{"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-14419"],"description":["Our previous work on the histone H3.3 chaperone HIRA revealed its importance for maintaining the targeting of H3.3 to its pre-existing sites. In concert with replication fork-coupled deposition of the replicative H3.1 variant, this establishes boundaries of H3.3/H3.1, which define early replication initiation zones, which are disrupted in the absence of HIRA (Gatto et al., 2022). We have also recently shown a role of HIRA for active gene organisation and compartment A interactions by Hi-C.  Here, we performed a HIRA rescue experiment in HIRA KO HeLa cells combined with a G1/S synchronisation to assay the recovery of H3.1 and H3.3 distribution (prior to S phase entry) by SNAP capture-seq and the pattern of nascent DNA synthesis in early S phase (2h) by EdU-seq. We also include H3.3 SNAP capture-seq from an asynchronous HIRA rescue we performed to assay recovery of genome organisation by Hi-C (submitted as a separate ArrayExpress entry)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - For H3.1/H3.3-SNAP ChIP-seq, we collected either G1/S-arrested cells by a double thymidine block (t0) or asynchronous cells (asynch). For EdU-seq, used to map sites of ongoing DNA synthesis, we released G1/S synchronized cells in S-phase as described in (Gatto et al., 2022). Ninety minutes after release of cells from the G1/S block, we performed a 30min pulse labelling by adding EdU (25μM) to the medium. For all experiments, we collected 4 million cells/condition.","Nucleic Acid Extraction - We performed SNAP capture-seq of G1/S-synchronised cells by double thymidine block as described in (Forest et al., 2024; Gatto et al., 2022).","Sequencing - Samples were sequenced on Illumina NovaSeq 6000 (PE100) at the Next Generation Sequencing (NGS) platform of Institut Curie.","Growth Protocol - We used HeLa cells stably expressing H3.1-SNAP-HA or H3.3-SNAP-HA which were knocked out for HIRA (KO, CRISPR/Cas9 HIRA KO) and transfected them with plasmids expressing with YFP (control) or HIRA-YFP 48 prior to collection as in (Ray-Gallet et al., 2018). Cell lines were grown and synchronized at the G1/S transition using a double thymidine block as described in (Forest et al., 2024; Gatto et al., 2022). All cell lines were tested negative for mycoplasma.","Library Construction - We prepared sequencing libraries at the Next Generation Sequencing (NGS) platform from Institut Curie with the Illumina TruSeq ChIP kit."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["ChIP-seq"],"species":["Homo sapiens"],"pubmed_title":["HIRA defines early replication initiation zones independently of their genome compartment"],"pubmed_authors":["Tina Karagyozova","Jean-Pierre Quivy","Alberto Gatto","Marc Mart-Renom","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":"EdU-seq and H3 variant SNAP capture-seq in HIRA KO HeLa cells rescued with HIRA","description":"Our previous work on the histone H3.3 chaperone HIRA revealed its importance for maintaining the targeting of H3.3 to its pre-existing sites. In concert with replication fork-coupled deposition of the replicative H3.1 variant, this establishes boundaries of H3.3/H3.1, which define early replication initiation zones, which are disrupted in the absence of HIRA (Gatto et al., 2022). We have also recently shown a role of HIRA for active gene organisation and compartment A interactions by Hi-C.  Here, we performed a HIRA rescue experiment in HIRA KO HeLa cells combined with a G1/S synchronisation to assay the recovery of H3.1 and H3.3 distribution (prior to S phase entry) by SNAP capture-seq and the pattern of nascent DNA synthesis in early S phase (2h) by EdU-seq. We also include H3.3 SNAP capture-seq from an asynchronous HIRA rescue we performed to assay recovery of genome organisation by Hi-C (submitted as a separate ArrayExpress entry).","dates":{"release":"2025-08-07T00:00:00Z","modification":"2025-08-08T00:01:52.837Z","creation":"2024-09-04T21:29:34.599Z"},"accession":"E-MTAB-14419","cross_references":{"ENA":["ERP163839"],"Biostudies":["E-MTAB-14416","E-MTAB-14415","E-MTAB-14417"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002692","EFO_0005518","EFO_0004184"],"doi":["10.1101/2024.08.29.610220"]}}