GEO series

Ablation of Linker Histone H1.4 Reveals Focal Regulation of AP-1 Directed Enhancers and Chromatin Accessibility [4sU]

GSE286581 Homo sapiens (human) Other 6 samples Submitted 2025/07/21 Platform GPL16791

At a glance

human · 6 samples

Organism: Homo sapiens (human)
Samples: 6 samples: 2 × 4sUseq UL3 vs 2 × 4sUseq UL3 dH1 cloneA vs 2 × 4sUseq UL3 dH1 cloneBGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI.
Paper: Ablation of histone H1.4 reveals the focal regulation of AP-1 directed enhancersiScience · 2025

Summary (written by the submitters)

Linker histone H1 and the four nucleosomal histone proteins form the greater chromatosome superstructure of chromatin. While a critical component of the epigenetic landscape, the specific role of H1 has remained elusive due in part to compensation by other H1 family members, a lack of genome-wide analyses, and suitable model systems. Ablation of H1.4 in a human osteosarcoma line with high H1-4 expression resulted in broad changes in DNA accessibility as well as gene expression.

Read the full summary ↓

Genes in critical signaling pathways are upregulated with H1.4 loss (RAR, acetylcholine/glutaminergic receptors) while extracellular matrix and collagen biosynthesis genes are repressed. The gene loci of the same critical pathways were enriched in differentially accessible chromatin after loss of H1.4, and many of this differential chromatin overlaps regions of known enhancer regions. The AP-1 binding motif was highly enriched at sites with reduced accessibility while sites with gained chromatin accessibility were enriched in more basal factor motifs (TBP, SRF). At sites of altered chromatin accessibility following H1.4-loss, concomitant changes to core histone proteins were observed (H3K27ac and H3K4me1), and the changes in PTMs was concordant with the change in accessibility. Alterations to chromatin accessibility and epigenetic activity were enriched at regions with known enhancer-like chromatin, and the size of the altered chromatin footprints were consistent with enhancer regions. Sites which gain chromatin accessibility localize to polycomb, heterochromatin and quiescent/low chromatin states, but were found to gain RNA transcription in cells lacking H1.4. Broad changes in chromatin accessibility and activity, as well as robust changes in gene transcription when H1.4 is abolished, place linker H1.4 as a hitherto underappreciated regulator of transcription response patterns as well as a dynamic member of regulatory chromatin.

Published in

Ablation of histone H1.4 reveals the focal regulation of AP-1 directed enhancers

Gokey NG, Ward JM, Milliman EJ et al. · iScience 2025 · PMID 41054521 · doi:10.1016/j.isci.2025.113426

This dataset

Open GSE286581 in finder → Find more human datasets →

Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE286581_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA1209948. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41054521) ↗

Study design

2 × 4sUseq UL3 vs 2 × 4sUseq UL3 dH1 cloneA vs 2 × 4sUseq UL3 dH1 cloneB

Supports a between-group comparison across 6 samples.

How we read this: 3 replicated groups read from 6 sample titles; they account for 6 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM8729783 4sUseq UL3 Rep1 4sUseq UL3
GSM8729784 4sUseq UL3 Rep2 4sUseq UL3
GSM8729785 4sUseq UL3 dH1 cloneA Rep1 4sUseq UL3 dH1 cloneA
GSM8729786 4sUseq UL3 dH1 cloneA Rep2 4sUseq UL3 dH1 cloneA
GSM8729787 4sUseq UL3 dH1 cloneB Rep1 4sUseq UL3 dH1 cloneB
GSM8729788 4sUseq UL3 dH1 cloneB Rep2 4sUseq UL3 dH1 cloneB

Datasets on a similar topic

GSE204911 Mapping genotypes to chromatin accessibility profiles in single cells [Genotyping GoT-ChA amplicon] 27 samples shares accessibility, chromatin
GSE201820 CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis [H2_HiC] 8 samples shares accessibility, chromatin
GSE281238 Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility 7 samples shares accessibility, chromatin
GSE273054 Differential chromatin accessibility analysis elucidates mechanisms of coronary artery disease-associated genetic variation 119 samples shares accessibility, chromatin
GSE244594 Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry 84 samples shares accessibility, chromatin
GSE160298 The chromatin accessibility landscape of T-Cell Acute Lymphoblastic Leukemia 80 samples shares accessibility, chromatin
GSE204912 Mapping genotypes to chromatin accessibility profiles in single cells 55 samples shares accessibility, chromatin
GSE287902 BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run] 40 samples shares accessibility, chromatin

Search all human datasets in GEO →

Share this dataset

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.