title: RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast.
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.
authors.affiliation: Department of Biological Chemistry and Molecular Pharmacology, Harvard University, 240 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Tae Soo
authors.initials: TS
authors.lastname: Kim
authors.forename: Chih Long
authors.initials: CL
authors.lastname: Liu
authors.forename: Moran
authors.initials: M
authors.lastname: Yassour
authors.forename: John
authors.initials: J
authors.lastname: Holik
authors.forename: Nir
authors.initials: N
authors.lastname: Friedman
authors.forename: Stephen
authors.initials: S
authors.lastname: Buratowski
authors.forename: Oliver J
authors.initials: OJ
authors.lastname: Rando
mesh_terms: D000483:Alleles; D050260:Carbohydrate Metabolism / Q000235:genetics; D030541:Databases, Genetic; D003958:Diamide / Q000633:toxicity; D004789:Enzyme Activation / Q000187:drug effects; D015966:Gene Expression Regulation, Fungal / Q000187:drug effects; D005800:Genes, Fungal / Q000235:genetics; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D011485:Protein Binding / Q000187:drug effects; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000201:enzymology* / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D013312:Stress, Physiological / Q000235:genetics*; D013696:Temperature; D014158:Transcription, Genetic / Q000187:drug effects
chemical_list: D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins; D003958:Diamide; D012319:RNA Polymerase II; C511736:RPB1 protein, S cerevisiae