Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress
Author(s)
Marguerat, Samuel
Lawler, Katherine
Brazma, Alvis
Baehler, Juerg
Type
Journal Article
Abstract
The cooperation of transcriptional and post-transcriptional levels of control to shape gene regulation is only partially understood. Here we show that a combination of two simple and non-invasive genomic techniques, coupled with kinetic mathematical modeling, affords insight into the intricate dynamics of RNA regulation in response to oxidative stress in the fission yeast Schizosaccharomyces pombe. This study reveals a dominant role of transcriptional regulation in response to stress, but also points to the first minutes after stress induction as a critical time when the coordinated control of mRNA turnover can support the control of transcription for rapid gene regulation. In addition, we uncover specialized gene expression strategies associated with distinct functional gene groups, such as simultaneous transcriptional repression and mRNA destabilization for genes encoding ribosomal proteins, delayed mRNA destabilization with varying contribution of transcription for ribosome biogenesis genes, dominant roles of mRNA stabilization for genes functioning in protein degradation, and adjustment of both transcription and mRNA turnover during the adaptation to stress. We also show that genes regulated independently of the bZIP transcription factor Atf1p are predominantly controlled by mRNA turnover, and identify putative cis-regulatory sequences that are associated with different gene expression strategies during the stress response. This study highlights the intricate and multi-faceted interplay between transcription and RNA turnover during the dynamic regulatory response to stress.
Date Issued
2014-06-01
Date Acceptance
2014-05-09
Citation
RNA Biology, 2014, 11 (6), pp.702-714
ISSN
1547-6286
Publisher
Taylor & Francis
Start Page
702
End Page
714
Journal / Book Title
RNA Biology
Volume
11
Issue
6
Copyright Statement
© 2014 Landes Bioscience
This is an open-access article licensed under a Creative Commons Attribution 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.
This is an open-access article licensed under a Creative Commons Attribution 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.
Identifier
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000341971700009&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
Subjects
Science & Technology
Life Sciences & Biomedicine
Biochemistry & Molecular Biology
fission yeast
mathematical modeling
mRNA turnover
oxidative stress
RNA Polymerase II
post-transcriptional control
gene regulation
Atf1
ribosome biogenesis
GENOME-WIDE ANALYSIS
GLOBAL ANALYSIS
REGULATED GENES
STABILITY
DEGRADATION
ELEMENTS
RATES
PRINCIPLES
DISCOVERY
TURNOVER
Publication Status
Published
Date Publish Online
2014-07-09