Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs

Abstract

Eukaryotic transcriptomes are characterized by widespread transcription of noncoding and antisense RNAs1,2,3, which is linked to key chromosomal processes, such as chromatin remodelling, gene regulation and heterochromatin assembly4,5,6,7. However, these transcripts can be deleterious, and their accumulation is suppressed by several mechanisms including degradation by the nuclear exosome8,9. The mechanisms by which cells differentiate coding RNAs from transcripts targeted for degradation are not clear. Here we show that the variant histone H2A.Z, which is loaded preferentially at the 5′ ends of genes by the Swr1 complex containing a JmjC domain protein, mediates suppression of antisense transcripts in the fission yeast Schizosaccharomyces pombe genome. H2A.Z is partially redundant in this regard with the Clr4 (known as SUV39H in mammals)-containing heterochromatin silencing complex that is also distributed at euchromatic loci, and with RNA interference component Argonaute (Ago1). Loss of Clr4 or Ago1 alone has little effect on antisense transcript levels, but cells lacking either of these factors and H2A.Z show markedly increased levels of antisense RNAs that are normally degraded by the exosome. These analyses suggest that as well as performing other functions, H2A.Z is a component of a genome indexing mechanism that cooperates with heterochromatin and RNAi factors to suppress read-through antisense transcripts.

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Figure 1: Δpht1 causes upregulated antisense transcripts.
Figure 2: H2A.Z acts in a synergistic manner with ClrC and Ago1 to suppress antisense transcripts.
Figure 3: Read-through antisense transcripts are suppressed by the exosome.
Figure 4: H2A.Z and heterochromatin factors suppress antisense RNAs targeted by the exosome.

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Primary accessions

Gene Expression Omnibus

Data deposits

Microarray data are available at the NCBI Gene Expression Omnibus (GEO) repository under the accession number GSE17271.

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Acknowledgements

We thank K. Noma for strain constructions, D. McPheeters for the run-on protocol, M. Lichten, F. Reyes-Turcu, E. Bartlett and H. Cam for comments on the manuscript, P. Fitzgerald for designing microarrays, and D. Venzon for advice with data analyses. This research was supported by the Intramural Research Program, and under Contract N01-CO-12400 of the National Institutes of Health, National Cancer Institute.

Author Contributions M.Zo., T.F. and S.I.S.G. designed research, M.Zo., T.F., K.Z. and M.Zh. performed experiments, B.C. contributed reagents, M.Zo., T.F., T.D.V. and S.I.S.G. analysed data, and S.I.S.G. wrote the paper.

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Correspondence to Shiv I. S. Grewal.

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Zofall, M., Fischer, T., Zhang, K. et al. Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs. Nature 461, 419–422 (2009). https://doi.org/10.1038/nature08321

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