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Arabidopsis thaliana

ABSTRACT: Analysis of genome-wide distribution of histone H4 acetylation in hda19 mutant and of HDA19 bound regions in the wild-type in response to shoot induction

PROVIDER: PRJDB13417 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR360270.fastq.gz	Fastqsanger.gz
	DRR360271.fastq.gz	Fastqsanger.gz
	DRR360272.fastq.gz	Fastqsanger.gz
	DRR360273.fastq.gz	Fastqsanger.gz
	DRR360274.fastq.gz	Fastqsanger.gz

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Dynamic competing histone H4 K5K8 acetylation and butyrylation are hallmarks of highly active gene promoters

Project description:Newly discovered histone lysine acylations increase the functional diversity of nucleosomes well beyond acetylation. Here, we focus on histone butyrylation in the context of sperm cell differentiation. Specifically, we investigate the butyrylation of histone H4 lysine 5 and 8 at gene promoters, where acetylation guides the binding of Brdt, a bromodomain-and-extra-terminal protein, thereby mediating stage-specific gene expression programs. Genome-wide mapping data show that highly active Brdt-bound gene promoters systematically harbour competing histone acetylation and butyrylation marks at H4 K5 and K8. Histone butyrylation, despite acting as a direct stimulator of transcription, competes with acetylation, especially at H4 K5, to prevent Brdt binding. The observed in vivo H4 K5K8 acetylation butyrylation state at active promoters is reproduced in vitro where p300 indistinctly acetylates and butyrylates H4 K5 and K8. Altogether, highly active gene promoter regions are characterized by alternating H4 acetylation and butyrylation sustaining direct gene activation and a dynamic bromodomain binding.

2016-07-13 | GSE77277 | GEO

Genome-wide analysis of histone H3 acetylation levels of wild type, hda6, hdc1, and hda19 in short day conditions [ChIP-seq]

Project description:To investigate whether the expression of upregulated genes in hdc1 and hda19 is assoiated with histone acetylation levels increased in the hdc1 and hda19 mutants, We carried out ChIP-seq to examine histone H3 acetylation at the whole-genome level.

2018-12-28 | GSE124414 | GEO

Arabidopsis thaliana: wild type vs. scl15 mutant

Project description:Epigenetic regulation of gene expression is critical for controlling embryonic properties during the embryo-to-seedling phase transition. Here we report that a HISTONE DEACETYLASE19 (HDA19)-associated regulator, SCARECROW LIKE15 (SCL15), is essential for repressing the seed maturation program in vegetative tissues. SCL15 is expressed and GFP-tagged SCL15 predominantly localizes to the vascular bundles, particularly in the phloem companion cells and neighbouring specialized cells. Mutation of SCL15 leads to a global shift in gene expression in seedlings to a profile resembling late embryogenesis in seeds. In scl15 seedlings, many genes involved in seed maturation are markedly derepressed and 12S globulin accumulates; this is correlated with elevated levels of histone acetylation at a subset of seed-specific loci. SCL15 physically interacts with HDA19 and direct targets of HDA19-SCL15 association are identified. These studies revealed that SCL15 acts as an HDA19-associated regulator to repress embryonic traits in seedlings. Two-condition experiment: wild type vs. scl15 mutant seedlings. Biological replicates: 3 wild type and 3 mutant, independently grown and harvested. One replicate per array. Dye-swaps were performed.

2015-03-30 | E-GEOD-67395 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:Analysis of gene expression in hda19 mutant in response to shoot induction

| PRJDB13418 | ENA

Identification of candidate enhancer elements in unstimulated and stimulated dendritic cells and fibroblasts

Project description:To identify candidate enhancer elements we analyzed the distribution of two histone modifications associated with enhancers - H3K4me1 and H3K27ac - and one histone modification associated with active transcription - H4 acetylation.

2012-11-19 | GSE32380 | GEO

Genome-wide analysis of SAS-I-mediated H4 K16 acetylation

Project description:The MYST HAT Sas2 is part of the SAS-I complex. The target for acetylation by Sas2 is Lys16 of histone H4 (H4 K16Ac). This acetylation site marks euchromatic regions and opposes the spreading of heterochromatin at telomere-proximal regions. Changes of SAS-I-mediated H4 K16Ac on a genome-wide scale comparing wt and sas2M-bM-^HM-^F cells were investigated in this study. We found a pronounced, genome-wide loss of H4 K16 acetylation in the body of transcribed genes in the absence of Sas2. Furthermore, the influence of Sas2 on gene expression was investigated in RNA expression arrays. H4 K16Ac and H4 in wt and sas2M-bM-^HM-^F was ChIPed. ChIP experiments were performed three times with independent chromatin preparations.

2012-01-18 | E-GEOD-19962 | biostudies-arrayexpress

Genome-wide maps of linker histone H1 lysine 85 acetylation in HCT116 cells

Project description:We identify acetylation of linker histone H1 lysine 85 as a novel histone acetylation mark, which regulates chromatin structure and genome stability upon DNA damage. By performing a chromatin immunoprecipitation and deep sequencing assay, we identified the genome-wide distribution patterns of H1 lysine 85 acetylation in HCT116 cells. We found that H1K85ac largely bound intergenic regions (53%) and gene bodies (39%), whereas only 7% H1K85ac bound regions 2 kb upstream of the transcription start sites (TSSs). As the proportion of H1K85ac bound to potential promoter regions was not significantly different to that of the random peaks (~6%), these data suggest that H1K85ac may not be mainly involved in general transcriptional regulation.

2018-04-18 | GSE113238 | GEO

Genetic dissection of NuA4-directed chromatin transactions throughout the S. cerevisiae genome

Project description:Acetylation of histone tails has long been associated with gene activation. Exactly how acetylation regulates gene expression is not fully known. Acetylation events at specific sites or collections of sites on histones elicit distinct outcomes. Here we examine the downstream consequences of histone acetylation by the histone H4 acetyltransferase NuA4 on a genomic scale. Evidence is presented that Bdf1, which is known to bind to acetylated lysine H4 tails in vitro, binds to nucleosomes in vivo and that this binding is dependent upon Esa1, the catalytic subunit of NuA4. Loss of NuA4 results in a coordinate depletion of Bdf1, the transcription complex assembly factor TFIID, and the H2A.Z assembly complex SWR-C at highly acetylated promoter regions. This finding is consistent with known interactions between Bdf1 and TFIID and SWR-C. Loss of Bdf1 results in little or no depletion of TFIID or SWR-C at these promoter regions, possibly due to substitution by the Bdf1 paralog Bdf2. Consistent with this possibility, loss of Bdf1 results in accumulation of Bdf2 at sites normally bound by Bdf1. Together, the findings presented here strengthen the proposed cascade of events whereby nucleosome H4 acetylation by NuA4 at promoters target Bdf1, which then recruits TFIID and SWR-C to assemble the transcription machinery. Keywords: chIP-chip, histone acetylation, transcription factor recruitment

2007-06-06 | GSE6707 | GEO

A link between Sas2-mediated H4 K16 acetylation, chromatin assembly in S-phase by CAF-I and Asf1, and nucleosome assembly by Spt6 during transcription

Project description:The histone acetyltransferase Sas2 is part of the SAS-I complex and acetylates lysine 16 of histone H4 (H4 K16Ac) in the genome of Saccharomyces cerevisiae. Sas2-mediated H4 K16Ac is strongest over the coding region of genes with low expression. However, it is unclear how Sas2-mediated acetylation is incorporated into chromatin. Our previous work has shown physical interactions of SAS with the histone chaperones CAF-I and Asf1, suggesting a link between SAS-I mediated acetylation and chromatin assembly. Here, we find that Sas2-dependent H4 K16Ac in bulk histones requires passage of the cells through the S-phase of the cell cycle, and the rate of increase in H4 K16Ac depends on both CAF-I and Asf1, whereas steady-state levels and genome-wide distribution of H4 K16Ac shows only mild changes in their absence. Furthermore, H4 K16Ac is deposited in chromatin at genes upon repression, and this deposition requires the histone chaperone Spt6, but not CAF-I, Asf1, HIR or Rtt106. Altogether, our data indicate that Spt6 controls H4 K16Ac levels by incorporating K16-unacetylated H4 in strongly transcribed genes. Upon repression, Spt6 association is decreased, resulting in less deposition of K16-unacetylated and therefore in a concomitant increase of H4 K16Ac that is recycled during transcription.

2015-09-14 | E-MTAB-2638 | biostudies-arrayexpress

ChIP from Candida albicans cells (3153A-parental and Sor125(55)-mutant) with H3pan-ac and H4pan-ac

Project description:Sorbose resistant Candida albicans mutant strain [Sor125(55)] derived from parental strain [3153A] has characteristic Ch5 monosomy plus Ch4/7b trisomy. ChIP-chip data showed marked elevation of H4 histone acetylation on monosomic Ch5 in Sor125(55) mutant compared with parental strain (3153A). There was no remarkable diffrence in H4 acetylation level on other chromosomes between those strains and no difference in H3 acetylation on all chromosomes.

2017-10-31 | GSE81684 | GEO

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