Global Effects on Gene Expression in Fission Yeast by Silencing and RNA Interference Machineries

Abstract

Histone modifications influence gene expression in complex ways. The RNA interference (RNAi) machinery can repress transcription by recruiting histone-modifying enzymes to chromatin, although it is not clear whether this is a general mechanism for gene silencing or whether it requires repeated sequences such as long terminal repeats (LTRs). We analyzed the global effects of the Clr3 and Clr6 histone deacetylases, the Clr4 methyltransferase, the zinc finger protein Clr1, and the RNAi proteins Dicer, RdRP, and Argonaute on the transcriptome of Schizosaccharomyces pombe (fission yeast). The clr mutants derepressed similar subsets of genes, many of which also became transcriptionally activated in cells that were exposed to environmental stresses such as nitrogen starvation. Many genes that were repressed by the Clr proteins clustered in extended regions close to the telomeres. Surprisingly few genes were repressed by both the silencing and RNAi machineries, with transcripts from centromeric repeats and Tf2 retrotransposons being notable exceptions. We found no correlation between repression by RNAi and proximity to LTRs, and the wtf family of repeated sequences seems to be repressed by histone deacetylation independent of RNAi. Our data indicate that the RNAi and Clr proteins show only a limited functional overlap and that the Clr proteins play more global roles in gene silencing.

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at http://mcb.asm.org/.

ACKNOWLEDGMENTS

We thank Stanley Brown and members of the Department of Genetics, University of Copenhagen, for comments on the manuscript and the experiments, Janne Verhein-Hansen for technical assistance, Nefeli Nikdaidou-Katsaridou and Al Ivens for array printing, Valerie Wood for help with data analysis, and Derek Goto for RT-PCR analysis of meu transcripts and for general resourcefulness.

We acknowledge the support of the National Science Foundation (grant DBI0077774 to R.M.), the National Institutes of Health (grant GM067014 to R.M.), Cancer Research UK (J.B.), the Novo Nordisk Foundation, and the Danish Research Council (G.T.). T.V. was supported by a postdoctoral fellowship from the National Cancer Institute.