Genome-wide H3K4me3 analysis in Arabidopsis
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PROVIDER: PRJNA767683 | ENA |
REPOSITORIES: ENA
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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
Project description:Genome-wide H3K27me3 and H3K4me3 analyses in Arabidopsis
| PRJNA767679 | ENA
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 | GSE185120 | GEO
Project description:Genome-wide H3K27me3 analysis in Arabidopsis
| PRJNA767682 | ENA
Project description:Genome-wide analysis of H3K4me3 in NOS1+ mouse enteric neurons
| PRJNA579930 | ENA
Project description:The genome-wide analysis of H3K4me3 in human umbilical cord blood
| PRJNA718913 | ENA
Project description:Background. Post-translational modifications of histones play important roles in regulating transcription by modulating the structural properties of the chromatin. In plants, methylation of histone H3 lysine4 (H3K4me) is associated with genes and required for normal plant development. Results. We have characterized the genome-wide distribution patterns of mono-, di- and trimethylation of H3K4 (H3K4me1, H3K4me2 and H3K4me3, respectively) in Arabidopsis thaliana using chromatin immunoprecipitation and high-resolution whole-genome tiling microarrays (ChIP-chip). All three types of H3K4me are found to be almost exclusively genic, and two thirds of Arabidopsis genes contain at least one type of H3K4me in seedlings. H3K4me2 and H3K4me3 accumulate predominantly in promoters and 5’ genic regions, whereas H3K4me1 is distributed within transcribed regions. In addition, H3K4me3-containing genes are highly expressed with low levels of tissue specificity, but H3K4me1 or H3K4me2 may not be directly involved in transcriptional activation. Furthermore, a genome-wide preferential co-localization of H3K4me3 and H3K27me3 found in mammals does not appear to exist in plants, but H3K4me2 and H3K27me3 co-localize at a higher-than-expected frequency. Finally, the relationship between H3K4me and DNA methylation was explored by comparing the genome-wide distribution patterns of H3K4me1, H3K4me2 and H3K4me3 in wild type plants and the met1 DNA methyltransferase mutant. Conclusions. H3K4me plays widespread roles in regulating gene expression in plants. Although many aspects of the mechanisms and functions of H3K4me appear to be conserved among all three kingdoms, we observed significant differences in the relationship between H3K4me and transcription or other epigenetic pathways in plants and mammals.
2009-02-01 | GSE13613 | GEO
Project description:Arabidopsis telomeric repeat binding factors (TRBs) can bind telomeric DNA sequences to protect telomeres from degradation. TRBs can also recruit Polycomb Repressive Complex 2 (PRC2) to deposit tri-methylation of H3 lysine 27 (H3K27me3) over certain target loci. Here, we demonstrate that TRBs also associate and colocalize with JUMONJI14 (JMJ14) and trigger H3K4me3 demethylation at some loci. The trb1/2/3 triple mutant and the jmj14-1 mutant show an increased level of H3K4me3 over TRB and JMJ14 binding sites, resulting in up-regulation of their target genes. Furthermore, tethering TRBs to the promoter region of genes with an artificial zinc finger (TRB-ZF) successfully triggers target gene silencing, as well as H3K27me3 deposition, and H3K4me3 removal. Interestingly, JMJ14 is predominantly recruited to ZF off-target sites with low levels of H3K4me3, which is accompanied with TRB-ZFs triggered H3K4me3 removal at these loci. These results suggest that TRB proteins coordinate PRC2 and JMJ14 activities to repress target genes via H3K27me3 deposition and H3K4me3 removal.
2023-02-22 | MSV000091349 | MassIVE
Project description:To characterize genome-wide H3K4me3 and H3K27me3 chromatin-state of HL-60 cells.
2018-06-13 | GSE100485 | GEO
Project description:Plants experience a wide array of environmental stimuli to form a memory of adversity. Histone modification plays roles in plant stress memory, of which the mechanisms of H3K4me3 of low temperature memory in plants are poorly understood although H3K4me3 is a key histone modification. Combined with phenotypic analysis, chip-seq, and transcriptome analyses were performed to investigate the potential H3K4me3 contributions for different phases of recurring cold stresses Arabidopsis plants. We then performed gene expression profiling analysis using data obtained from RNA-seq of different low temperature treatments.
2023-09-01 | GSE217609 | GEO