An enhancer screen identifies new suppressors of small-RNA-mediated epigenetic gene silencing

Yukiko Shimada; Sarah H Carl; Merle Skribbe; Valentin Flury; Tahsin Kuzdere; Georg Kempf; Marc Bühler

doi:10.1371/journal.pgen.1009645

An enhancer screen identifies new suppressors of small-RNA-mediated epigenetic gene silencing

PLoS Genet. 2021 Jun 22;17(6):e1009645. doi: 10.1371/journal.pgen.1009645. eCollection 2021 Jun.

Authors

Yukiko Shimada¹, Sarah H Carl^{1

2}, Merle Skribbe^{1

3}, Valentin Flury^{1

3}, Tahsin Kuzdere^{1

3}, Georg Kempf¹, Marc Bühler^{1

3}

Affiliations

¹ Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
² Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
³ University of Basel, Basel, Switzerland.

Abstract

Small non-protein coding RNAs are involved in pathways that control the genome at the level of chromatin. In Schizosaccharomyces pombe, small interfering RNAs (siRNAs) are required for the faithful propagation of heterochromatin that is found at peri-centromeric repeats. In contrast to repetitive DNA, protein-coding genes are refractory to siRNA-mediated heterochromatin formation, unless siRNAs are expressed in mutant cells. Here we report the identification of 20 novel mutant alleles that enable de novo formation of heterochromatin at a euchromatic protein-coding gene by using trans-acting siRNAs as triggers. For example, a single amino acid substitution in the pre-mRNA cleavage factor Yth1 enables siRNAs to trigger silent chromatin formation with unparalleled efficiency. Our results are consistent with a kinetic nascent transcript processing model for the inhibition of small-RNA-directed de novo formation of heterochromatin and lay a foundation for further mechanistic dissection of cellular activities that counteract epigenetic gene silencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles
Amino Acid Substitution
Centromere / chemistry
Centromere / metabolism
Chromatin Assembly and Disassembly
Gene Expression Profiling
Gene Expression Regulation, Fungal*
Gene Silencing*
Heterochromatin / chemistry
Heterochromatin / metabolism
Kinetics
Models, Genetic
Molecular Sequence Annotation
Mutation
RNA, Messenger / genetics*
RNA, Messenger / metabolism
RNA, Small Interfering / genetics*
RNA, Small Interfering / metabolism
Schizosaccharomyces / genetics*
Schizosaccharomyces / metabolism
mRNA Cleavage and Polyadenylation Factors / genetics*
mRNA Cleavage and Polyadenylation Factors / metabolism

Substances

Heterochromatin
RNA, Messenger
RNA, Small Interfering
mRNA Cleavage and Polyadenylation Factors

Grants and funding

This work has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 681213 - REpiReg) (M.B.) and the Novartis Research Foundation (M.B.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.