Genome-wide profiling of γH2AX in Arabidopsis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA514446 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The R-loop, composed of a DNA-RNA hybrid and the displaced single-stranded DNA, regulates diverse cellular processes. However, how cellular R-loops are sensed remain poorly understood. Here we report the discovery of the evolutionally conserved ALBA proteins (AtALBA1&2) functioning as the R-loops sensor of genic regions in higher plant Arabidopsis thaliana. AtALBA1 and 2 form a heterodimer protein complex and localize in the nucleus. While AtALBA1 binds to the DNA-RNA hybrid strand, AtALBA2 associates with single-stranded DNA in the R-loops. AtALBA1&2 preferentially binds to the genic R-loop regions that are associated with active epigenetic marks. Depletion of AtALBA1 or AtALBA2 results in hypersensitivity of plants to DNA damaging agents. Our results demonstrate the unprotected R-loops by loss of AtALBA1&2 are main source of DNA damage through γH2AX ChIP-seq.
2019-04-17 | GSE124943 | GEO
Project description:We investigated the RNAPII and γH2AX occupancy genome wide by ChIP-Seq in MLL2 F/F and FC/FC80 MEF cells. We found that a week after MLL2 excision (FC/FC cells), a group of genes present higher levels of γH2AX and RNAPII near the TSS, as compared to the control (F/F cells). H3K4Me1, H3K4M2 and H3K4Me3 levels near the TSS were also studied.
2016-04-13 | GSE73124 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE34655: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - mRNA-seq GSE34656: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - small RNA-seq GSE34657: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - Bisulfite-seq Refer to individual Series
2011-12-22 | E-GEOD-34658 | biostudies-arrayexpress
Project description:In the testis of the mice, most spermatogonia are in pachytene stage. We have harvested spermatogonia from 3-week-old mice. As γH2AX is the marker of the XY body, we performed RNA-seq following RNA-ChIP using anti-γH2AX antibody in germ cells to report the γH2AX associated RNA in mouse spermatocytes, while IgG as the negative control. Process of RNA-ChIP for germ cells was as the ChIP protocol with some modifications.
2021-09-26 | GSE184711 | GEO
Project description:BRAHMA (BRM) is a conserved SWI/SNF-type chromatin remodeling ATPase implicated in many key nuclear events. Histone H3 Lysine 27 (H3K27) demethylases specifically remove the repressive histone mark, trimethylation of H3K27 (H3K27me3). Both proteins are thought to play active roles in regulating gene activities at the chromatin level, but their genome-wide coordination remains to be determined. In Arabidopsis thaliana, RELATIVE OF EARLY FLOWERING 6 (REF6, also known as JMJ12) is the first identified plant H3K27 demethylase. Here, genome-wide analyses revealed that REF6 targets to thousands of genes across the Arabidopsis genome and co-localizes with BRM at more than 1,000 genes, many of which are genes involved in response to various stimuli, especially plant hormones. Loss of REF6 activity results in decreased BRM occupancy at hundreds of BRM-REF6 co-targets, indicating that REF6 is required for the recruitment of BRM to chromatin. Further, REF6 targets to genomic loci that contains the CTCTGTTT motif in vivo
2016-03-31 | PXD003583 | Pride
Project description:Genome-wide profiling of EDM3 dependent H3K9me2 in Arabidopsis thaliana
| PRJNA427433 | ENA
Project description:We perform genome-wide profiling of H3K9me2 in the Arabidopsis thaliana edm3 mutant. By var-seq, we identified EDM3 as a nuclear-localized protein featuring a single RNA-recognition motif (RRM). Similar to PHD finger-containing histone binding protein EDM2, EDM3 promotes high levels of H3K9me2 at RPP7 and controls transcripts of this NLR gene by suppressing proximal polyadenylation and promoting the synthesis of full-length RPP7-coding mRNAs. Our results showed that EDM3 affects levels of this epigenetic mark at a set of genes and transposons, the vast majority of which also feature EDM2-dependent H3K9me2.
2020-01-29 | GSE108490 | GEO
Project description:The goal of this study is to find out the relationship between ER-mediated transcription and DNA damage induced by estrogen(E2) and BRCA1 deficiency in MCF7. The DNA damage is marked by chromatin binding of γH2AX using ChIP-seq.
2022-04-07 | GSE200154 | GEO
Project description:Inspired by the important roles of the special chromatin structure R-loops, here we report a new method, ssDRIP-seq, for genome-wide identification of R-loops, and demonstrate its high efficiency, low bias, and strand-specificity when profiling the R-loops in Arabidopsis. Using this single-strand DNA ligation based library construction technique, we find that Arabidopsis R-loops are formed in both the sense and antisense orientations of genes, and prefer both AT and GC skews. R-loops are prevalent in regions with multiple chromatin modifications, and are negatively correlated with CG DNA hypermethylation. R-loops are strongly enriched in gene promoters and gene bodies, highly associated with noncoding RNA and repetitive genomic regions, and correlated with activated and repressed gene loci. In summary, our analysis reveals that R-loop is a common feature of the Arabidopsis genome, and suggests diverse roles for R-loops in genome organization and gene regulation, thereby providing novel insights into plant nuclear genome formation and function.
2017-05-31 | GSE95765 | GEO
Project description:To explore the bivalent histone modifications in the Arabidopsis genome, we examined genome-wide histone 3 lysine-27 trimethylation (H3K27me3) and histone 3 lysine-4 trimethylation (H3K4me3) in 5-day-old seedlings (Col-0) by ChIP-seq. We found that more than 1300 genes loci contain both H3K27me3 and H3K4me3.
2023-02-28 | GSE185121 | GEO