Periodic mRNA synthesis and degradation co‐operate during cell cycle gene expression

Molecular Systems Biology

Philipp Eser¹  Carina Demel¹  Kerstin C Maier¹  Björn Schwalb¹  Nicole Pirkl¹  Dietmar E Martin¹  Patrick Cramer¹ 

[1] Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany

关键词: cell cycle;    gene regulation;    mRNA degradation;    mRNA turnover;    periodic transcription;   

DOI  :  10.1002/msb.134886

来源: Wiley

【 摘 要 】

Abstract

During the cell cycle, the levels of hundreds of mRNAs change in a periodic manner, but how this is achieved by alterations in the rates of mRNA synthesis and degradation has not been studied systematically. Here, we used metabolic RNA labeling and comparative dynamic transcriptome analysis (cDTA) to derive mRNA synthesis and degradation rates every 5 min during three cell cycle periods of the yeast Saccharomyces cerevisiae. A novel statistical model identified 479 genes that show periodic changes in mRNA synthesis and generally also periodic changes in their mRNA degradation rates. Peaks of mRNA degradation generally follow peaks of mRNA synthesis, resulting in sharp and high peaks of mRNA levels at defined times during the cell cycle. Whereas the timing of mRNA synthesis is set by upstream DNA motifs and their associated transcription factors (TFs), the synthesis rate of a periodically expressed gene is apparently set by its core promoter.

Synopsis

Genome-scale measurement of changes in mRNA synthesis and degradation rates during the yeast cell cycle identifies genes with periodic synthesis and degradation and reveals a tight temporal coupling of both processes.

• The first high-resolution time series of mRNA synthesis and degradation rates during the cell cycle is presented.
• A novel statistical algorithm identifies periodically expressed genes and parameters of their temporal profile.
• The timing of periodic expression is set by upstream DNA motifs and the associated transcription factors, whereas the synthesis rate is set by the core promoter.
• Sharp and high peaks of mRNA levels are obtained by a temporal coupling of periodic mRNA synthesis and degradation maxima.

【 授权许可】

CC BY   
© 2014 The Authors.

Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.