Project description:To test if H3K27Ac contributes to chromatin accessibility at enhancers, we globally reduced H3K27Ac levels by chemical inhibition of the histone acetylase p300 (with the small molecule A-485, final concentration 3 μM). This dataset includes ChIP-seq data for H3K27Ac with spike-in normalization, comparing DMSO and A-485 treated samples in mouse cells (i.e., XY 159 knock-out of the three DNA methyl transferases (DNMT TKO) mESCs). Two biological replicates were generated for each treatment condition. In summary, after treating the cells for 24h, cross-link ChIP-seq was performed. The protocol was adapted from (Trovato et al., 2024), with minor modifications. Chromatin was sheared using the Bioruptor Pico (Diagenode) and incubated with the antibody against H3K27ac (ab4729, Abcam) for 1 h at room temperature with rotation. Bead-immunocomplexes were reversed cross-linked after RNA and protein digestion. DNA was then purified using 1.4X SPRI-select beads. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit (New England Biolabs) and sequenced on Aviti Cloudbreak Low 2x150 (250 M clusters/run). Input samples were generated alongside the immunoprecipitated (IP) samples. Exogenous chromatin (from Drosophila Schneider 2 (S2) cells), prepared with the same protocol was added to each reaction as spike-in. Reads were processed, aligned, and normalized using QuasR, deepTools, and DESeq2 to generate coverage files and identify differential enrichment (https://github.com/Krebslabrep/TF-chromatin.git).
Project description:This data set comprises population (47 samples) measurements of transcription factor DNA binding (PU.1 and RPB2) and histone modification (H3K27ac, H3K4me1 and H3k4me3) levels for a subset of the 1000 Genomes Project CEPH samples. This data was generated as part of the following study: - Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. Cell. 2015 Aug 27;162(5):1039-50. doi: 10.1016/j.cell.2015.08.001. Epub 2015 Aug 20. An additional set of 111 samples from the 1000 Genomes Project (GBR and TSI populations) were also assayed for three histone modifications (H3K27ac, H3K4me1 and H3k4me3). This data was generated as part of the following study: - Chromatin 3D interactions mediate genetic effects on regulatory networks.
Project description:H3k27ac assessment by ChIPseq was performed on 16h-activated naïve CD4+ T cells with variables of RARα expression and RA concentration.
Project description:To determine the positions of promoters and enhancers in developing Xenopus laevis epithelial progenitors, we performed ChIPseq on the histone modifications H3K4me3 and H3K27ac. We also performed ChIPseq on the transcription factors foxj1 (in the presence or absence of rfx2), myb (in the presence or absence of multicilin), and rad21. Some embryos were harvested as wild-types; in other experiments, we injected embryos with mRNAs encoding FLAG-foxj1 (with and without rfx2 morpholino) or GFP-myb (with and without an inducible form of multicilin (mcidas-HGR)). We then isolated epithelial progenitors surgically and, when injected with multicilin, induced at mid-stage 11. We then harvested chromatin at 9 hours after induction (roughly stage 18) and performed ChIPseq using antibodies against endogenous targets (H3K4me3, H3K27ac, rad21) or protein tags (FLAG, GFP). We then sequenced these libraries, aligned the reads to the X. laevis genome (version 9.1) with bwa mem and called peaks with HOMER, using input as background.
Project description:ChIPseq data for human glioblastoma patients, EGAS00001003953. Mix of input, H3K27ac, H3K27me1, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9me3 and BRD, 20 human samples, 2 cell lines (LN229, ZH487).
Project description:In cancer cells, enhancer hijacking mediated by chromosomal alterations and/or increase of histone H3 lysine 27 acetylation (H3K27ac) can support oncogene expression. However, how the chromatin conformation of enhancer-promoter interactions is affected by these events is unclear. Here, by comparing chromatin structure and H3K27ac levels in normal and lymphoma B-cells, we show that enhancer-promoter interacting regions assume different conformations according to the local abundance of H3K27ac. Genetic or pharmacologic depletion of H3K27ac decreases the frequency and the spreading of these interactions, altering oncogene expression. Moreover, enhancer hijacking mediated by chromosomal translocations influences the epigenetic status of the regions flanking the breakpoint, prompting the formation of distinct intra-chromosomal interactions in the two homologous chromosomes. These interactions are accompanied by allele-specific gene expression changes. Overall, our work indicates that H3K27ac dynamics modulate interaction frequency between regulatory regions and can lead to allele-specific chromatin configurations to sustain oncogene expression.
Project description:Analysis of ETO2, MYB, EP300 binding as well as H3K27ac, H3K4me1 and H3M27me3 occupancy by ChIP-seq in HEL cells treated with DMSO or dCBP-1 (0.5uM) for 3h or expressing shRNA targeting MYB (shMYB) or genetically inactivated for ETO2 (ETO2ko)