GEO series

Epigenomic manipulation reveals the relationship between locus specific chromatin dynamics and gene expression [Hi-C]

GSE282761 Homo sapiens (human) Other 8 samples Submitted 2025/11/18 Platform GPL30173

At a glance

human · 8 samples

Organism: Homo sapiens (human)
Samples: 8 samples: 2 × 24hr Control Hi-C vs 2 × 24hr SAHA Hi-C vs 2 × 48hr Control Hi-C vs 2 × 48hr SAHA Hi-CGroups 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: Disruption of histone acetylation homeostasis reveals multilayered chromatin regulation for transcriptional resiliencyEpigenetics & chromatin · 2025

Summary (written by the submitters)

Dysregulation of epigenetic processes leads to a plethora of abnormalities including disease states such as cancer. Therapies focused on epigenetic modulation alter gene expression to correct dysfunction, though the mechanisms and perpetuation of these states is unknown. Here, we use integrated epigenomics and three-dimensional chromatin structure-function analyses after acute histone deacetylase inhibitor cancer drug treatment (suberoylanilide hydroxamic acid in lung cancer cells).

Read the full summary ↓

Treatment induced substantial (13%) genomic rearrangement that rebounds despite persistent gene expression changes and spreading of acetylation. The chromatin functional landscape (accessibility, active transcription modification, and gene expression) is controlled and locus-specific, while chromatin contacts are globally altered resulting in a moderate weakening of topologically associating domains. Chromatin states are more dynamic at transcriptionally active loci while genes with reduced expression are epigenetically stable suggesting chromatin architectural turnover and nucleosome remodeling is locus-specific and underlies the bidirectional expression changes. Thus, local 3D chromatin and genome structural dynamics is integral for loci regulation in response to epigenomic perturbation. The partial persistence of these altered features may have larger implications for efficacy of epigenetic drugs in amelioration of disease states.

Published in

Disruption of histone acetylation homeostasis reveals multilayered chromatin regulation for transcriptional resiliency

Venu V, Small EM, Roth C et al. · Epigenetics & chromatin 2025 · PMID 41044756 · doi:10.1186/s13072-025-00631-4

This dataset

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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 (GSE282761_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 PRJNA1135966. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41044756) ↗

Study design

2 × 24hr Control Hi-C vs 2 × 24hr SAHA Hi-C vs 2 × 48hr Control Hi-C vs 2 × 48hr SAHA Hi-C

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 8 sample titles; they account for 8 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

GSM8650136 24hr Control Hi-C Bio rep 1 24hr Control Hi-C
GSM8650137 24hr Control Hi-C Bio rep 2 24hr Control Hi-C
GSM8650138 24hr SAHA Hi-C Bio rep 1 24hr SAHA Hi-C
GSM8650139 24hr SAHA Hi-C Bio rep 2 24hr SAHA Hi-C
GSM8650140 48hr Control Hi-C Bio rep 1 48hr Control Hi-C
GSM8650141 48hr Control Hi-C Bio rep 2 48hr Control Hi-C
GSM8650142 48hr SAHA Hi-C Bio rep 1 48hr SAHA Hi-C
GSM8650143 48hr SAHA Hi-C Bio rep 2 48hr SAHA Hi-C

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