Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae

The assessment of transcriptional regulation requires a genome-wide survey of active RNA polymerases. Thus, we combined the nuclear run-on assay, which labels and captures nascent transcripts, with high-throughput DNA sequencing to examine transcriptional activity in exponentially growing Saccharomy...

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Main Authors:	McKinlay, Anastasia, Araya, Carlos L., Fields, Stanley
Format:	Online
Language:	English
Published:	Genetics Society of America 2011
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276176/

id	pubmed-3276176
recordtype	oai_dc
spelling	pubmed-32761762012-03-01 Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae McKinlay, Anastasia Araya, Carlos L. Fields, Stanley Investigation The assessment of transcriptional regulation requires a genome-wide survey of active RNA polymerases. Thus, we combined the nuclear run-on assay, which labels and captures nascent transcripts, with high-throughput DNA sequencing to examine transcriptional activity in exponentially growing Saccharomyces cerevisiae. Sequence read data from these nuclear run-on libraries revealed that transcriptional regulation in yeast occurs not only at the level of RNA polymerase recruitment to promoters but also at postrecruitment steps. Nascent synthesis signals are strongly enriched at TSS throughout the yeast genome, particularly at histone loci. Nascent transcripts reveal antisense transcription for more than 300 genes, with the read data providing support for the activity of distinct promoters driving transcription in opposite directions rather than bidirectional transcription from single promoters. By monitoring total RNA in parallel, we found that transcriptional activity accounts for 80% of the variance in transcript abundance. We computed RNA stabilities from nascent and steady-state transcripts for each gene and found that the most stable and unstable transcripts encode proteins whose functional roles are consistent with these stabilities. We also surveyed transcriptional activity after heat shock and found that most, but not all, heat shock-inducible genes increase their abundance by increasing their RNA synthesis. In summary, this study provides a genome-wide view of RNA polymerase activity in yeast, identifies regulatory steps in the synthesis of transcripts, and analyzes transcript stabilities. Genetics Society of America 2011-12-01 /pmc/articles/PMC3276176/ /pubmed/22384366 http://dx.doi.org/10.1534/g3.111.000810 Text en Copyright © 2011 McKinlay et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	McKinlay, Anastasia Araya, Carlos L. Fields, Stanley
spellingShingle	McKinlay, Anastasia Araya, Carlos L. Fields, Stanley Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae
author_facet	McKinlay, Anastasia Araya, Carlos L. Fields, Stanley
author_sort	McKinlay, Anastasia
title	Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae
title_short	Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae
title_full	Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae
title_fullStr	Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae
title_full_unstemmed	Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae
title_sort	genome-wide analysis of nascent transcription in saccharomyces cerevisiae
description	The assessment of transcriptional regulation requires a genome-wide survey of active RNA polymerases. Thus, we combined the nuclear run-on assay, which labels and captures nascent transcripts, with high-throughput DNA sequencing to examine transcriptional activity in exponentially growing Saccharomyces cerevisiae. Sequence read data from these nuclear run-on libraries revealed that transcriptional regulation in yeast occurs not only at the level of RNA polymerase recruitment to promoters but also at postrecruitment steps. Nascent synthesis signals are strongly enriched at TSS throughout the yeast genome, particularly at histone loci. Nascent transcripts reveal antisense transcription for more than 300 genes, with the read data providing support for the activity of distinct promoters driving transcription in opposite directions rather than bidirectional transcription from single promoters. By monitoring total RNA in parallel, we found that transcriptional activity accounts for 80% of the variance in transcript abundance. We computed RNA stabilities from nascent and steady-state transcripts for each gene and found that the most stable and unstable transcripts encode proteins whose functional roles are consistent with these stabilities. We also surveyed transcriptional activity after heat shock and found that most, but not all, heat shock-inducible genes increase their abundance by increasing their RNA synthesis. In summary, this study provides a genome-wide view of RNA polymerase activity in yeast, identifies regulatory steps in the synthesis of transcripts, and analyzes transcript stabilities.
publisher	Genetics Society of America
publishDate	2011
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276176/
_version_	1611505150994677760

Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae

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