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. 2011 Jan 7;41(1):56-66.
doi: 10.1016/j.molcel.2010.12.009.

Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci

Kenichi Yamane  1 , Takeshi Mizuguchi, Bowen Cui, Martin Zofall, Ken-ichi Noma, Shiv I S Grewal
Affiliations

Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci

Kenichi Yamane et al. Mol Cell. .

Abstract

Heterochromatin impacts various nuclear processes by providing a recruiting platform for diverse chromosomal proteins. In fission yeast, HP1 proteins Chp2 and Swi6, which bind to methylated histone H3 lysine 9, associate with SHREC (Snf2/HDAC repressor complex) and Clr6 histone deacetylases (HDACs) involved in heterochromatic silencing. However, heterochromatic silencing machinery is not fully defined. We describe a histone chaperone complex containing Asf1 and HIRA that spreads across silenced domains via its association with Swi6 to enforce transcriptional silencing. Asf1 functions in concert with a Clr6 HDAC complex to silence heterochromatic repeats, and it suppresses antisense transcription by promoting histone deacetylation. Furthermore, we demonstrate that Asf1 and SHREC facilitate nucleosome occupancy at heterochromatic regions but TFIIIC transcription factor binding sites within boundary elements are refractory to these factors. These analyses uncover a role for Asf1 in global histone deacetylation and suggest that HP1-associated histone chaperone promotes nucleosome occupancy to assemble repressive heterochromatin.

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Figures

Figure 1
Figure 1. Asf1 Affects Heterochromatic Silencing in S. pombe
(A) Purification of Asf1 and CAF-1. SDS-PAGE followed by coomassie blue staining of untagged control, Asf1-TAP and Pcf3-TAP purification. Purified fractions were subjected to tandem MS (LC-MS/MS). (B) Coomassie blue staining of Asf1-TAP purification from wild type and asf1-1 mutant. (C) Heterochromatic silencing of reporter genes inserted at pericentromeric repeats (otr1R::ura4+) and silent mat locus (Kint2::ura4+). Serial dilution plating on counter-selective fluoroorotic acid (FOA) medium used to assay ura4+ expression. (D) asf1-1 affects silencing of heterochromatic repeats and Tf2. qPCR was used to assay expression of indicated loci. Values shown were normalized to act1+ expression. Error bars indicate standard deviations from three independent experiments. (E) Defective TGS in mutants results in elevated levels of dg/dh siRNAs. siRNAs levels were analyzed by northern blot. (F) Mutations in Asf1/HIRA impair mating-type switching. In contrast to colonies formed by wild-type homothallic (h90) cells, which switch mating-type efficiently and stain dark with iodine vapors, colonies formed by h90 asf1 and HIRA mutants stain light, owing to defective mating-type switching. Δclr4 is shown as a control.
Figure 2
Figure 2. Swi6-dependent and –independent Localization of Histone Chaperone
(A) asf1-1 and hip1Δ maintain heterochromatin signatures of H3K9me, Swi6, and Chp2. Strains carrying otr1R::ura4+ and ura4DS/E minigene at the endogenous locus were used to perform ChIP. Intensities of bands representing otr1R::ura4+ and ura4DS/E in ChIP and input lanes were used to calculate relative fold enrichment values shown. (B) qPCR using DNA isolated from either immunoprecipitated chromatin or input DNA was used to calculate relative fold enrichment at centromeres. Error bars indicate standard deviations from three independent experiments. (C) Swi6 interacts with Hip1. Strains expressing functional FLAG-epitope tagged Hip1 (Hip1-FLAG) and/or TAP-tagged Swi6 (TAP-Swi6) were used to perform purification. Purified fractions from untagged or TAP-tagged Swi6 samples were analyzed by western blotting using anti-FLAG antibody. (D and E) Hip1 localization across silent mat locus and subtelomeres requires Swi6. ChIP-chip was used to determine Hip1-FLAG distribution in wild type and swi6Δ cells. At silent mat locus, heterochromatic domain containing mat2 and mat3 loci as well as cenH is surrounded by IR-L and IR-R boundary elements. The subtelomeric region of right arm of chromosome II includes tlh2 gene sharing homology to dh, LTRs (blue boxes) and ORFs (open boxes).
Figure 3
Figure 3. Asf1 Acts in Concert with Clr6 HDAC to Promote Heterochromatic Silencing
(A) The expression levels of dg [otr(dg)] and dh [otr(dh)] centromeric repeats and cenH in indicated strains were analyzed by qPCR. All values were normalized to act1+ expression. Error bars indicate standard deviations from three independent experiments. (B) Asf1 interacts with Clr6 complex-II. Strain expressing FLAG-tagged Asf1 (Asf1-FLAG) or control untagged strain was used to perform the immunoaffinity purification using anti-FLAG antibody. Purified fractions were analyzed by western blotting with antibodies against Alp13 and Clr6. (C) asf1-1 and hip1Δ show increase in bulk histone acetylation levels, similar to alp13Δ. Histones extracted from indicated strains were analyzed by western blotting using anti-H3K9ac and anti-H3 antibodies. (D and E) ChIP-chip analyses of histone acetylation were performed using anti-H3K9ac antibody. Percentage of upregulated probes (mutant/WT signal intensity ratio > 1.5) corresponding to ORF and intergenic regions are plotted (D). Like alp13Δ, asf1-1 shows increased acetylation in coding regions of genes. A representative region of the genome is shown (E).
Figure 4
Figure 4. Asf1 Suppresses Antisense Transcription and Protects Genomic Integrity
(A) Expression profiling of asf1-1, hip1Δ, and alp13Δ was performed using microarrays containing probes corresponding to both DNA strands. Changes in RNA signal intensities were calculated for each probe. Plotted are number and percentage of upregulated probes (mutant/WT signal intensity ratio > 1.5) corresponding to sense and antisense strands. (B) asf1 and hip1 mutants show antisense upregulation at loci affected by alp13Δ. Ratios of RNA signal intensities for forward and reverse strand probes in mutant versus wild type were converted to color codes and plotted. Black rectangles on top and bottom of solid line indicate genes transcribed in forward and reverse directions, respectively. (C) High resolution view of antisense upregulation at hrp1 gene. Strand-specific RT-PCR performed using RNA prepared from indicated strains is shown. (D) Hierarchical clustering of mutants based on similarities in the distribution of upregulated antisense RNAs. Pearson’s correlation coefficients calculated from pairwise comparisons of mutant expression profiles were converted into color codes. (E) Asf1 and Alp13 protect DNA from damage by genotoxins. Chromosomal DNA samples from indicated strains treated with 0 or 0.5mU/ ml bleomycin for 90 minutes were analyzed by pulse-field gel electrophoresis.
Figure 5
Figure 5. Asf1 and SHREC Promote Nucleosome Occupancy at Heterochromatic Loci
Nucleosome occupancies in wild type, clr3-735 (which carry D232N mutation in Clr3 HDAC domain), asf1-1 and clr3-735 asf1-1 mutants were measured using MNase-chip. Major heterochromatic regions at silent mat locus (A), centromere 2 (B) and subtelomeric region (C) were analyzed for differences in nucleosome occupancy. The regions showing minimum log2 difference of 2 between wild type and clr3-735asf1-1 datasets are highlighted. Red arrows indicate regions showing lower nucleosome occupancy in single and/or double mutants as compared to wild type. Schematic diagrams indicating main features of heterochromatin domains are included (A-C). (A) At silent mat locus, heterochromatic domain containing mat2 and mat3 loci as well as cenH is surrounded by IR-L and IR-R boundary elements. REII and REIII represent cis-acting silencers. (B) At centromeres, heterochromatin coats dg/dh repeats and a portion of inner repeats (imr) that surround central (cnt) core domain. Vertical black lines and boxes indicate individual copies or clusters of tRNAs. (C) Heterochromatin at subtelomeric loci covers several ORFs including SPAC212.11 sharing homology to dh. Blue lines denote LTRs.
Figure 6
Figure 6. Nucleosome Occupancy at a Recombinational Enhancer and Boundary Elements
(A) Nucleosome occupancies in indicated mutants, as determined by MNase-chip, are plotted for a region containing mat3M, SRE element containing Swi2-binding site, and IR-R boundary element. Blue arrows indicate NFRs unaffected by mutations in Asf1 or SHREC. Red arrow indicates location of an NFR in IR-R most prominent in asf1clr3 double mutant. (B) DNaseI- or MNase-treated chromatin fractions from wild-type cells were digested with HindIII and then analyzed by Southern blotting with a mat-specific probe (black rectangle). Lane N indicates naked DNA treated with MNase. HS1 and HS2 indicate the positions of DNaseI and MNase hypersensitive sites.
Figure 7
Figure 7. Model Showing Involvement of HP1-associated Asf1/HIRA, Clr6 and SHREC in Histone Deacetylation and Nucleosome Occupancy at Heterochromatic Regions
RNAPII transcription of dg/dh repeats generates transcripts that are processed by RNAi machinery (RITS, RNA-dependent RNA polymerase, Rdp1, and Dicer, Dcr1) into siRNAs. Asf1 facilitates histone deacetylation by Clr6 complex-II after the passage of RNAP II to reassemble repressive chromatin. Clr4 binding to H3K9me via its chromodomain facilitates heterochromatin spreading. H3K9me also recruits Chp1, Chp2 and Swi6. Whereas Chp1 tethers RNAi machinery to chromatin for cis-PTGS, Chp2 and Swi6 associate with Asf1/HIRA, Clr6-complex-II and/or SHREC involved in deacetylation of histones and transcriptional silencing. Asf1/HIRA and SHREC promote nucleosome occupancy and positioning to exclude NFRs, which is presumably critical for preventing access to transcriptional and recombinational machineries. The prevention of nucleosome turnover by these effectors may have important implications for the maintenance of heterochromatin.
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