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

Tae Soo Kim, Chih Long Liu, Moran Yassour, John Holik, Nir Friedman, Stephen Buratowski, Oliver J. Rando*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

43 Scopus citations


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.

Original languageAmerican English
Article numberR75
JournalGenome Biology
Issue number7
StatePublished - 16 Jul 2010

Bibliographical note

Funding Information:
We thank Audrey Gasch, Paul Kaufman, and members of the Rando lab for comments on this manuscript. Work was supported by NIGMS grant GM079205, HFSP, and the Burroughs Wellcome Fund (OJR), and the US-Israel Bi-National Foundation and a European Union FP7 ‘Model-In’ collaborative grant (NF).


Dive into the research topics of 'RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast'. Together they form a unique fingerprint.

Cite this