Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions

Börlin, Christoph Sebastian,1989Chalmers tekniska högskola,Chalmers University of Technology (author)

One of the fundamental processes that determine cellular fate is regulation of gene transcription. Understanding these regulatory processes is therefore essential for understanding cellular responses to changes in environmental conditions. At the core promoter, the regulatory region containing the transcription start site (TSS), all inputs regulating transcription are integrated. Here, we used Cap Analysis of Gene Expression (CAGE) to analyze the pattern of TSSs at four different environmental conditions (limited in ethanol, limited in nitrogen, limited in glucose and limited in glucose under anaerobic conditions) using the Saccharomyces cerevisiae strain CEN.PK113-7D. With this experimental setup, we were able to show that the TSS landscape in yeast is stable at different metabolic states of the cell. We also show that the spatial distribution of transcription initiation events, described by the shape index, has a surprisingly strong negative correlation with measured gene expression levels, meaning that genes with higher expression levels tend to have a broader distribution of TSSs. Our analysis supplies a set of high-quality TSS annotations useful for metabolic engineering and synthetic biology approaches in the industrially relevant laboratory strain CEN.PK113-7D, and provides novel insights into yeast TSS dynamics and gene regulation.

Cvetesic, Nevena (author)
Holland, Petter,1985Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)holland (author)
Bergenholm, David,1987Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)davidju (author)
Siewers, Verena,1976Novo Nordisk Fonden,Novo Nordisk Foundation,Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)siewers (author)
Lenhard, BorisUniversitetet i Bergen,University of Bergen (author)
Nielsen, Jens B,1962Chalmers tekniska högskola,Chalmers University of Technology,Novo Nordisk Fonden,Novo Nordisk Foundation,Danmarks Tekniske Universitet,Technical University of Denmark(Swepub:cth)nielsenj (author)
Chalmers tekniska högskolaNovo Nordisk Fonden (creator_code:org_t)

By the author/editor: Börlin, Christop ...; Cvetesic, Nevena; Holland, Petter, ...; Bergenholm, Davi ...; Siewers, Verena, ...; Lenhard, Boris; show more...; Nielsen, Jens B, ...; show less...

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Microbiology

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Bioinformatics a ...

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