GEO series

HIRA-mediated H3.3 deposition preserves hepatocyte cell identity during non-proliferative liver aging

GSE324042 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 2 samples Submitted 2026/04/02 Platform GPL34475

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 2 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Mus musculus (mouse)
Samples: 2 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: HIRA-mediated H3.3 deposition preserves hepatocyte cell identity during liver agingResearch square · 2026

Summary (written by the submitters)

Age-associated functional decline is partly driven by progressive chromatin degeneration. Conversely, maintenance of chromatin integrity preserves cell identity and promotes healthy aging, albeit through different mechanisms in proliferating and non-proliferating cells. However, whether tissue regeneration with its associated cell proliferation can rescue defects in epigenetic maintenance in otherwise non-proliferative cells remains unclear.

Read the full summary ↓

The histone chaperone HIRA deposits the histone variant H3.3 in a DNA replication–independent manner, leading to its accumulation in aging, non-proliferating cells. Here, we show that hepatocyte-specific loss of HIRA causes loss of cell identity, metabolic dysfunction, and accelerated fibrotic pathology with age. Transcriptomic and epigenomic analyses indicate that HIRA–H3.3 preserves chromatin integrity and sustains transcription of highly expressed genes. Partial hepatectomy, associated with induced proliferation, restores cell identity with compensatory deposition of canonical histones H3.1/2. Together, these results demonstrate that HIRA-mediated H3.3 deposition is essential for safeguarding cell identity and tissue function during aging of non-proliferating cells, but this function can be rescued by tissue regeneration with associated cell proliferation.

Published in

HIRA-mediated H3.3 deposition preserves hepatocyte cell identity during liver aging

Adams P, Arnold R, Teneche M et al. · Research square 2026 · PMID 42282022 · doi:10.21203/rs.3.rs-9261217/v1

This dataset

Open GSE324042 in finder → Find more mouse ChIP / ATAC / CUT&Tag datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE324042_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1433269 and SRA study SRP681614. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42282022) ↗

Samples in this study

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+ 2 more — browse all 2 samples with per-sample file links →

Datasets on a similar topic

GSE324283 HIRA-mediated H3.3 deposition preserves hepatocyte cell identity during non-proliferative liver aging [CUT&Tag] 18 samples shares non-proliferative, hira-mediated, deposition, hepatocyte, preserves, identity, liver, aging
GSE324372 HIRA-mediated H3.3 deposition preserves hepatocyte cell identity during non-proliferative liver aging [RNA-Seq 2] 20 samples shares non-proliferative, hira-mediated, deposition, hepatocyte, preserves, identity, liver, aging
GSE324284 HIRA-mediated H3.3 deposition preserves hepatocyte cell identity during non-proliferative liver aging [RNA-Seq HIRAKO_1Y] 18 samples shares non-proliferative, hira-mediated, deposition, hepatocyte, preserves, identity, liver, aging
GSE224825 Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis [Prox1 OE MEF/4in1 ATAC-seq] 12 samples shares hepatocyte, identity, liver
GSE224831 Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis [Prox1 OE iHep Timecourse RNA-seq] 16 samples shares hepatocyte, identity, liver
GSE224830 Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis [Prox1 OE iHep Timecourse scRNA-seq] 13 samples shares hepatocyte, identity, liver
GSE294859 Distinct hepatocyte adaptations during gestation and lactation [pregnant_liver_mm10_CUT_RUN] 10 samples shares hepatocyte, liver
GSE281035 PAR3-mediated coordination of hepatocyte proliferation, maturation, and architecture in liver development and regeneration 128 samples shares hepatocyte, liver

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.