Evolution and Functional Trajectory of Sir1 in Gene Silencing

Abstract

We used the budding yeasts Saccharomyces cerevisiae and Torulaspora delbrueckii to examine the evolution of Sir-based silencing, focusing on Sir1, silencers, the molecular topography of silenced chromatin, and the roles of SIR and RNA interference (RNAi) genes in T. delbrueckii. Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) analysis of Sir proteins in T. delbrueckii revealed a different topography of chromatin at the HML and HMR loci than was observed in S. cerevisiae. S. cerevisiae Sir1, enriched at the silencers of HMLα and HMRa, was absent from telomeres and did not repress subtelomeric genes. In contrast to S. cerevisiae SIR1's partially dispensable role in silencing, the T. delbrueckii SIR1 paralog KOS3 was essential for silencing. KOS3 was also found at telomeres with T. delbrueckii Sir2 (Td-Sir2) and Td-Sir4 and repressed subtelomeric genes. Silencer mapping in T. delbrueckii revealed single silencers at HML and HMR, bound by Td-Kos3, Td-Sir2, and Td-Sir4. The KOS3 gene mapped near HMR, and its expression was regulated by Sir-based silencing, providing feedback regulation of a silencing protein by silencing. In contrast to the prominent role of Sir proteins in silencing, T. delbrueckii RNAi genes AGO1 and DCR1 did not function in heterochromatin formation. These results highlighted the shifting role of silencing genes and the diverse chromatin architectures underlying heterochromatin.

Supplemental material for this article may be found at http://dx.doi.org/10.1128/MCB.01013-15.

ACKNOWLEDGMENTS

This work was supported by an NSF predoctoral fellowship to A.E. and by a grant from the National Institutes of Health to J.R. (GM31105). We thank the Vincent J. Coates Genomics Sequencing Laboratory at the University of California, Berkeley, supported by National Institutes of Health S10 Instrumentation grants S10-RR029668 and S10-RR027303.

We also thank Devin Scannell for generously providing Torulaspora strains, Peter Combs and Jackie Villalta for sequencing reagents, and members of the Rine laboratory for thoughtful discussion, especially Oliver Zill and Debbie Thurtle.

Additional information

Funding

National Science Foundation (NSF) provided funding to Aisha Ellahi through a Graduate Research Fellowship.