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A novel BRAT1-BRP1 complex recognizes histone acetylation and mediates active DNA demethylation and transcriptional activation in Arabidopsis

ABSTRACT: A novel BRAT1-BRP1 complex recognizes histone acetylation and mediates active DNA demethylation and transcriptional activation in Arabidopsis

PROVIDER: PRJNA280955 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1970640_1.fastq.gz	Fastqsanger.gz
	SRR1970640_2.fastq.gz	Fastqsanger.gz
	SRR1970650_1.fastq.gz	Fastqsanger.gz
	SRR1970650_2.fastq.gz	Fastqsanger.gz
	SRR1970641_1.fastq.gz	Fastqsanger.gz

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A novel BRAT1–BRP1 complex recognizes histone acetylation and mediates active DNA demethylation and transcriptional activation in Arabidopsis [BS-Seq]

Project description:Active DNA demethylation is an important epigenetic phenomenon in many eukaryotes. In Arabidopsis thaliana, ROS1, a 5-methylcytosine DNA glycosylase, is responsible for active DNA demethylation via a base excision repair process. Here, we found that Bromodomain and ATPase domain-containing protein 1 (BRAT1) associates with BRP1 (BRAT1 Partner 1) and forms a tight BRAT1–BRP1 complex required for DNA demethylation. To identify hypermethylated loci at the whole-genome level in brat1, brp1, and ros1, we performed whole-genome bisulfite sequencing. Compare the DNA methylation profiles of 10-day old seedlings materials of mutants (brat1, brp1, and ros1) to wild type by whole-genome bisulfite sequencing.

2015-04-14 | E-GEOD-67798 | biostudies-arrayexpress

A novel BRAT1–BRP1 complex recognizes histone acetylation and mediates active DNA demethylation and transcriptional activation in Arabidopsis [BS-Seq]

2015-04-14 | GSE67798 | GEO

Histone acetylation recruits the SWR1 complex to regulate active DNA demethylation in Arabidopsis

Project description:The eukaryotic genome is divided into regions of heterochromatin and euchromatin. The histone variant H2A.Z specifically localizes at euchromatin and displays a genome-wide anti-correlation with DNA methylation. DNA methylation plays a central role in the epigenetic regulation of many eukaryotic genomes. Active DNA demethylation is critical for controlling the epigenome in plants and mammals. Yet, little is known about how DNA demethylases are recruited to target loci. Here we report that SWR1, a conserved histone H2A.Z deposition complex, regulates DNA demethylation in Arabidopsis thaliana by recruiting the plant DNA demethylase ROS1. A forward genetic screen for anti-silencing mutants identified two SWR1 components, PIE1 and ARP6, as cellular factors required for ROS1-mediated DNA demethylation. We further discovered two bromodomain-containing proteins, the methyl-DNA-binding protein AtMBD9, and NPX1, a plant homolog of ScBDF1 in yeast, as components of the SWR1 complex in Arabidopsis. AtMBD9 and NPX1 function redundantly in preventing DNA hypermethylation and transcriptional gene silencing by recognizing histone acetylation marks established by IDM1, a known regulator of DNA demethylation. We show that IDM1 is required for H2A.Z deposition in many genomic regions targeted for active DNA demethylation. We found that H2A.Z interacts with ROS1 and is required for locus-specific DNA demethylation and antisilencing. Our results reveal a role of H2A.Z in active DNA demethylation, and a mechanism through which DNA demethylases can be recruited to target regions by specific histone acetylation marks.

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Histone acetylation recruits the SWR1 complex to regulate active DNA demethylation in Arabidopsis

Project description:Histone acetylation recruits the SWR1 complex to regulate active DNA demethylation in Arabidopsis

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PHF8 mediates histone demethylation events in cell cycle progression

Project description:This SuperSeries is composed of the following subset Series: GSE22477: PHF8 mediates histone demethylation events in cell cycle progression [expression] GSE22478: PHF8 mediates histone demethylation events in cell cycle progression [ChIP-Seq] Refer to individual Series

2010-08-31 | E-GEOD-22400 | biostudies-arrayexpress

Histone acetylation and DNA demethylation of T-cells result in an anaplastic large cell lymphoma-like phenotype.

Project description:A characteristic feature of anaplastic large cell lymphoma (ALCL) is the significant reduction of the T-cell expression program despite its T-cell origin, a finding very similar to the loss of B-cell identity of classical Hodgkin lymphoma (cHL). Previously we demonstrated that epigenetic mechanisms are active in cHL to induce this peculiar phenotype. The results show that combined DNA demethylation and histone acetylation of T-cell lines induce an almost complete extinction of the T-cell phenotype, including the down-regulation of essential T-cell receptor signalling pathway genes such as CD3, LCK and ZAP70, as well as an up-regulation of ALCL-characteristic genes. In contrast, combined DNA demethylation and histone acetylation of ALCL cells is not able to reconstitute their T-cell phenotype. This clearly demonstrates that similar epigenetic mechanisms are active in ALCL and cHL which are responsible for the extinction of their cell type characteristic phenotype. We subjected T-cell lymphoma/leukemia cell lines and ALCL cell lines (n=4, each) to epigenetic modifiers to evoke DNA demethylation and the histone acetylation. Global gene expression profiling (Affymetrix) was performed from treated and untreated cell lines which were evaluated by real-time RT-PCR and Western Blot analysis.

2012-08-19 | E-GEOD-26101 | biostudies-arrayexpress

A novel BRAT1-BRP1 complex recognizes histone acetylation and mediates active DNA demethylation and transcriptional activation in Arabidopsis

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-04-14 | E-GEOD-67799 | biostudies-arrayexpress

The GTE4–EML chromatin reader complex concurrently recognizes histone acetylation and H3K4 trimethylation in Arabidopsis

Project description:Histone acetylation and H3K4 trimethylation (H3K4me3) are associated with active transcription. However, how they cooperate to regulate transcription in plants remains largely unclear. Our study revealed that GLOBAL TRANSCRIPTION FACTOR GROUP E 4 (GTE4) binds to acetylated histones and forms a complex with the functionally redundant H3K4me3-binding EMSY-like proteins EML1 or EML2 (EML1/2) in Arabidopsis thaliana. The eml1 eml2 (eml1/2) double mutant exhibits a similar morphological phenotype to gte4, and most of the differentially expressed genes in gte4 were coregulated in eml1/2. Through chromatin immunoprecipitation followed by deep sequencing, we found that GTE4 and EML2 co-occupy protein-coding genes enriched with both histone acetylation and H3K4me3, exerting a synergistic effect on the association of the GTE4–EML complex with chromatin. The association of GTE4 with chromatin requires both its bromodomain and EML-interacting domain. This study identified a complex and uncovered how it cooperatively recognizes histone acetylation and H3K4me3 to facilitate gene transcription at the whole-genome level in Arabidopsis.

2024-12-24 | GSE245273 | GEO

Active DNA demethylation controls transgenerational epigenetic stability

Project description:Active DNA demethylation controls transgenerational epigenetic stability

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Active DNA Demethylation by DNMT3A and DNMT3B - Mechanistic Aspect and In Vivo Evidence

Project description:The DNA methylation program is at the bottom layer of the epigenetic regulatory cascade of vertebrate development. While the methylation at C-5 position of the cytosine (C) residues on the vertebrate genomes is achieved through the catalytic activities of the DNA methyltransferases (DNMTs), the conversion of the methylated cytosine (5mC) could be accomplished by the combined actions of the TET enzyme and DNA repair. Interestingly, it has been found recently that the mouse and human DNMTs also possess active DNA demethylation activity in vitro in a Ca2+- and redox condition-dependent manner. We report here the study of tracking down the fate of the methyl group removed from 5mC on DNA during in vitro demethylation reaction by mouse de novo DNMTs, i.e. DNMT3A and DNMT3B. Remarkably, the methyl group becomes covalently linked to the catalytic cysteines utilized by the two de novo DNMTs in their DNA methylation reactions. Thus, the forward and reverse reactions of DNA methylations by the DNMTs may utilize the same cysteine residue(s) as the active site despite of their distinctive pathways. Secondly, we demonstrate that active DNA demethylation of a heavily methylated GFP reporter plasmid by ectopically expressed DNMT3A or DNMT3B occurs in vivo in transfected human HEK 293 cells in culture. Furthermore, the extent of DNA demethylation by the DNMTs in this cell-based system is affected by Ca2+ homeostasis as well as by mutation of their putative active cysteines. These findings substantiate the roles of the vertebrate DNMTs as double-edged swords in DNA methylation-demethylation in vitro as well as in a cellular context.

2022-02-24 | PXD003401 | Pride

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