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Hi-C to compare 3D genome organisation in HIRA KO HeLa cells rescued with HIRA

ABSTRACT: Hi-C to compare 3D genome organisation in HIRA KO HeLa cells rescued with HIRA

PROVIDER: PRJEB79847 | ENA |

REPOSITORIES: ENA

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Hi-C to compare 3D genome organisation in HIRA KO HeLa cells rescued with HIRA

Project description:We performed Hi-C in asynchronous HeLa cells that knock-out (KO) for the H3.3-specific chaperone HIRA and bear an exogenous H3.1-SNAP and H3.3-SNAP gene transfected with HIRA-YFP (HIRA) or YFP only (control) plasmid.

2025-08-07 | E-MTAB-14431 | biostudies-arrayexpress

Hi-C to compare 3D genome organisation in WT to HIRA KO HeLa cells

Project description:Hi-C to compare 3D genome organisation in WT to HIRA KO HeLa cells

| PRJEB79848 | ENA

EdU-seq and H3 variant SNAP capture-seq in HIRA KO HeLa cells rescued with HIRA

Project 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).

2025-08-07 | E-MTAB-14419 | biostudies-arrayexpress

Hi-C to compare 3D genome organisation in WT to HIRA KO HeLa cells

Project description:We performed Hi-C in asynchronous HeLa cells that are wild-type (WT) or knock-out (KO) for the H3.3-specific chaperone HIRA and bear an exogenous H3.1-SNAP and H3.3-SNAP gene.

2025-08-07 | E-MTAB-14433 | biostudies-arrayexpress

EdU-seq and H3 variant SNAP capture-seq in HIRA KO HeLa cells rescued with HIRA

Project description:EdU-seq and H3 variant SNAP capture-seq in HIRA KO HeLa cells rescued with HIRA

| PRJEB79724 | ENA

Total RNA-seq in WT and HIRA KO HeLa cells

Project description:We performed total RNA-seq of G1/S-synchronised HeLa cells that are wild-type (WT) or knock-out (KO) for the H3.3-specific chaperone HIRA and bear an exogenous H3.1-SNAP and H3.3-SNAP gene.

2025-08-07 | E-MTAB-14417 | biostudies-arrayexpress

Chromatin accessibility by ATAC-seq in WT and HIRA KO HeLa cells

Project description:We profiled accessibility by ATAC-seq of G1/S-synchronised HeLa cells that are wild-type (WT) or knock-out (KO) for the H3.3-specific chaperone HIRA and bear an exogenous H3.1-SNAP and H3.3-SNAP gene.

2025-08-07 | E-MTAB-14415 | biostudies-arrayexpress

Distribution of active (H3K4me1, H3K4me3, H3K27ac) and inactive (H3K9me3, H3K27me3) histone PTMs in WT and HIRA KO HeLa cells

Project 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.

2025-08-07 | E-MTAB-14416 | biostudies-arrayexpress

Total RNA-seq in WT and HIRA KO HeLa cells

Project description:Total RNA-seq in WT and HIRA KO HeLa cells

| PRJEB79723 | ENA

Expression data from Control and HIRA knockdown cells

Project description:The HIRA chaperone complex, comprised of HIRA, UBN1 and CABIN1, collaborates with histone-binding protein ASF1a to incorporate histone variant H3.3 into chromatin in a DNA replication-independent manner. To better understand its function and mechanism, we integrated HIRA, UBN1, ASF1a and histone H3.3 ChIP-seq and gene expression analyses. Most HIRA-binding sites co-localize with UBN1, ASF1a and H3.3 at active promoters and active and weak/poised enhancers. At promoters, binding of HIRA/UBN1/ASF1a correlates with the level of gene expression. HIRA is required for deposition of histone H3.3 at its binding sites. There are marked differences in nucleosome and co-regulator composition at different classes of HIRA-bound regulatory site. Underscoring this, we report novel physical interactions between the HIRA complex and transcription factors, a chromatin insulator and an ATP-dependent chromatin-remodelling complex. Our results map the distribution of the HIRA chaperone across the chromatin landscape and point to different interacting partners at functionally distinct regulatory sites. We used microarrays to detail the global programme of gene expression after knockdown of HIRA HeLa cells were nucleofacted with Dharmacon control siRNA and siRNA to HIRA and RNA was isolated 72 hours after transfection in four biological replicates

2013-04-18 | E-GEOD-45022 | biostudies-arrayexpress

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