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

Tae Soo Kim1, Chih Long Liu26, Moran Yassour34, John Holik2, Nir Friedman35, Stephen Buratowski1 and Oliver J Rando2*

Author Affiliations

1 Department of Biological Chemistry and Molecular Pharmacology, Harvard University, 240 Longwood Avenue, Boston, MA 02115, USA

2 Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, USA

3 School of Computer Science and Engineering, The Hebrew University, Givat Ram Campus, Jerusalem 91904, Israel

4 The Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA

5 The Alexander Silberman Institute of Life Science, The Hebrew University, Givat Ram Campus, Jerusalem 91904, Israel

6 Current address: Division of Immunology and Rheumatology, Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA

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Genome Biology 2010, 11:R75  doi:10.1186/gb-2010-11-7-r75

Published: 16 July 2010



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.


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.