The Organization of Histone H3 Modifications as Revealed by a Panel of Specific Monoclonal Antibodies

Kimurâ, Hiroshi; Hayashi‐Takanaka, Yoko; Goto, Yuji; Takizawa, Nanako; Nozaki, Naohito

doi:10.1247/csf.07035

Cited by 288 publications

(282 citation statements)

References 29 publications

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“…Among the modifications, acetylation at H3K27 (H3K27Ac) has been established to be primarily localized to active promoter and enhancer regions 32 . Accordingly, we performed ChIP-seq for H3K27Ac 33 and examined whether the ChIP-peaks for Ad4BP/SF-1 overlapped with the H3K27Ac-containing regions. Indeed, the Ad4BP/SF-1 ChIP-peaks coincided with the H3K27Ac regions in the Aldoa, Eno1, Hk1, Pfkp, Gapdh and Pkm2 genes, but not in the Pfkl, Pgam1 and Ldha genes ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Glycolytic genes are targets of the nuclear receptor Ad4BP/SF-1

et al. 2014

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Genetic deficiencies in transcription factors can lead to the loss of certain types of cells and tissue. The steroidogenic tissue-specific nuclear receptor Ad4BP/SF-1 (NR5A1) is one such gene, because mice in which this gene is disrupted fail to develop the adrenal gland and gonads. However, the specific role of Ad4BP/SF-1 in these biological events remains unclear. Here we use chromatin immunoprecipitation sequencing to show that nearly all genes in the glycolytic pathway are regulated by Ad4BP/SF-1. Suppression of Ad4BP/SF-1 by small interfering RNA reduces production of the energy carriers ATP and nicotinamide adenine dinucleotide phosphate, as well as lowers expression of genes involved in glucose metabolism. Together, these observations may explain tissue dysgenesis as a result of Ad4BP/SF-1 gene disruption in vivo. Considering the function of estrogen-related receptor a, the present study raises the possibility that certain types of nuclear receptors regulate sets of genes involved in metabolic pathways to generate energy carriers.

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Section: Resultsmentioning

confidence: 99%

Glycolytic genes are targets of the nuclear receptor Ad4BP/SF-1

et al. 2014

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“…H23 cells were fixed for 5 min at room temperature and permeabilized with 1% Triton X-100 in PBS for 20 min at room temperature. After blocking with Blocking One P (Nacalai tesque) for 20 min at room temperature, cells were incubated with 2 μg/ml Cy3-conjugated anti H4K5acK8ac antibody with 2–10 μg/ml Alexa Fluor 488-conjugated histone modification-specific antibody (H3K27ac/CMA309, H3K4me1/CMA302, or H3K4me3/CMA304) [63] and 1 μg/ml Hoechst33342 for 2.5 hours at room temperature. Fluorescence images were acquired using a confocal microscope (FV1000; Olympus) with a 60× UPlanApoN oil immersion lens (NA 1.40).…”

Section: Methodsmentioning

confidence: 99%

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

Handoko¹,

Kaczkowski²,

Hon³

et al. 2018

Epigenetics

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The bromodomain and extra-terminal domain (BET) proteins are promising drug targets for cancer and immune diseases. However, BET inhibition effects have been studied more in the context of bromodomain-containing protein 4 (BRD4) than BRD2, and the BET protein association to histone H4-hyperacetylated chromatin is not understood at the genome-wide level. Here, we report transcription start site (TSS)-resolution integrative analyses of ChIP-seq and transcriptome profiles in human non-small cell lung cancer (NSCLC) cell line H23. We show that di-acetylation at K5 and K8 of histone H4 (H4K5acK8ac) co-localizes with H3K27ac and BRD2 in the majority of active enhancers and promoters, where BRD2 has a stronger association with H4K5acK8ac than H3K27ac. Although BET inhibition by JQ1 led to complete reduction of BRD2 binding to chromatin, only local changes of H4K5acK8ac levels were observed, suggesting that recruitment of BRD2 does not influence global histone H4 hyperacetylation levels. This finding supports a model in which recruitment of BET proteins via histone H4 hyperacetylation is predominant over hyperacetylation of histone H4 by BET protein-associated acetyltransferases. In addition, we found that a remarkable number of BRD2-bound genes, including MYC and its downstream target genes, were transcriptionally upregulated upon JQ1 treatment. Using BRD2-enriched sites and transcriptional activity analysis, we identified candidate transcription factors potentially involved in the JQ1 response in BRD2-dependent and -independent manner.

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“…For an antibody to pass dot blot analysis required that at least 75% of the total signal be specific to the cognate peptide. Mouse monoclonal antibodies against H3K9me2 (clone 6D11), H3K9me3 (clone 2F3), H3K27me3 (clone1E7), H3K36me2 (2C3), and H3K36me3 (13C9) were gifts from Hiroshi Kimura (Osaka University) (Kimura et al 2008 , MES-4 (SDI SDQ0791) , SDC-3 and DPY-27 (Ercan et al 2007), DPY-26 and MIX-1 (Ercan et al 2009), and HTZ-1 (Whittle et al 2008). DPY-28 antibody was kindly provided by Kirsten Hagstrom.…”

Section: Methods Antibodiesmentioning

confidence: 99%

Broad chromosomal domains of histone modification patterns in C. elegans

Liu¹,

Rechtsteiner²,

Egelhofer³

et al. 2010

Genome Res.

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Chromatin immunoprecipitation identifies specific interactions between genomic DNA and proteins, advancing our understanding of gene-level and chromosome-level regulation. Based on chromatin immunoprecipitation experiments using validated antibodies, we define the genome-wide distributions of 19 histone modifications, one histone variant, and eight chromatin-associated proteins in Caenorhabditis elegans embryos and L3 larvae. Cluster analysis identified five groups of chromatin marks with shared features: Two groups correlate with gene repression, two with gene activation, and one with the X chromosome. The X chromosome displays numerous unique properties, including enrichment of monomethylated H4K20 and H3K27, which correlate with the different repressive mechanisms that operate in somatic tissues and germ cells, respectively. The data also revealed striking differences in chromatin composition between the autosomes and between chromosome arms and centers. Chromosomes I and III are globally enriched for marks of active genes, consistent with containing more highly expressed genes, compared to chromosomes II, IV, and especially V. Consistent with the absence of cytological heterochromatin and the holocentric nature of C. elegans chromosomes, markers of heterochromatin such as H3K9 methylation are not concentrated at a single region on each chromosome. Instead, H3K9 methylation is enriched on chromosome arms, coincident with zones of elevated meiotic recombination. Active genes in chromosome arms and centers have very similar histone mark distributions, suggesting that active domains in the arms are interspersed with heterochromatin-like structure. These data, which confirm and extend previous studies, allow for in-depth analysis of the organization and deployment of the C. elegans genome during development.

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The Organization of Histone H3 Modifications as Revealed by a Panel of Specific Monoclonal Antibodies

Cited by 288 publications

References 29 publications

Glycolytic genes are targets of the nuclear receptor Ad4BP/SF-1

Glycolytic genes are targets of the nuclear receptor Ad4BP/SF-1

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

Broad chromosomal domains of histone modification patterns in C. elegans

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