Distinct roles of HDAC complexes in promoter silencing, antisense suppression and DNA damage protection

Abstract

Histone acetylation is important in regulating DNA accessibility. Multifunctional Sin3 proteins bind histone deacetylases (HDACs) to assemble silencing complexes that selectively target chromatin. We show that, in fission yeast, an essential HDAC, Clr6, exists in two distinct Sin3 core complexes. Complex I contains an essential Sin3 homolog, Pst1, and other factors, and predominantly targets gene promoters. Complex II contains a nonessential Sin3 homolog, Pst2, and several conserved proteins. It preferentially targets transcribed chromosomal regions and centromere cores. Defects in complex II abrogate global protective functions of chromatin, causing increased accessibility of DNA to genotoxic agents and widespread antisense transcripts that are processed by the exosome. Notably, the two Clr6 complexes differentially repress forward and reverse centromeric repeat transcripts, suggesting that these complexes regulate transcription in heterochromatin and euchromatin in similar manners, including suppression of spurious transcripts from cryptic start sites.

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Figure 1: Identification of Clr6 and Alp13 binding partners.
Figure 2: Clr6 forms distinct complexes: I/I′ and II.
Figure 3: Clr6 complexes have different roles in histone deacetylation.
Figure 4: Clr6 complex II represses antisense transcription.
Figure 5: Complexes I and II repress centromeric repeats.
Figure 6: Rrp6 and Set2 both regulate antisense transcripts.
Figure 7: Complexes I and II have distinct roles in maintaining genomic integrity.
Figure 8: Model showing differential roles of the Clr6 complexes.

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Acknowledgements

We thank J. Nakayama and A. Malikzay for helpful contributions, H. Levin (National Institute of Child Health and Human Development, NIH), K. Ekwall (Karolinska Institutet), R. Maraia (National Institute of Child Health and Human Development, NIH) for strains, M. Lichten, O. Sordet and J. Sabl for help in editing the manuscript and K. Noma, G. Mizuguchi, D. Eyre and M. Lichten for helpful discussions and protocols. This research was supported by the Intramural Research Program of the NIH, National Cancer Institute.

Author information

S.I.S.G. and E.N. designed experiments; E.N. performed all biochemical and genetic experiments; E.N and H.P.C. performed the microarray experiments; T.Y. analyzed DNA prepared from bleomycin-treated cells by pulse-field gel electrophoresis; R.K. analyzed purified protein samples by mass spectrometry; P.C.F. helped analyze microarray expression data; S.I.S.G and E.N. wrote the paper; S.I.S.G. and H.P.C. edited the paper.

Correspondence to Shiv I S Grewal.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Genetic and biochemical characterization of Clr6-associated factors. (PDF 3008 kb)

Supplementary Fig. 2

Complexes I and II differentially affect histone acetylation at the promoters and the coding regions of genes. (PDF 222 kb)

Supplementary Fig. 3

Complexes I and II preferentially regulate sense and antisense transcripts. (PDF 63 kb)

Supplementary Fig. 4

Complex II suppresses antisense transcription at the zer1 and hrp1 coding regions. (PDF 558 kb)

Supplementary Fig. 5

Antisense transcription does not correlate with detectable levels of heterochromatic modifications at euchromatic loci. (PDF 2626 kb)

Supplementary Fig. 6

Complex I, but not complex II, is required for silencing of donor mating-type loci. (PDF 553 kb)

Supplementary Fig. 7

Distribution of H3K9 methylation in alp13rrp6 double mutant strain. (PDF 927 kb)

Supplementary Fig. 8

set2 and rrp6 mutant strains are sensitive to bleomycin treatment. (PDF 260 kb)

Supplementary Table 1

Loci showing upregulated antisense transcripts in alp13Δ mutant background. (PDF 39 kb)

Supplementary Table 2

Clr6 complex I and complex II subunits in S. pombe and their homologs in S. cerevisiae and mammals. (PDF 92 kb)

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Nicolas, E., Yamada, T., Cam, H. et al. Distinct roles of HDAC complexes in promoter silencing, antisense suppression and DNA damage protection. Nat Struct Mol Biol 14, 372–380 (2007). https://doi.org/10.1038/nsmb1239

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