This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Although most studies of mRNA abundance analyze steady-state levels, it is critical to directly measure RNA synthesis in order to understand gene regulation. We combined the nuclear run-on (NRO) assay, which uses RNA labeling and capture of nascent transcripts, with high throughput DNA sequencing to examine transcription of exponentially growing Saccharomyces cerevisiae. The accumulation of sequencing reads in the NRO sample is consistent with transcriptional regulation not only at the level of RNA polymerase promoter recruitment but also at multiple post-recruitment steps, particularly promoter-proximal pausing. For example, all but one yeast core histone gene showed strong promoter-proximal pausing, suggesting that transition to productive elongation is necessary for rapid induction of histone synthesis in S phase. We examined the NRO sample for antisense transcripts and observed these for 310 genes, but we found no evidence for widespread bidirectional transcription from a single divergent promoter. Instead, the antisense data appear to reflect the activity of distinct promoters driving transcription in opposite directions. By calculating the ratio of NRO transcription to total RNA for each gene, we could estimate RNA stability, and we found that the most stable and unstable transcripts encode proteins whose functional roles are consistent with these stabilities. Transcription was also analyzed after a brief heat shock treatment of yeast, which revealed that most heat shock-inducible genes increase their RNA abundance by increasing their RNA synthesis. In sum, the combination of the NRO assay and high throughput sequencing allows an assessment genome-wide of RNA polymerase activity in yeast, identifying regulatory steps of RNA synthesis and RNA stability.
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