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Cell cycle- and chaperone-mediated regulation of H3K56ac incorporation in yeast

ABSTRACT: Acetylation of histone H3 lysine 56 is a covalent modification best-known as a mark of newly-replicated chromatin, but has also been linked to replication-independent histone replacement. Here, we measured H3K56ac levels at single-nucleosome resolution in asynchronously growing yeast cultures, as well as in yeast proceeding synchronously through the cell cycle. We developed a quantitative model of H3K56ac kinetics, which shows that H3K56ac is largely explained by the genomic replication timing and the turnover rate of each nucleosome, suggesting that cell cycle profiles of H3K56ac should reveal most first-time nucleosome incorporation events. However, since the deacetylases Hst3/4 prevent use of H3K56ac as a marker for histone deposition during M phase, we also directly measured M phase histone replacement rates. We report a global decrease in turnover rates during M phase, and a further specific decrease in turnover among early origins of replication, which switch from rapidly-replaced in G1 phase to stable-bound during M phase. Finally, by measuring H3 replacement in yeast deleted for the H3K56 acetyltransferase Rtt109 and its two co-chaperones Asf1 and Vps75, we find evidence that Rtt109 and Asf1 preferentially enhance histone replacement at rapidly-replaced nucleosomes, whereas Vps75 appears to inhibit histone turnover at those loci. These results provide a broad perspective on histone replacement/incorporation throughout the cell cycle, and suggest that H3K56 acetylation provides a positive feedback loop by which replacement of a nucleosome enhances subsequent replacement at the same location.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE12822 | GEO | 2008/10/04

SECONDARY ACCESSION(S): PRJNA111129

REPOSITORIES: GEO

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Project description:Acetylation of histone H3 lysine 56 is a covalent modification best-known as a mark of newly-replicated chromatin, but has also been linked to replication-independent histone replacement. Here, we measured H3K56ac levels at single-nucleosome resolution in asynchronously growing yeast cultures, as well as in yeast proceeding synchronously through the cell cycle. We developed a quantitative model of H3K56ac kinetics, which shows that H3K56ac is largely explained by the genomic replication timing and the turnover rate of each nucleosome, suggesting that cell cycle profiles of H3K56ac should reveal most first-time nucleosome incorporation events. However, since the deacetylases Hst3/4 prevent use of H3K56ac as a marker for histone deposition during M phase, we also directly measured M phase histone replacement rates. We report a global decrease in turnover rates during M phase, and a further specific decrease in turnover among early origins of replication, which switch from rapidly-replaced in G1 phase to stable-bound during M phase. Finally, by measuring H3 replacement in yeast deleted for the H3K56 acetyltransferase Rtt109 and its two co-chaperones Asf1 and Vps75, we find evidence that Rtt109 and Asf1 preferentially enhance histone replacement at rapidly-replaced nucleosomes, whereas Vps75 appears to inhibit histone turnover at those loci. These results provide a broad perspective on histone replacement/incorporation throughout the cell cycle, and suggest that H3K56 acetylation provides a positive feedback loop by which replacement of a nucleosome enhances subsequent replacement at the same location. To characterize incorporation of H3K56ac in yeast, several sets of ChIP-chip experiments were performed, along with a set of gene expression microarrays. The following describes each individual set, the number of biological and array replicates performed, dye-flip replicates if performed, the total number of arrays, and the applicable figures in the manuscript. Except for Item D (gene expression), all arrays were ChIP-chip experiments. A. Mid-log H3K56ac measurement. 3 biological replicates, 1 array replicate each of K56Ac ChIP with Grunstein Lab antibody. 2 biological replicates, 2 array replicates each of K56Ac ChIP with Upstate antibody. 7 total arrays. Figure 1A-C, 3, S1, S2A, S6, S7. B. Cell cycle - H3K56ac measurements. 1 biological replicate, 3 array replicates each of K56Ac ChIP with Upstate antibody. 17 time points (10 min. unavailable in third array replicate). 50 total arrays. Figures 2, 3, 4, S4, S5, S7, S8. C. G1 phase turnover. 1 biological replicate (3 time points) with 1 dye-flip replicate each time point (45 minutes replaced with 60 minutes for dye-flip replicate). 6 total arrays. Tables S2, S3. D. Cell cycle - mRNA measurements. 2 biological replicates, 1 array replicate each. 34 total arrays. Figure S3. E. M phase turnover rates. 2 biological replicates, second biological replicate has one dye-flip replicate. 17 total arrays. Figure 5. F. Deletion mutants in H3K56ac pathway for G1-arrested cells. Strains: wild-type parental strain (PKY4212; 2 biological replicates), asf1D (strain 2 biological replicates), vps75D (3 biological replicates, third biological replicate having two array replicates), rtt109D (2 biological replicates, each with one dye-flip replicate). 12 total arrays. Figure 6.

Project description:Histones are the protein components of the basic unit of chromatin, the core particle of the nucleosome. They play a central role in defining chromatin states associated with distinct cell fates and are classified into replicative and non-replicative/replacement histone variants. While the latter do not exhibit S phase regulation in their expression, the replicative histone variants show a major peak in expression early during S phase to support chromatin assembly during replication of the genome. Their expression is tightly regulated during the cell-cycle both transcriptionally and post-transcriptionally and involves a number of actors. During replication in human cells, two main chaperones ensure the deposition of H3-H4 onto DNA: Chromatin assembly factor 1 (CAF-1) and Anti-silencing factor 1 (ASF1). Interestingly, on the one hand, ASF1 binds the newly synthesized replicative histones H3.1/H3.2-H4 to hand them off to the downstream chaperone, CAF-1, for deposition onto the duplicated DNA strands in a DNA synthesis-coupled (DSC) manner. On the other hand, ASF1 also promotes the recycling of parental histones during replication. In addition, ASF1 binds the non-replicative variant H3.3 and hands it off to the downstream chaperone Histone regulator A (HIRA) for deposition of H3.3 in a DNA synthesis independent (DSI) manner. Finally, in human cells, ASF1 but not CAF-1, also provides a buffering system for histone excess generated in response to stalled replication, indicating yet another role for ASF1 in regulating the flow of replicative histones in higher eukaryotes. However, to date, roles of these chaperones in histone RNA metabolism in mammals had remained unexplored. This is particularly interesting to consider given that in budding yeast, where there are no distinct replicative and non-replicative H3 variants, the single ASF1 ortholog participates in activating transcription of histone genes in S phase and transcriptional repression outside S phase in combination with Hir1, the budding yeast counterpart of HIRA. We thus decided to explore how the key histone chaperones involved in DNA synthesis-coupled chromatin assembly could contribute to the critical regulation of expression of replicative histone genes in human cells during S phase. From total RNA extracted from asynchronous and synchronized human cells, we performed RNA-seq and found that most of the annotated replicative histone genes decreased in expression upon ASF1 depletion by siRNA during S phase compared to the control condition with siRNA againt GFP. However, by 4sU-labeled RNA-seq we detected an increase in newly synthesized replicative histone transcripts. These findings indicate that the decrease in expression of replicative histone genes in ASF1-depleted cells cannot be due to a decrease at the level of transcription. We then inspected closely the sequences at the 3’ end of the replicative histone transcripts in our RNA-seq data and detected a defect of their 3’ processing. Thus, we propose that in mammals ASF1 plays a role in the unique regulation of replicative histone RNA metabolism.

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Cell cycle- and chaperone-mediated regulation of H3K56ac incorporation in yeast

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