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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.

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Mismatches between mRNA production and changes in PolII occupancy. (a) Scatterplot of mRNA change versus PolII occupancy change. PolII data are taken from mid-CDS probes, and change from 0 to 30 minutes of diamide treatment is shown on the x-axis. mRNA data from Gasch et al. [18] is shown on the y-axis. The red line shows the LOWESS fit of mRNA/PolII change. (b) Example genes with excess, typical, and a dearth of mRNA produced per change in PolII occupancy. Data for mRNA change and PolII change at mid-CDS are plotted at the same scale. (c) Definition of mRNA excess per PolII change. As in (b), but for 30 minutes of heat shock. Genes that fall more than 0.5 above (red) or below (green) the LOWESS fit (red line) of mRNA/PolII change are indicated. (d) Genes with excess mRNA production are subject to extensive overlapping noncoding transcription. Average extent of overlap with other transcripts defined in Xu et al. [22] are shown for the three gene classes defined in (c).
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Figure 4: Mismatches between mRNA production and changes in PolII occupancy. (a) Scatterplot of mRNA change versus PolII occupancy change. PolII data are taken from mid-CDS probes, and change from 0 to 30 minutes of diamide treatment is shown on the x-axis. mRNA data from Gasch et al. [18] is shown on the y-axis. The red line shows the LOWESS fit of mRNA/PolII change. (b) Example genes with excess, typical, and a dearth of mRNA produced per change in PolII occupancy. Data for mRNA change and PolII change at mid-CDS are plotted at the same scale. (c) Definition of mRNA excess per PolII change. As in (b), but for 30 minutes of heat shock. Genes that fall more than 0.5 above (red) or below (green) the LOWESS fit (red line) of mRNA/PolII change are indicated. (d) Genes with excess mRNA production are subject to extensive overlapping noncoding transcription. Average extent of overlap with other transcripts defined in Xu et al. [22] are shown for the three gene classes defined in (c).

Mentions: However, close examination of PolII changes within any given cluster reveal numerous examples where mRNA changes are not matched by PolII abundance changes. To investigate this phenomenon further, we compared the change in PolII abundance over mid-CDS probes and the corresponding change in mRNA abundance at varying times after induction of the stress response (Figure 4a,c; Additional file 7). We observed the expected positive correlation between PolII changes and changes in mRNA abundance, but there was significant variation as well - changes in PolII abundance typically accounted for approximately 50% of variance in mRNA abundance in this analysis. Examples of genes exhibiting high or low mRNA production per change in PolII occupancy are shown in Figure 4b.


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)

Mismatches between mRNA production and changes in PolII occupancy. (a) Scatterplot of mRNA change versus PolII occupancy change. PolII data are taken from mid-CDS probes, and change from 0 to 30 minutes of diamide treatment is shown on the x-axis. mRNA data from Gasch et al. [18] is shown on the y-axis. The red line shows the LOWESS fit of mRNA/PolII change. (b) Example genes with excess, typical, and a dearth of mRNA produced per change in PolII occupancy. Data for mRNA change and PolII change at mid-CDS are plotted at the same scale. (c) Definition of mRNA excess per PolII change. As in (b), but for 30 minutes of heat shock. Genes that fall more than 0.5 above (red) or below (green) the LOWESS fit (red line) of mRNA/PolII change are indicated. (d) Genes with excess mRNA production are subject to extensive overlapping noncoding transcription. Average extent of overlap with other transcripts defined in Xu et al. [22] are shown for the three gene classes defined in (c).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Mismatches between mRNA production and changes in PolII occupancy. (a) Scatterplot of mRNA change versus PolII occupancy change. PolII data are taken from mid-CDS probes, and change from 0 to 30 minutes of diamide treatment is shown on the x-axis. mRNA data from Gasch et al. [18] is shown on the y-axis. The red line shows the LOWESS fit of mRNA/PolII change. (b) Example genes with excess, typical, and a dearth of mRNA produced per change in PolII occupancy. Data for mRNA change and PolII change at mid-CDS are plotted at the same scale. (c) Definition of mRNA excess per PolII change. As in (b), but for 30 minutes of heat shock. Genes that fall more than 0.5 above (red) or below (green) the LOWESS fit (red line) of mRNA/PolII change are indicated. (d) Genes with excess mRNA production are subject to extensive overlapping noncoding transcription. Average extent of overlap with other transcripts defined in Xu et al. [22] are shown for the three gene classes defined in (c).
Mentions: However, close examination of PolII changes within any given cluster reveal numerous examples where mRNA changes are not matched by PolII abundance changes. To investigate this phenomenon further, we compared the change in PolII abundance over mid-CDS probes and the corresponding change in mRNA abundance at varying times after induction of the stress response (Figure 4a,c; Additional file 7). We observed the expected positive correlation between PolII changes and changes in mRNA abundance, but there was significant variation as well - changes in PolII abundance typically accounted for approximately 50% of variance in mRNA abundance in this analysis. Examples of genes exhibiting high or low mRNA production per change in PolII occupancy are shown in Figure 4b.

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
Related in: MedlinePlus