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MacroH2A1.1 and PARP-1 cooperate to regulate transcription by promoting CBP-mediated H2B acetylation.

Chen H, Ruiz PD, Novikov L, Casill AD, Park JW, Gamble MJ - Nat. Struct. Mol. Biol. (2014)

Bottom Line: Here, we demonstrate that in primary human cells, macroH2A1 participates in two physically and functionally distinct types of chromatin marked by either H3K27me3 or nine histone acetylations.Using RNA sequencing, we found that macroH2A1-regulated genes, which have roles in cancer progression, are specifically found in macroH2A1-containing acetylated chromatin.Through the recruitment of PARP-1, macroH2A1.1 promotes the CBP-mediated acetylation of H2B K12 and K120, which either positively or negatively regulates the expression of macroH2A1-target genes.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, USA.

ABSTRACT
The histone variant macroH2A1 regulates gene expression important for differentiation, stem-cell reprogramming and tumor suppression. Here, we demonstrate that in primary human cells, macroH2A1 participates in two physically and functionally distinct types of chromatin marked by either H3K27me3 or nine histone acetylations. Using RNA sequencing, we found that macroH2A1-regulated genes, which have roles in cancer progression, are specifically found in macroH2A1-containing acetylated chromatin. Of the two macroH2A1 variants, macroH2A1.1 and macroH2A1.2, the former is suppressed in cancer and can interact with PARP-generated poly(ADP-ribose). Through the recruitment of PARP-1, macroH2A1.1 promotes the CBP-mediated acetylation of H2B K12 and K120, which either positively or negatively regulates the expression of macroH2A1-target genes. Although macroH2A1-regulated H2B acetylation is a common feature of primary cells, this regulation is typically lost in cancer cells. Consequently, our results provide insight into macroH2A1.1's role in cancer suppression.

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MacroH2A1-regulated genes are marked by specific histone acetylations.(a) Pie chart depicting the fraction of genes positively and negatively regulated by macroH2A1 depletion in IMR90 cells using RNA-seq with a cutoff of absolute Log2 fold change of 0.6 and a p < 0.05 (n = 3 independent cell cultures).(b) Meta-gene analysis of ChIP-seq data for the indicated histone marks from IMR90 cells. Genes were separated into macroH2A1-regulated (n=596) and unregulated groups (n=17,073). The data in each group represent ten 1 kb windows upstream of the TSS, 30 windows spanning the gene body, and ten 1 kb windows downstream of the end of the gene. The vertical dotted lines depict the location of the TSS (left) and the end of the gene (right).(c) All genes were divided into eight categories based on the presence of macroH2A1, H2BK12ac and H3K27me3 (see Supplementary Fig. 4). The enrichment of macroH2A1-regulated genes in each of the eight classes is expressed as the log2 odds ratio. Error bars, 95% confidence interval. * p < 0.01; ** p < 1×10−9 from Fisher’s exact tests.
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Figure 2: MacroH2A1-regulated genes are marked by specific histone acetylations.(a) Pie chart depicting the fraction of genes positively and negatively regulated by macroH2A1 depletion in IMR90 cells using RNA-seq with a cutoff of absolute Log2 fold change of 0.6 and a p < 0.05 (n = 3 independent cell cultures).(b) Meta-gene analysis of ChIP-seq data for the indicated histone marks from IMR90 cells. Genes were separated into macroH2A1-regulated (n=596) and unregulated groups (n=17,073). The data in each group represent ten 1 kb windows upstream of the TSS, 30 windows spanning the gene body, and ten 1 kb windows downstream of the end of the gene. The vertical dotted lines depict the location of the TSS (left) and the end of the gene (right).(c) All genes were divided into eight categories based on the presence of macroH2A1, H2BK12ac and H3K27me3 (see Supplementary Fig. 4). The enrichment of macroH2A1-regulated genes in each of the eight classes is expressed as the log2 odds ratio. Error bars, 95% confidence interval. * p < 0.01; ** p < 1×10−9 from Fisher’s exact tests.

Mentions: To understand how these different chromatin environments influence macroH2A1 function, we performed RNA-seq on control and macroH2A1-depleted IMR90 cells and identified 596 macroH2A1-regulated autosomal genes (Fig. 2a). IPA analysis indicated that macroH2A1 regulated genes are enriched for a variety of cancer related functions (Table 1 and Supplementary Table 3). Computational analysis of gene expression data from squamous cell lung cancer tumors indicated that macroH2A1-regulated genes, specifically those downregulated in macroH2A1-depleted IMR90 cells, are significantly enriched for genes with altered expression in lung cancer (Supplementary Fig. 2). Reduction of macroH2A1.1 levels, due to changes in alternative splicing are a hallmark of lung cancer10,12. We found that genes that positively correlated with changes in macroH2A1.1 splicing across the squamous cell lung cancer data are significantly enriched for genes positively regulated by macroH2A1 in IMR90 cells. Interestingly, loss of macroH2A1 in IMR90 cells enhanced cancer-relevant phenotypes including proliferation and anchorage-independent growth (Supplementary Fig. 2). Overall, these findings support a role for macroH2A1 in suppression of oncogenesis and metastasis10,12-15,29.


MacroH2A1.1 and PARP-1 cooperate to regulate transcription by promoting CBP-mediated H2B acetylation.

Chen H, Ruiz PD, Novikov L, Casill AD, Park JW, Gamble MJ - Nat. Struct. Mol. Biol. (2014)

MacroH2A1-regulated genes are marked by specific histone acetylations.(a) Pie chart depicting the fraction of genes positively and negatively regulated by macroH2A1 depletion in IMR90 cells using RNA-seq with a cutoff of absolute Log2 fold change of 0.6 and a p < 0.05 (n = 3 independent cell cultures).(b) Meta-gene analysis of ChIP-seq data for the indicated histone marks from IMR90 cells. Genes were separated into macroH2A1-regulated (n=596) and unregulated groups (n=17,073). The data in each group represent ten 1 kb windows upstream of the TSS, 30 windows spanning the gene body, and ten 1 kb windows downstream of the end of the gene. The vertical dotted lines depict the location of the TSS (left) and the end of the gene (right).(c) All genes were divided into eight categories based on the presence of macroH2A1, H2BK12ac and H3K27me3 (see Supplementary Fig. 4). The enrichment of macroH2A1-regulated genes in each of the eight classes is expressed as the log2 odds ratio. Error bars, 95% confidence interval. * p < 0.01; ** p < 1×10−9 from Fisher’s exact tests.
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Figure 2: MacroH2A1-regulated genes are marked by specific histone acetylations.(a) Pie chart depicting the fraction of genes positively and negatively regulated by macroH2A1 depletion in IMR90 cells using RNA-seq with a cutoff of absolute Log2 fold change of 0.6 and a p < 0.05 (n = 3 independent cell cultures).(b) Meta-gene analysis of ChIP-seq data for the indicated histone marks from IMR90 cells. Genes were separated into macroH2A1-regulated (n=596) and unregulated groups (n=17,073). The data in each group represent ten 1 kb windows upstream of the TSS, 30 windows spanning the gene body, and ten 1 kb windows downstream of the end of the gene. The vertical dotted lines depict the location of the TSS (left) and the end of the gene (right).(c) All genes were divided into eight categories based on the presence of macroH2A1, H2BK12ac and H3K27me3 (see Supplementary Fig. 4). The enrichment of macroH2A1-regulated genes in each of the eight classes is expressed as the log2 odds ratio. Error bars, 95% confidence interval. * p < 0.01; ** p < 1×10−9 from Fisher’s exact tests.
Mentions: To understand how these different chromatin environments influence macroH2A1 function, we performed RNA-seq on control and macroH2A1-depleted IMR90 cells and identified 596 macroH2A1-regulated autosomal genes (Fig. 2a). IPA analysis indicated that macroH2A1 regulated genes are enriched for a variety of cancer related functions (Table 1 and Supplementary Table 3). Computational analysis of gene expression data from squamous cell lung cancer tumors indicated that macroH2A1-regulated genes, specifically those downregulated in macroH2A1-depleted IMR90 cells, are significantly enriched for genes with altered expression in lung cancer (Supplementary Fig. 2). Reduction of macroH2A1.1 levels, due to changes in alternative splicing are a hallmark of lung cancer10,12. We found that genes that positively correlated with changes in macroH2A1.1 splicing across the squamous cell lung cancer data are significantly enriched for genes positively regulated by macroH2A1 in IMR90 cells. Interestingly, loss of macroH2A1 in IMR90 cells enhanced cancer-relevant phenotypes including proliferation and anchorage-independent growth (Supplementary Fig. 2). Overall, these findings support a role for macroH2A1 in suppression of oncogenesis and metastasis10,12-15,29.

Bottom Line: Here, we demonstrate that in primary human cells, macroH2A1 participates in two physically and functionally distinct types of chromatin marked by either H3K27me3 or nine histone acetylations.Using RNA sequencing, we found that macroH2A1-regulated genes, which have roles in cancer progression, are specifically found in macroH2A1-containing acetylated chromatin.Through the recruitment of PARP-1, macroH2A1.1 promotes the CBP-mediated acetylation of H2B K12 and K120, which either positively or negatively regulates the expression of macroH2A1-target genes.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, USA.

ABSTRACT
The histone variant macroH2A1 regulates gene expression important for differentiation, stem-cell reprogramming and tumor suppression. Here, we demonstrate that in primary human cells, macroH2A1 participates in two physically and functionally distinct types of chromatin marked by either H3K27me3 or nine histone acetylations. Using RNA sequencing, we found that macroH2A1-regulated genes, which have roles in cancer progression, are specifically found in macroH2A1-containing acetylated chromatin. Of the two macroH2A1 variants, macroH2A1.1 and macroH2A1.2, the former is suppressed in cancer and can interact with PARP-generated poly(ADP-ribose). Through the recruitment of PARP-1, macroH2A1.1 promotes the CBP-mediated acetylation of H2B K12 and K120, which either positively or negatively regulates the expression of macroH2A1-target genes. Although macroH2A1-regulated H2B acetylation is a common feature of primary cells, this regulation is typically lost in cancer cells. Consequently, our results provide insight into macroH2A1.1's role in cancer suppression.

Show MeSH
Related in: MedlinePlus