundance of mRNA in a cell is determined by the relative rates of production (transcription and processing) and destruction, integrated over time. Thus, while mRNA levels are easily measured using microarrays or deep sequencing, the correspondence between mRNA changes and transcriptional changes in response to a given perturbation is imperfect. This is widely understood, but the ease of mRNA measurements has led most genomic analyses of transcriptional regulation t
%U http://genomebiology.com/2010/11/7/R75