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KMT2C and KMT2D amplify GRHL2-driven enhancer activation [CUT&Tag]

GSE325799 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 80 samples Submitted 2026/03/28 Platform GPL34328
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 80 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
80 samples: 40 conditions, mostly in duplicateGroups 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)
The activation of cis-regulatory enhancers is essential for cell fate specification by driving cell type-specific gene expression. Differentiation models are widely used to study enhancer biology but the asynchronous and interdependent nature of gene regulatory changes during cell state transitions can complicate mechanistic studies.
Read the full summary ↓
To overcome these limitations, here we develop a tamoxifen-gated system for acute enhancer activation in embryonic stem cells (ESCs) based on GRHL2, a pioneer transcription factor which naturally becomes expressed as naive ESCs differentiate into the formative ESC state. Using this system, we investigate the functional relationship between GRHL2 and the histone mono-methyltransferases KMT2C and KMT2D (KMT2C/D). GRHL2 readily binds its target sites independent of KMT2C/D. However, in the absence of KMT2C/D, there are dramatic reductions in H3K4me1/2, P300 recruitment, and H3K27ac deposition at these sites as well as diminished transcriptional activation. Still, strikingly, a basal level of active enhancer mark acquisition and transcriptional activation occurs. Consistent with these findings, during the naive to formative ESC differentiation, GRHL2 enhancer remodeling and target expression is also strongly but incompletely dependent on KMT2C/D. Together, these results define a functional co-activator relationship in which KMT2C/D act as important amplifiers of GRHL2-driven enhancer activation in ESCs and establish a rapid inducible system for dissecting the kinetics and enzymatic dependencies of pioneer transcription factor mediated enhancer remodeling.
This dataset
Open GSE325799 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 GSE325799_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 PRJNA1441644 and SRA study SRP686072. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
40 conditions, mostly in duplicate
Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtO… ×2 Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam… ×2 Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8… ×2 Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 … ×2 Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtO… ×2 Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam… ×2 Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8… ×2 Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 … ×2 +32 more

Supports a between-group comparison across 80 samples.

How we read this: 40 replicated groups read from 80 sample titles; they account for 80 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

+ 40 more — browse all 80 samples with per-sample file links →

Datasets on a similar topic

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