Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions
Journal article, 2019

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.

Author

Christoph Sebastian Börlin

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Nevena Cvetesic

MRC Clinical Sciences Centre

Petter Holland

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

David Bergenholm

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Verena Siewers

Novo Nordisk Foundation Center for Biosustainability

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Boris Lenhard

MRC Clinical Sciences Centre

University of Bergen

Jens B Nielsen

Technical University of Denmark (DTU)

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Novo Nordisk Foundation Center for Biosustainability

FEMS Yeast Research

1567-1356 (ISSN) 1567-1364 (eISSN)

Vol. 19 2

Subject Categories

Microbiology

Bioinformatics and Systems Biology

Genetics

DOI

10.1093/femsyr/foy128

PubMed

30590648

More information

Latest update

1/28/2019