{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Tina Karagyozova"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14416"],"description":["We profiled the enrichment of active (H3K4me1, H3K4me3, H3K27ac) and inactive (H3K9me3, H3K27me3) histone PTMs in cells that are wild-type (WT) or knock-out (KO) for the H3.3-specific chaperone HIRA. We performed native ChIP-seq following MNase digestion to isolate nucleosomes in H3.1-SNAP and H3.3-SNAP-bearing HeLa cells. We had previously assayed the distribution of the H3.1 and H3.3 histone variants (Gatto et al., 2022) in the same cell lines, so we generated this PTM ChIP-seq data to compare the behaviour of the variants with that of H3 modifications."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Sequencing libraries were prepared at the NGS (Next-Generation Sequencing) platform at Institut Curie with the Illumina TruSeq ChIP kit.","Sequencing - All libraries were sequenced on Illumina NovaSeq 6000 (PE100).","Nucleic Acid Extraction - We performed ChIP-seq using the native nucleosomes isolation procedure described in Gatto et al. (2022) with small modifications. We used 5 million cells per IP and Dynabeads Protein A-conjugated antibodies against histone PTMs for immunoprecipitation. All steps were performed at 4°C and in the presence of Protease inhibitors (Roche) and 1mM TSA in every buffer to prevent protease and HDAC activity, respectively. For each IP reaction, we prepared 50μL of Ab-conjugated beads by blocking for 4 hours in Bead blocking buffer (2.5% BSA in PBS-T, 1mg/mL tRNA), washing once in 0.02% PBS-T and incubating for 15-30min with the antibodies (diluted in 0.2mL 0.02% PBS-T) on a rotating wheel. Ab-conjugated beads were then washed twice with 0.02% PBS-T and resuspended in 0.2mL 0.02% PBS-T. Native nucleosomes (80μL per IP) from up to 3 samples were pooled, diluted in 5x volumes of Incubation buffer (50mM Tris-HCl pH 7.5, 100mM NaCl, 0.5% BSA) and pre-cleared by incubating with Dynabeads Protein A (15μL per input pool) for 30 min on a rotating wheel. We kept 20μL (1%) pre-cleared chromatin as input sample. We incubated the remaining (460μL/IP) with the Ab-conjugated beads (washed once in Incubation buffer) overnight on a rotating wheel. Beads were washed and DNA was purified from the IPed material as described for SNAP-seq in Gatto et al. (2022).  Ab used: PTM     Provider        Cat. no Amount per ChIP (ug) H3K4me1 abcam         ab8895 4 H3K4me3 Active Motif 39915 4 H3K9me3 Active Motif 39765 10 H3K27ac Active Motif 39133 5 H3K7me3 Active Motif 39155 5","Sample Collection - We collected 5 million cells per IP by trypsinization.","Growth Protocol - We used HeLa cells stably expressing H3.1-SNAP-HA or H3.3-SNAP-HA which were either wild-type (WT, CRISPR/Cas9 GFP KO) or knock-out for HIRA (KO, CRISPR/Cas9 HIRA KO), as described in Ray-Gallet et al. (2018). We cultured cells in DMEM complete medium (Dulbecco’s Modified Eagle’s Medium with D-Glucose, L-Glutamine and Pyruvate) supplemented with 10% fetal calf serum, 100U/mL Penicillin and 100mg/mL Streptomycin."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"pubmed_abstract":["The mammalian genome, organised into chromatin, adopts a three-dimensional (3D) folding within the cell nucleus with spatially segregated active and repressed compartments, termed A and B. However, how nucleosome deposition impacts these levels of organisation is unknown. Here, we monitored changes in 3D genome folding by Hi-C after impairing the chaperone HIRA, involved in histone H3.3 deposition. In the absence of HIRA, H3.3 enrichment decreases in compartment A that also shows weaker interactions. At this scale, histone post-translational modifications (PTMs) do not follow H3.3 changes. In line with impaired H3.3 nucleosome maintenance, compartment A accessibility measured by ATAC-seq increases. Specifically, at active genes, accessibility increases in gene bodies but decreases at promoters where compensation by H3.1 reduces nucleosome turnover. Notably, regions flanking active genes show reduced insulation. We conclude that the HIRA-dependent pathway involved in H3.3 deposition is key to maintain higher order organisation in active regions and impact compartmentalisation independently of histone PTMs."],"study_type":["ChIP-seq"],"species":["Homo sapiens"],"pubmed_title":["HIRA-dependent provision of histone H3.3 in active chromatin ensures genome compartmentalisation"],"pubmed_authors":["Tina Karagyozova","Jean-Pierre Quivy","Marc Marti-Renom","Alberto Gatto","Tina Karagyozova, Alberto Gatto, Audrey Forest, Jean-Pierre Quivy, Marc Marti-Renom, Leonid Mirny, Geneviève Almouzni","Audrey Forest","Leonid Mirny","Geneviève Almouzni"],"additional_accession":[]},"is_claimable":false,"name":"Distribution of active (H3K4me1, H3K4me3, H3K27ac) and inactive (H3K9me3, H3K27me3) histone PTMs in WT and HIRA KO HeLa cells","description":"We profiled the enrichment of active (H3K4me1, H3K4me3, H3K27ac) and inactive (H3K9me3, H3K27me3) histone PTMs in cells that are wild-type (WT) or knock-out (KO) for the H3.3-specific chaperone HIRA. We performed native ChIP-seq following MNase digestion to isolate nucleosomes in H3.1-SNAP and H3.3-SNAP-bearing HeLa cells. We had previously assayed the distribution of the H3.1 and H3.3 histone variants (Gatto et al., 2022) in the same cell lines, so we generated this PTM ChIP-seq data to compare the behaviour of the variants with that of H3 modifications.","dates":{"release":"2025-08-07T00:00:00Z","modification":"2025-08-08T00:02:22.876Z","creation":"2024-09-04T21:28:17.41Z"},"accession":"E-MTAB-14416","cross_references":{"ENA":["ERP163837"],"Biostudies":["E-MTAB-14419","E-MTAB-14415","E-MTAB-14417","E-MTAB-10619"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002692","EFO_0005518","EFO_0004184"],"doi":["10.1101/2024.08.27.609896"]}}