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Histone succinylation directly inhibits Jumonji domain demethylases and stabilizes repressive chromatin states [RNA-Seq]

GSE331257 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2026/05/22 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 24 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
24 samples: 6 conditions, mostly with about 4 replicates eachGroups 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; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Summary (written by the submitters)
We investigate the relationship between histone succinylation and Jumonji C (JmjC) domain-containing histone demethylases, a class of enzymes that catalyzes the removal of histone methylation. By using quantitative proteomics and peptide pull-down assays, we identified Jumonji demethylases as candidate interactors of succinylated histone peptides.
Read the full summary ↓
Biochemical assays demonstrate that succinylated histone peptides bind and inhibit the demethylase activity of KDM4D and KDM6B in a dose-dependent manner. Notably, these two demethylases are responsible for the removal of the silencing marks H3K9me2/3 and H3K27me2/3. We increased histone succinylation in a HepG2/C3A cell model by providing supraphysiological sodium succinate and demonstrated that H3K9me2/3 and H3K27me2/3 increased in relative abundance as well. CUT&Tag and ChIP–mass spectrometry revealed co-occurrence of succinylation with repressive methylation marks, together with reduced levels of transcribed RNA. Altogether, these findings support a model in which histone succinylation contributes to maintaining the silencing marks H3K9me2/3 and H3K27me2/3 on chromatin by locally inhibiting Jumonji domain demethylases. This work establishes a mechanistic link between metabolic state and chromatin regulation and suggests a role for histone succinylation in the maintenance of heterochromatin.
This dataset
Open GSE331257 in finder → Find more human RNA-seq 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 GSE331257_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1467578 and SRA study SRP701622. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly with about 4 replicates each
HepG2/C3A cells, control, 48h treatment, biol ×4 HepG2/C3A cells, control, 96h treatment, biol ×4 HepG2/C3A cells, 10 mM sodium acetate, 48h tr… ×4 HepG2/C3A cells, 10 mM sodium acetate, 96h tr… ×4 HepG2/C3A cells, 10 mM sodium succinate, 48h … ×4 HepG2/C3A cells, 10 mM sodium succinate, 96h … ×4

Supports a between-group comparison across 24 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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
Datasets on a similar topic

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