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Transcription-coupled recruitment of human CHD1 and CHD2 influences chromatin accessibility and histone H3 and H3.3 occupancy at active chromatin regions.

Siggens L, Cordeddu L, Rönnerblad M, Lennartsson A, Ekwall K - Epigenetics Chromatin (2015)

Bottom Line: CHD2 depletion causes increased histone H3 and reduced histone variant H3.3 occupancy.We conclude that transcription-coupled recruitment of CHD1 and CHD2 occurs at transcribed gene TSSs and at intragenic and intergenic enhancer-like sites.The recruitment of CHD1 and CHD2 regulates the architecture of active chromatin regions through chromatin accessibility and nucleosome disassembly.

View Article: PubMed Central - PubMed

Affiliation: Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Huddinge, 141 83 Sweden.

ABSTRACT

Background: CHD1 and CHD2 chromatin remodeling enzymes play important roles in development, cancer and differentiation. At a molecular level, the mechanisms are not fully understood but include transcriptional regulation, nucleosome organization and turnover.

Results: Here we show human CHD1 and CHD2 enzymes co-occupy active chromatin regions associated with transcription start sites (TSS), enhancer like regions and active tRNA genes. We demonstrate that their recruitment is transcription-coupled. CHD1 and CHD2 show distinct binding profiles across active TSS regions. Depletion of CHD1 influences chromatin accessibility at TSS and enhancer-like chromatin regions. CHD2 depletion causes increased histone H3 and reduced histone variant H3.3 occupancy.

Conclusions: We conclude that transcription-coupled recruitment of CHD1 and CHD2 occurs at transcribed gene TSSs and at intragenic and intergenic enhancer-like sites. The recruitment of CHD1 and CHD2 regulates the architecture of active chromatin regions through chromatin accessibility and nucleosome disassembly.

No MeSH data available.


Related in: MedlinePlus

CHD1 and CHD2 are recruited to active but not weak or inactive promoters in association with Pol II. (A) CHD1 and CHD2 occupancy is strongest in the active promoter chromatin state in K562 H1 embryonic stem cell (ESC) and GM12878 cells. CHD1 and CHD2 chromatin immunoprecipitation high throughput sequencing (ChIP-seq) data were normalized to input. Box plots illustrate the median and 25th to 75th percentile with whisker length determined by the Tukey method. In all cell types examined for both CHD1 and CHD2, enrichment at active promoters is statistically higher than at weak and inactive promoters (Kruskall-Wallis test with Dunn’s post test correction, k = 3, P <0.0001) (B) H3K4me2 and H3K4me3 are present at both active and weak promoters, while Pol II enrichment distinguishes the active and weak promoter chromatin state. (C) Examples of the transcription start site (TSS) of genes marked by H3K4me2/3 with differential Pol II, CHD1 and CHD2 binding. The GAL1K1 promoter - TSS1 is marked by H3K4me2/3 but is not bound by Pol II, CHD1 or CHD2, while the H3F3B promoter, TSS2, is strongly bound by Pol II along with CHD1 and CHD2. TSS3 of the UNK gene promoter displays H3K4me2/3 enrichment on a similar scale to the H3F3B gene but has weaker Pol II, CHD1 and CHD2 binding.
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Fig1: CHD1 and CHD2 are recruited to active but not weak or inactive promoters in association with Pol II. (A) CHD1 and CHD2 occupancy is strongest in the active promoter chromatin state in K562 H1 embryonic stem cell (ESC) and GM12878 cells. CHD1 and CHD2 chromatin immunoprecipitation high throughput sequencing (ChIP-seq) data were normalized to input. Box plots illustrate the median and 25th to 75th percentile with whisker length determined by the Tukey method. In all cell types examined for both CHD1 and CHD2, enrichment at active promoters is statistically higher than at weak and inactive promoters (Kruskall-Wallis test with Dunn’s post test correction, k = 3, P <0.0001) (B) H3K4me2 and H3K4me3 are present at both active and weak promoters, while Pol II enrichment distinguishes the active and weak promoter chromatin state. (C) Examples of the transcription start site (TSS) of genes marked by H3K4me2/3 with differential Pol II, CHD1 and CHD2 binding. The GAL1K1 promoter - TSS1 is marked by H3K4me2/3 but is not bound by Pol II, CHD1 or CHD2, while the H3F3B promoter, TSS2, is strongly bound by Pol II along with CHD1 and CHD2. TSS3 of the UNK gene promoter displays H3K4me2/3 enrichment on a similar scale to the H3F3B gene but has weaker Pol II, CHD1 and CHD2 binding.

Mentions: We analyzed CHD1 and CHD2 occupancy by calculating the enrichment of CHD1 and CHD2 from ChIP-seq data in relation to the chromatin states delineated by Ernst et al.[28]. The chromatin states established by Ernst et al. were based on ChIP-seq data of combinatorial patterns of eight histone modifications and the insulator binding protein CTCF [28]. The promoter and enhancer chromatin states are summarized in Table 1. In relation to promoter chromatin states; H3K4me2/3 and high H3K9/K27ac define the active promoter state. The weak promoter state is lower in H3K9/27 ac compared to the active promoter state, and H3K27me3 defines the inactive promoter. Enrichment of CHD1 and CHD2 was strongest at the active promoter chromatin state (Figure 1A). In all three cell types examined for both CHD1 and CHD2, the enrichment observed at active promoters was significantly higher than at weak or inactive promoters (Kruskall-Wallis, k = 3, P <0.0001). Previous studies have demonstrated in model organisms and human cells that CHD1 remodelers are recruited to promoters in a gene expression-dependent manner [29, 30]. Importantly, the weak promoter state from the ENCODE project is also defined by H3K4me2/me3 [28]. This suggested that H3K4 methylation is therefore not sufficient for recruiting CHD1 to promoters in vivo since occupancy is strongly reduced or absent at weak promoters, which are marked by H3K4me2/3.Table 1


Transcription-coupled recruitment of human CHD1 and CHD2 influences chromatin accessibility and histone H3 and H3.3 occupancy at active chromatin regions.

Siggens L, Cordeddu L, Rönnerblad M, Lennartsson A, Ekwall K - Epigenetics Chromatin (2015)

CHD1 and CHD2 are recruited to active but not weak or inactive promoters in association with Pol II. (A) CHD1 and CHD2 occupancy is strongest in the active promoter chromatin state in K562 H1 embryonic stem cell (ESC) and GM12878 cells. CHD1 and CHD2 chromatin immunoprecipitation high throughput sequencing (ChIP-seq) data were normalized to input. Box plots illustrate the median and 25th to 75th percentile with whisker length determined by the Tukey method. In all cell types examined for both CHD1 and CHD2, enrichment at active promoters is statistically higher than at weak and inactive promoters (Kruskall-Wallis test with Dunn’s post test correction, k = 3, P <0.0001) (B) H3K4me2 and H3K4me3 are present at both active and weak promoters, while Pol II enrichment distinguishes the active and weak promoter chromatin state. (C) Examples of the transcription start site (TSS) of genes marked by H3K4me2/3 with differential Pol II, CHD1 and CHD2 binding. The GAL1K1 promoter - TSS1 is marked by H3K4me2/3 but is not bound by Pol II, CHD1 or CHD2, while the H3F3B promoter, TSS2, is strongly bound by Pol II along with CHD1 and CHD2. TSS3 of the UNK gene promoter displays H3K4me2/3 enrichment on a similar scale to the H3F3B gene but has weaker Pol II, CHD1 and CHD2 binding.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4305392&req=5

Fig1: CHD1 and CHD2 are recruited to active but not weak or inactive promoters in association with Pol II. (A) CHD1 and CHD2 occupancy is strongest in the active promoter chromatin state in K562 H1 embryonic stem cell (ESC) and GM12878 cells. CHD1 and CHD2 chromatin immunoprecipitation high throughput sequencing (ChIP-seq) data were normalized to input. Box plots illustrate the median and 25th to 75th percentile with whisker length determined by the Tukey method. In all cell types examined for both CHD1 and CHD2, enrichment at active promoters is statistically higher than at weak and inactive promoters (Kruskall-Wallis test with Dunn’s post test correction, k = 3, P <0.0001) (B) H3K4me2 and H3K4me3 are present at both active and weak promoters, while Pol II enrichment distinguishes the active and weak promoter chromatin state. (C) Examples of the transcription start site (TSS) of genes marked by H3K4me2/3 with differential Pol II, CHD1 and CHD2 binding. The GAL1K1 promoter - TSS1 is marked by H3K4me2/3 but is not bound by Pol II, CHD1 or CHD2, while the H3F3B promoter, TSS2, is strongly bound by Pol II along with CHD1 and CHD2. TSS3 of the UNK gene promoter displays H3K4me2/3 enrichment on a similar scale to the H3F3B gene but has weaker Pol II, CHD1 and CHD2 binding.
Mentions: We analyzed CHD1 and CHD2 occupancy by calculating the enrichment of CHD1 and CHD2 from ChIP-seq data in relation to the chromatin states delineated by Ernst et al.[28]. The chromatin states established by Ernst et al. were based on ChIP-seq data of combinatorial patterns of eight histone modifications and the insulator binding protein CTCF [28]. The promoter and enhancer chromatin states are summarized in Table 1. In relation to promoter chromatin states; H3K4me2/3 and high H3K9/K27ac define the active promoter state. The weak promoter state is lower in H3K9/27 ac compared to the active promoter state, and H3K27me3 defines the inactive promoter. Enrichment of CHD1 and CHD2 was strongest at the active promoter chromatin state (Figure 1A). In all three cell types examined for both CHD1 and CHD2, the enrichment observed at active promoters was significantly higher than at weak or inactive promoters (Kruskall-Wallis, k = 3, P <0.0001). Previous studies have demonstrated in model organisms and human cells that CHD1 remodelers are recruited to promoters in a gene expression-dependent manner [29, 30]. Importantly, the weak promoter state from the ENCODE project is also defined by H3K4me2/me3 [28]. This suggested that H3K4 methylation is therefore not sufficient for recruiting CHD1 to promoters in vivo since occupancy is strongly reduced or absent at weak promoters, which are marked by H3K4me2/3.Table 1

Bottom Line: CHD2 depletion causes increased histone H3 and reduced histone variant H3.3 occupancy.We conclude that transcription-coupled recruitment of CHD1 and CHD2 occurs at transcribed gene TSSs and at intragenic and intergenic enhancer-like sites.The recruitment of CHD1 and CHD2 regulates the architecture of active chromatin regions through chromatin accessibility and nucleosome disassembly.

View Article: PubMed Central - PubMed

Affiliation: Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Huddinge, 141 83 Sweden.

ABSTRACT

Background: CHD1 and CHD2 chromatin remodeling enzymes play important roles in development, cancer and differentiation. At a molecular level, the mechanisms are not fully understood but include transcriptional regulation, nucleosome organization and turnover.

Results: Here we show human CHD1 and CHD2 enzymes co-occupy active chromatin regions associated with transcription start sites (TSS), enhancer like regions and active tRNA genes. We demonstrate that their recruitment is transcription-coupled. CHD1 and CHD2 show distinct binding profiles across active TSS regions. Depletion of CHD1 influences chromatin accessibility at TSS and enhancer-like chromatin regions. CHD2 depletion causes increased histone H3 and reduced histone variant H3.3 occupancy.

Conclusions: We conclude that transcription-coupled recruitment of CHD1 and CHD2 occurs at transcribed gene TSSs and at intragenic and intergenic enhancer-like sites. The recruitment of CHD1 and CHD2 regulates the architecture of active chromatin regions through chromatin accessibility and nucleosome disassembly.

No MeSH data available.


Related in: MedlinePlus