Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae

G3: Genes, Genomes, Genetics

Stanley Fields³  Anastasia McKinlay¹  Carlos L. Araya² 

[1] Department of Genome SciencesHoward Hughes Medical Institute, University of Washington, Seattle, Washington 98195Department of Genome SciencesDepartment of Genome SciencesHoward Hughes Medical Institute, University of Washington, Seattle, Washington 98195Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195Department of Genome SciencesHoward Hughes Medical Institute, University of Washington, Seattle, Washington 98195;Department of Genome SciencesDepartment of Genome SciencesDepartment of Genome Sciences;Department of Genome SciencesHoward Hughes Medical Institute, University of Washington, Seattle, Washington 98195Department of MedicineDepartment of Genome SciencesDepartment of Genome SciencesHoward Hughes Medical Institute, University of Washington, Seattle, Washington 98195Department of MedicineHoward Hughes Medical Institute, University of Washington, Seattle, Washington 98195Department of Genome SciencesHoward Hughes Medical Institute, University of Washington, Seattle, Washington 98195Department of MedicineDepartment of MedicineDepartment of Genome SciencesHoward Hughes Medical Institute, University of Washington, Seattle, Washington 98195Department of Medicine

关键词: yeast;    Saccharomyces cerevisiae;    transcription;    nuclear run-on assay;    high-throughput sequencing;    RNA stability;   

DOI  :  10.1534/g3.111.000810

学科分类：生物科学（综合）

来源: Genetics Society of America

【 摘 要 】

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.

【 授权许可】

Unknown