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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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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.

2019-08-01 | GSE115170 | GEO

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 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

| PRJNA473996 | ENA

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

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

Active Demethylation of Both Maternal and Paternal Genomes in Mouse Zygotes

Project description:The epigenomes of mammalian sperm and oocytes, characterized by gamete-specific 5-methylcytosine (5mC) patterns, are reprogrammed in early embryogenesis to establish full developmental potential. It is broadly accepted that the paternal genome is actively demethylated in the zygote while the maternal genome undergoes passive demethylation thanks to DNA replication over the subsequent cleavage divisions. Here we reveal that both maternal and paternal genomes undergo widespread active and passive demethylation in the pronuclear zygote before the first mitotic division. Whereas the passive demethylation requires DNA replication, the active demethylation relies on enzymatic oxidation of 5mC, as deletion of the DNA dioxygenase, Tet3, but not the inhibition of replication, blocks the active demethylation. At actively demethylated loci, 5mCs appear to be processed to unmodified cytosines in a manner independent of the DNA glycosylase TDG. These observations suggest the occurrence of genuine active demethylation in both parental genomes following fertilization. An extra supportive Tet3 knock-out female pronuclear sample related to experiment Series GSE56650.

2016-09-01 | E-GEOD-60777 | biostudies-arrayexpress

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

Project description:To identify BRAT1 target loci at the whole-genome level, we performed RNA deep sequencing and examined the transcript levels of transposable elements and genes in the wild type, brat1, nrpe1, and brat1nrpe1. Compare the mRNA profiles of 10-day old seedlings materials of mutants (brat1, nrpe1, and brat1nrpe1) to wild type by Illumina suquencing.

2015-04-14 | E-GEOD-67797 | biostudies-arrayexpress

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