Project description:We performed colocalization studies of Spindlin1 and H3"K4me3-K9me3" and found two kinds of genome distribution patterns in overlapping peaks. One is that Spindlin1, H3K4me3 and H3K9me3 are distributed with sharp peaks in the promoter regions of some genes in euchromatin, and the other is that Spindlin1 and H3K4me3 coexist with sharp peaks in genome regions where H3K9me3 is widely distributed.
Project description:This study was carried out to investigate potential changes in the genome-wide distribution of h3k4me3, h3k27me3, and h3k9me3 in Uhrf1hepKO mouse livers compared to wild-type.
Project description:PRDM9 is a histone methyltransferase expressed in meiotic germ cells that determines the location of genetic recombination hotspots through binding of its allele-specific DNA binding domain. Here we characterize the genome-wide chromatin modification for two human PRDM9 alleles (A and C) in human cell lines. HEK293 cells were transfected with both alleles and an empty vector control. Resulting chromatin was subjected to H3K4me3 ChIP followed by high-throughput sequencing. We find that different PRDM9 allele largely modified chromatin in entirely different genomic regions in somatic cells determined by the protein's zinc-finger DNA binding domains. Many of the allele-specific peaks overlap sites of meiotic double-strand breaks found in vivo in human germ cells suggesting that transient expression of PRDM9 in somatic cells can reflect binding in vivo. Identify PRDM9-dependent H3K4me3 sites by comparing modified chromatin after expression of different human PRDM9 alleles in HEK293 cells.
Project description:We report the application of low input high-throughput profiling of histone modifications in mouse oocytes. Using antibodies against H3K4me3 (100 oocytes/replicate; 2 biological replicates per genotype) and H3K9me3 ( around 300 oocytes/replicate; 2 biological replicates per genotype), we find that they are mutually exclusive in oocytes and this property is lost in oocytes lacking Kdm4a. H3K9me3 is spread into regions of H3K4me3 postive open chromatin which is surprisingly, well preserved leading to a potential bivalency of scale. Altogether, KDM4A is important to keep H3K4me3 marked open chromatin clear of H3K9me3 spreading in oocytes.
Project description:This study describes the epigenetic profiling of the novel interactors of H3K4me3, H3K36me3 or H3K9me3. The interactors were ChIP-Seq profiled by their GFP tag in stably transfected HeLa (Kyoto) cells. The interactors include GATAD1, Sgf29, BAP18, TRRAP, PHF8, N-PAC and LRWD1 (including replicates), as well as an GFP ChIP-Seq profile on non-transfected HeLa cells (negative control). Also included are the profiles of the histone modifications themselves (H3K4me3, H3K27me3, H3K9me3, H3K36me3, H3K9/14Ac and H3K79me3)
Project description:This study describes the epigenetic profiling of the novel interactors of H3K4me3, H3K36me3 or H3K9me3. The interactors were ChIP-Seq profiled by their GFP tag in stably transfected HeLa (Kyoto) cells. The interactors include GATAD1, Sgf29, BAP18, TRRAP, PHF8, N-PAC and LRWD1 (including replicates), as well as an GFP ChIP-Seq profile on non-transfected HeLa cells (negative control). Also included are the profiles of the histone modifications themselves (H3K4me3, H3K27me3, H3K9me3, H3K36me3, H3K9/14Ac and H3K79me3) ChIP-Seq profiling of 8 proteins by their GFP tag in stably transfected cells HeLa (Kyoto) cells, 6 replicas, as well as ChIP-Seq profiling of 6 histone modifications in wt HeLa (Kyoto) cells
Project description:To study the effect of rs1192691 on histone modifications, we performed H3K27ac, H3K4me3, H3K27me3 and H3K9me3 in SKOV3(AA) and SKOV3(CC).
Project description:We used chromatin immunoprecipitation-coupled to deep sequencing (ChIP-seq) to profile genome-wide locations of H3K4 trimethylation (H3K4me3) and H3K9 trimethylation (H3K9me3) epigenetic marks in SUN-depleted mouse peritoneal macrophages.
Project description:Acute myeloid leukemia (AML) with rearrangement of the mixed-lineage leukemia (MLL) gene are the most aggressive hematopoietic malignancies. Previous studies demonstrated the distribution of several epigenetic modifications including H3K9me3, H3K79me2, H3K36me3, H3K4me3 and H3K27me3, in MLL-AF9 transformed murine cells. Here, we examined the H3K9me3 distribution in c-Kit+ cells (enriched with stem/progenitor cells) from both MLL-AF9 transformed murine cells in parallel with control wild-type cells, and found an overall lower distribution of H3K9me3 in leukemia stem cells than normal hematopoietic stem/progenitor cells.
Project description:Full title: Discrete genomic domains exhibit co-occurrence of H3K9me3 and H3K27me3 histone modifications throughout Drosophila development Trimethylation of histone H3 on lysine 9 (H3K9me3) and lysine 27 (H3K27me3) is strongly associated with gene silencing and transcriptional repression in both Drosophila and mammals. H3K9me3 is linked to the formation of heterochromatin, while H3K27me3 is a hallmark of repression of euchromatic genes by Polycomb group proteins. We examined the genomic distribution of the two modifications at high resolution over nine different stages of Drosophila development, and found that they are present in large overlapping domains in euchromatin. These dual-mark domains are stable throughout the life of the fly, and cover genomic regions greatly enriched in developmental regulatory genes with spatially restricted expression. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf