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

Kim TS, Liu CL, Yassour M, Holik J, Friedman N, Buratowski S, Rando OJ - Genome Biol. (2010)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

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

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.

Show MeSH
PolII can still be recruited even after shifting rpb1-1 to 37°C. (a-c) Examples of time course data from cells shifted to 37°C (left panel), treated with diamide (middle panel), or shifted to 37°C for 10 minutes before diamide addition (right panel). Panels (a, b) show regions where PolII is recruited to diamide-specific genes despite being at the rpb1-1 restrictive temperature, whereas (c) shows diamide-specific genes that fail to recruit PolII.
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Figure 6: PolII can still be recruited even after shifting rpb1-1 to 37°C. (a-c) Examples of time course data from cells shifted to 37°C (left panel), treated with diamide (middle panel), or shifted to 37°C for 10 minutes before diamide addition (right panel). Panels (a, b) show regions where PolII is recruited to diamide-specific genes despite being at the rpb1-1 restrictive temperature, whereas (c) shows diamide-specific genes that fail to recruit PolII.

Mentions: Surprisingly, PolII was recruited to a subset of diamide-specific genes under these conditions (Figure 6), indicating that not only can PolII maintain contact with the genome under these conditions, but it can still be recruited. PolII occupancy over some of these genes was not restricted to the promoter, suggesting that it might even transit the ORF under these conditions. Interestingly, only a subset of diamide-specific genes were capable of recruiting PolII after 10 minutes at the restrictive temperature. The difference between these two sets of diamide-specific genes is not apparent to us at present.


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

Kim TS, Liu CL, Yassour M, Holik J, Friedman N, Buratowski S, Rando OJ - Genome Biol. (2010)

PolII can still be recruited even after shifting rpb1-1 to 37°C. (a-c) Examples of time course data from cells shifted to 37°C (left panel), treated with diamide (middle panel), or shifted to 37°C for 10 minutes before diamide addition (right panel). Panels (a, b) show regions where PolII is recruited to diamide-specific genes despite being at the rpb1-1 restrictive temperature, whereas (c) shows diamide-specific genes that fail to recruit PolII.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2926786&req=5

Figure 6: PolII can still be recruited even after shifting rpb1-1 to 37°C. (a-c) Examples of time course data from cells shifted to 37°C (left panel), treated with diamide (middle panel), or shifted to 37°C for 10 minutes before diamide addition (right panel). Panels (a, b) show regions where PolII is recruited to diamide-specific genes despite being at the rpb1-1 restrictive temperature, whereas (c) shows diamide-specific genes that fail to recruit PolII.
Mentions: Surprisingly, PolII was recruited to a subset of diamide-specific genes under these conditions (Figure 6), indicating that not only can PolII maintain contact with the genome under these conditions, but it can still be recruited. PolII occupancy over some of these genes was not restricted to the promoter, suggesting that it might even transit the ORF under these conditions. Interestingly, only a subset of diamide-specific genes were capable of recruiting PolII after 10 minutes at the restrictive temperature. The difference between these two sets of diamide-specific genes is not apparent to us at present.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

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

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.

Show MeSH