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H4K12ac is regulated by estrogen receptor-alpha and is associated with BRD4 function and inducible transcription.

Nagarajan S, Benito E, Fischer A, Johnsen SA - Oncotarget (2015)

Bottom Line: Similar to BRD4, we observed that H4K12ac occupancy increases near the transcription start sites (TSS) of estrogen-induced genes as well as at distal ERα binding sites in an estrogen-dependent manner.Interestingly, H4K12ac occupancy highly correlates with BRD4 binding and enhancer RNA production on ERα-positive enhancers.Consistent with an importance in estrogen-induced gene transcription, H4K12ac occupancy globally increased in ER-positive cells relative to ER-negative cells and these levels were further increased by estrogen treatment in an ERα-dependent manner.

View Article: PubMed Central - PubMed

Affiliation: Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany.

ABSTRACT
Hormone-dependent gene expression requires dynamic and coordinated epigenetic changes. Estrogen receptor-positive (ER+) breast cancer is particularly dependent upon extensive chromatin remodeling and changes in histone modifications for the induction of hormone-responsive gene expression. Our previous studies established an important role of bromodomain-containing protein-4 (BRD4) in promoting estrogen-regulated transcription and proliferation of ER+ breast cancer cells. Here, we investigated the association between genome-wide occupancy of histone H4 acetylation at lysine 12 (H4K12ac) and BRD4 in the context of estrogen-induced transcription. Similar to BRD4, we observed that H4K12ac occupancy increases near the transcription start sites (TSS) of estrogen-induced genes as well as at distal ERα binding sites in an estrogen-dependent manner. Interestingly, H4K12ac occupancy highly correlates with BRD4 binding and enhancer RNA production on ERα-positive enhancers. Consistent with an importance in estrogen-induced gene transcription, H4K12ac occupancy globally increased in ER-positive cells relative to ER-negative cells and these levels were further increased by estrogen treatment in an ERα-dependent manner. Together, these findings reveal a strong correlation between H4K12ac and BRD4 occupancy with estrogen-dependent gene transcription and further suggest that modulators of H4K12ac and BRD4 may serve as new therapeutic targets for hormone-dependent cancers.

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H4K12ac correlates with BRD4 binding in estrogen-induced enhancer function(A) Average genomic binding profiles of H4K12ac around distal EREs and 5 kb upstream and downstream under vehicle (Veh) and estrogen-treated (E2) conditions. X-axis shows the distance from distal EREs in kilobase pairs. Center of ERE is marked with black dotted line. (B) Heatmaps showing genomic binding profiles of H4K12ac around ERE and 5 kb upstream and downstream under vehicle (Veh) and estrogen-treated (E2) conditions. Center of the heatmap represents center of ERE. Color key of the heatmaps is shown on the side. (C) Correlation plot showing the heatmap with the Pearson's correlation coefficient values for H4K12ac, BRD4, H3K27ac, ERα, FOXA1, GRO-seq, RNAPII and H3K27me3 on distal EREs and 1.5 kb upstream and downstream region of estrogen-induced genes. Color key of the heatmap is shown at the bottom of the plot. (D) High, medium, low and  groups were classified according to the H4K12ac signal under estrogen-treated conditions and then heatmaps were plotted for various ChIP-seq signals (H4K12ac E2, BRD4, nascent RNA transcription (GRO-seq), RNAPII, ERα, FOXA1 and H3K27me3) around distal EREs and 5 kb upstream and downstream. Center of the heatmap represents center of the distal ERE region. Color key of the heatmaps is shown on the side.
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Figure 2: H4K12ac correlates with BRD4 binding in estrogen-induced enhancer function(A) Average genomic binding profiles of H4K12ac around distal EREs and 5 kb upstream and downstream under vehicle (Veh) and estrogen-treated (E2) conditions. X-axis shows the distance from distal EREs in kilobase pairs. Center of ERE is marked with black dotted line. (B) Heatmaps showing genomic binding profiles of H4K12ac around ERE and 5 kb upstream and downstream under vehicle (Veh) and estrogen-treated (E2) conditions. Center of the heatmap represents center of ERE. Color key of the heatmaps is shown on the side. (C) Correlation plot showing the heatmap with the Pearson's correlation coefficient values for H4K12ac, BRD4, H3K27ac, ERα, FOXA1, GRO-seq, RNAPII and H3K27me3 on distal EREs and 1.5 kb upstream and downstream region of estrogen-induced genes. Color key of the heatmap is shown at the bottom of the plot. (D) High, medium, low and groups were classified according to the H4K12ac signal under estrogen-treated conditions and then heatmaps were plotted for various ChIP-seq signals (H4K12ac E2, BRD4, nascent RNA transcription (GRO-seq), RNAPII, ERα, FOXA1 and H3K27me3) around distal EREs and 5 kb upstream and downstream. Center of the heatmap represents center of the distal ERE region. Color key of the heatmaps is shown on the side.

Mentions: Given the association of BRD4 with enhancers [23, 32] and its recently established role in promoting eRNA transcription [10, 26, 27], we examined whether H4K12ac occupancy is also preferentially enriched on ERα- and FOXA1-bound enhancers. Indeed, we observed H4K12ac enrichment on distal EREs and this enrichment significantly increased following estrogen treatment as shown in aggregate plot and heatmap analyses (Fig. 2A-B). To further examine the association of H4K12ac at distal ERα-bound enhancers, correlation plot and heatmaps were generated for BRD4, as well as ERα, FOXA1 and H3K27ac on these regions (Fig. 2C, Fig. S2A). We observed that BRD4 and H3K27ac occupancy correlated with H4K12ac on distal enhancers. Notably, apart from its association with FOXA1 and BRD4, ERα binding correlated particularly well with H4K12ac and lesser with H3K27ac. Interestingly, RNAPII occupancy and nascent RNA transcription on enhancers, which are indicative of eRNA production, also correlated with H4K12ac occupancy. Genomic Regions Enrichment of Annotations Tool (GREAT) analyses [43] on distal intergenic regions which exhibited overlapping peaks of H3K27ac, H4K12ac and BRD4 demonstrated an enrichment of estrogen and breast cancer luminal upregulated and basal downregulated-related pathways (Fig. S2B-C). These findings support a strong association among H4K12ac, H3K27ac, BRD4 and ERα function on distal enhancer regions.


H4K12ac is regulated by estrogen receptor-alpha and is associated with BRD4 function and inducible transcription.

Nagarajan S, Benito E, Fischer A, Johnsen SA - Oncotarget (2015)

H4K12ac correlates with BRD4 binding in estrogen-induced enhancer function(A) Average genomic binding profiles of H4K12ac around distal EREs and 5 kb upstream and downstream under vehicle (Veh) and estrogen-treated (E2) conditions. X-axis shows the distance from distal EREs in kilobase pairs. Center of ERE is marked with black dotted line. (B) Heatmaps showing genomic binding profiles of H4K12ac around ERE and 5 kb upstream and downstream under vehicle (Veh) and estrogen-treated (E2) conditions. Center of the heatmap represents center of ERE. Color key of the heatmaps is shown on the side. (C) Correlation plot showing the heatmap with the Pearson's correlation coefficient values for H4K12ac, BRD4, H3K27ac, ERα, FOXA1, GRO-seq, RNAPII and H3K27me3 on distal EREs and 1.5 kb upstream and downstream region of estrogen-induced genes. Color key of the heatmap is shown at the bottom of the plot. (D) High, medium, low and  groups were classified according to the H4K12ac signal under estrogen-treated conditions and then heatmaps were plotted for various ChIP-seq signals (H4K12ac E2, BRD4, nascent RNA transcription (GRO-seq), RNAPII, ERα, FOXA1 and H3K27me3) around distal EREs and 5 kb upstream and downstream. Center of the heatmap represents center of the distal ERE region. Color key of the heatmaps is shown on the side.
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Figure 2: H4K12ac correlates with BRD4 binding in estrogen-induced enhancer function(A) Average genomic binding profiles of H4K12ac around distal EREs and 5 kb upstream and downstream under vehicle (Veh) and estrogen-treated (E2) conditions. X-axis shows the distance from distal EREs in kilobase pairs. Center of ERE is marked with black dotted line. (B) Heatmaps showing genomic binding profiles of H4K12ac around ERE and 5 kb upstream and downstream under vehicle (Veh) and estrogen-treated (E2) conditions. Center of the heatmap represents center of ERE. Color key of the heatmaps is shown on the side. (C) Correlation plot showing the heatmap with the Pearson's correlation coefficient values for H4K12ac, BRD4, H3K27ac, ERα, FOXA1, GRO-seq, RNAPII and H3K27me3 on distal EREs and 1.5 kb upstream and downstream region of estrogen-induced genes. Color key of the heatmap is shown at the bottom of the plot. (D) High, medium, low and groups were classified according to the H4K12ac signal under estrogen-treated conditions and then heatmaps were plotted for various ChIP-seq signals (H4K12ac E2, BRD4, nascent RNA transcription (GRO-seq), RNAPII, ERα, FOXA1 and H3K27me3) around distal EREs and 5 kb upstream and downstream. Center of the heatmap represents center of the distal ERE region. Color key of the heatmaps is shown on the side.
Mentions: Given the association of BRD4 with enhancers [23, 32] and its recently established role in promoting eRNA transcription [10, 26, 27], we examined whether H4K12ac occupancy is also preferentially enriched on ERα- and FOXA1-bound enhancers. Indeed, we observed H4K12ac enrichment on distal EREs and this enrichment significantly increased following estrogen treatment as shown in aggregate plot and heatmap analyses (Fig. 2A-B). To further examine the association of H4K12ac at distal ERα-bound enhancers, correlation plot and heatmaps were generated for BRD4, as well as ERα, FOXA1 and H3K27ac on these regions (Fig. 2C, Fig. S2A). We observed that BRD4 and H3K27ac occupancy correlated with H4K12ac on distal enhancers. Notably, apart from its association with FOXA1 and BRD4, ERα binding correlated particularly well with H4K12ac and lesser with H3K27ac. Interestingly, RNAPII occupancy and nascent RNA transcription on enhancers, which are indicative of eRNA production, also correlated with H4K12ac occupancy. Genomic Regions Enrichment of Annotations Tool (GREAT) analyses [43] on distal intergenic regions which exhibited overlapping peaks of H3K27ac, H4K12ac and BRD4 demonstrated an enrichment of estrogen and breast cancer luminal upregulated and basal downregulated-related pathways (Fig. S2B-C). These findings support a strong association among H4K12ac, H3K27ac, BRD4 and ERα function on distal enhancer regions.

Bottom Line: Similar to BRD4, we observed that H4K12ac occupancy increases near the transcription start sites (TSS) of estrogen-induced genes as well as at distal ERα binding sites in an estrogen-dependent manner.Interestingly, H4K12ac occupancy highly correlates with BRD4 binding and enhancer RNA production on ERα-positive enhancers.Consistent with an importance in estrogen-induced gene transcription, H4K12ac occupancy globally increased in ER-positive cells relative to ER-negative cells and these levels were further increased by estrogen treatment in an ERα-dependent manner.

View Article: PubMed Central - PubMed

Affiliation: Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany.

ABSTRACT
Hormone-dependent gene expression requires dynamic and coordinated epigenetic changes. Estrogen receptor-positive (ER+) breast cancer is particularly dependent upon extensive chromatin remodeling and changes in histone modifications for the induction of hormone-responsive gene expression. Our previous studies established an important role of bromodomain-containing protein-4 (BRD4) in promoting estrogen-regulated transcription and proliferation of ER+ breast cancer cells. Here, we investigated the association between genome-wide occupancy of histone H4 acetylation at lysine 12 (H4K12ac) and BRD4 in the context of estrogen-induced transcription. Similar to BRD4, we observed that H4K12ac occupancy increases near the transcription start sites (TSS) of estrogen-induced genes as well as at distal ERα binding sites in an estrogen-dependent manner. Interestingly, H4K12ac occupancy highly correlates with BRD4 binding and enhancer RNA production on ERα-positive enhancers. Consistent with an importance in estrogen-induced gene transcription, H4K12ac occupancy globally increased in ER-positive cells relative to ER-negative cells and these levels were further increased by estrogen treatment in an ERα-dependent manner. Together, these findings reveal a strong correlation between H4K12ac and BRD4 occupancy with estrogen-dependent gene transcription and further suggest that modulators of H4K12ac and BRD4 may serve as new therapeutic targets for hormone-dependent cancers.

Show MeSH
Related in: MedlinePlus