The Schizosaccharomyces pombe JmjC-Protein, Msc1, Prevents H2A.Z Localization in Centromeric and Subtelomeric Chromatin Domains

Luke Buchanan,Karl Ekwall,Mickaël Durand-Dubief,Annelie Strålfors,Rein Aasland,Cagri Sakalar,Anna Shevchenko,A Francis Stewart,Brian Wilhelm,Assen Roguev,Andrej Shevchenko

doi:10.1371/journal.pgen.1000726

Abstract

Eukaryotic genomes are repetitively packaged into chromatin by nucleosomes, however they are regulated by the differences between nucleosomes, which establish various chromatin states. Local chromatin cues direct the inheritance and propagation of chromatin status via self-reinforcing epigenetic mechanisms. Replication-independent histone exchange could potentially perturb chromatin status if histone exchange chaperones, such as Swr1C, loaded histone variants into wrong sites. Here we show that in Schizosaccharomyces pombe, like Saccharomyces cerevisiae, Swr1C is required for loading H2A.Z into specific sites, including the promoters of lowly expressed genes. However S. pombe Swr1C has an extra subunit, Msc1, which is a JumonjiC-domain protein of the Lid/Jarid1 family. Deletion of Msc1 did not disrupt the S. pombe Swr1C or its ability to bind and load H2A.Z into euchromatin, however H2A.Z was ectopically found in the inner centromere and in subtelomeric chromatin. Normally this subtelomeric region not only lacks H2A.Z but also shows uniformly lower levels of H3K4me2, H4K5, and K12 acetylation than euchromatin and disproportionately contains the most lowly expressed genes during vegetative growth, including many meiotic-specific genes. Genes within and adjacent to subtelomeric chromatin become overexpressed in the absence of either Msc1, Swr1, or paradoxically H2A.Z itself. We also show that H2A.Z is N-terminally acetylated before, and lysine acetylated after, loading into chromatin and that it physically associates with the Nap1 histone chaperone. However, we find a negative correlation between the genomic distributions of H2A.Z and Nap1/Hrp1/Hrp3, suggesting that the Nap1 chaperones remove H2A.Z from chromatin. These data describe H2A.Z action in S. pombe and identify a new mode of chromatin surveillance and maintenance based on negative regulation of histone variant misincorporation.

Highlights

Chromatin is based on a repetitive structural unit called the nucleosome
The regulatory properties of chromatin are mediated by the differences between nucleosomes, due to posttranslational modifications or presence of histone variants
Swr1 complex (Swr1C) has a regulatory subunit, Msc1, which is not required for H2A.Z promoter loading but prevents H2A.Z occupancy in the inner centromere and subtelomeric regions

Summary

Introduction

Chromatin is based on a repetitive structural unit called the nucleosome. the regulatory properties of chromatin are mediated by the differences between nucleosomes, due to posttranslational modifications or presence of histone variants. Trimethylation of histone 3 at lysine 4 (H3K4me3) characterizes nucleosomes around RNAP II promoters [5] while incorporation of the histone 3 variant CENP-A characterizes nucleosomes of the inner centromere [6]. How these differences arise and propagate, often at individual nucleosomes, is not clear, clues are available. Self-reinforcing feed-forward mechanisms can explain the propagation of nucleosomal states [7,8,9] These mechanisms rely upon a physical connection between a protein that binds a histone modification with an enzyme that catalyzes the same modification. Notable examples include the association between H3K9 methyltransferase Clr and H3K9 methylation [10], and Spp and Set for H3K4 methylation [11]

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