H3K9me-Independent Gene Silencing in Fission Yeast Heterochromatin by Clr5 and Histone Deacetylases

Klavs R Hansen,Idit Hazan,Jürg Bähler,Janne Verhein-Hansen,Stephen Watt,Amikam Cohen,Robert A Martienssen,Sreenath Shanker,Janet F Partridge,Geneviève Thon

doi:10.1371/journal.pgen.1001268

Abstract

Nucleosomes in heterochromatic regions bear histone modifications that distinguish them from euchromatic nucleosomes. Among those, histone H3 lysine 9 methylation (H3K9me) and hypoacetylation have been evolutionarily conserved and are found in both multicellular eukaryotes and single-cell model organisms such as fission yeast. In spite of numerous studies, the relative contributions of the various heterochromatic histone marks to the properties of heterochromatin remain largely undefined. Here, we report that silencing of the fission yeast mating-type cassettes, which are located in a well-characterized heterochromatic region, is hardly affected in cells lacking the H3K9 methyltransferase Clr4. We document the existence of a pathway parallel to H3K9me ensuring gene repression in the absence of Clr4 and identify a silencing factor central to this pathway, Clr5. We find that Clr5 controls gene expression at multiple chromosomal locations in addition to affecting the mating-type region. The histone deacetylase Clr6 acts in the same pathway as Clr5, at least for its effects in the mating-type region, and on a subset of other targets, notably a region recently found to be prone to neo-centromere formation. The genomic targets of Clr5 also include Ste11, a master regulator of sexual differentiation. Hence Clr5, like the multi-functional Atf1 transcription factor which also modulates chromatin structure in the mating-type region, controls sexual differentiation and genome integrity at several levels. Globally, our results point to histone deacetylases as prominent repressors of gene expression in fission yeast heterochromatin. These deacetylases can act in concert with, or independently of, the widely studied H3K9me mark to influence gene silencing at heterochromatic loci.

Highlights

The mating-type region of the fission yeast Schizosaccharomyces pombe affords a well-defined system to investigate how heterochromatic histone modifications affect gene expression [1] (Figure 1A)
In eukaryotes some histone modifications are preponderantly associated with silent chromosomal domains, the extent to which distinct modifications contribute to the silencing of gene expression is often not known
Contrary to a general assumption, we found that genes naturally present in the mating-type region of wildtype strains remain repressed in the absence of the H3K9 methyltransferase Clr4

Summary

Introduction

The mating-type region of the fission yeast Schizosaccharomyces pombe affords a well-defined system to investigate how heterochromatic histone modifications affect gene expression [1] (Figure 1A). Mat2-P and mat3-M contain the same genes and internal promoters of transcription as mat, these two cassettes are not expressed. They act as donors for gene conversions of mat in a process leading to matingtype switching. The tight gene silencing of mat2-P and mat3-M is essential for the viability of vegetative cells because co-expression of the P and M mating-type information triggers meiosis in starved cells [2]. Co-expression of the P and M mating-type information in haploid cells on the other hand, as might happen following expression of mat2-P and mat3-M, leads to haploid meiosis and cell death [2]

Methods

Results

Discussion

Conclusion