GEO series

KMT2C and KMT2D amplify GRHL2-driven enhancer activation [Cut&Run]

GSE325765 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 16 samples Submitted 2026/03/28 Platform GPL34328

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 16 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: 16 samples: 2 × Naive ESC, WT, GRHL2, vs 2 × Naive ESC, Kmt2cKO; Kmt2dKO, GRHL2, vs 2 × Form ESC, WT, GRHL2, vs 2 × Form ESC, Kmt2cKO; Kmt2dKO, GRHL2,Groups 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

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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 GSE325765_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 PRJNA1441582 and SRA study SRP686021. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

2 × Naive ESC, WT, GRHL2, vs 2 × Naive ESC, Kmt2cKO; Kmt2dKO, GRHL2, vs 2 × Form ESC, WT, GRHL2, vs 2 × Form ESC, Kmt2cKO; Kmt2dKO, GRHL2,

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 16 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

GSM9612734 Naive ESC, WT, GRHL2, rep1 Naive ESC, WT, GRHL2,
GSM9612735 Naive ESC, WT, GRHL2, rep2 Naive ESC, WT, GRHL2,
GSM9612736 Naive ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep1 Naive ESC, Kmt2cKO; Kmt…
GSM9612737 Naive ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep2 Naive ESC, Kmt2cKO; Kmt…
GSM9612738 Form ESC, WT, GRHL2, rep1 Form ESC, WT, GRHL2,
GSM9612739 Form ESC, WT, GRHL2, rep2 Form ESC, WT, GRHL2,
GSM9612740 Form ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep1 Form ESC, Kmt2cKO; Kmt2…
GSM9612741 Form ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep2 Form ESC, Kmt2cKO; Kmt2…
GSM9612742 Naive ESC, WT, GRHL2, rep1, techrep2
GSM9612743 Naive ESC, WT, GRHL2, rep2, techrep2
GSM9612744 Naive ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep1, techrep2
GSM9612745 Naive ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep2, techrep2
GSM9612746 Form ESC, WT, GRHL2, rep1, techrep2
GSM9612747 Form ESC, WT, GRHL2, rep2, techrep2
GSM9612748 Form ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep1, techrep2
GSM9612749 Form ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep2, techrep2

Datasets on a similar topic

GSE325799 KMT2C and KMT2D amplify GRHL2-driven enhancer activation [CUT&Tag] 80 samples shares kmt2c, kmt2d, grhl2-driven, activation, enhancer, amplify
GSE237390 Loss of Kmt2c or Kmt2d drives brain metastasis via KDM6A-dependent upregulation of MMP3 [ChIP-seq] 54 samples shares kmt2c, kmt2d
GSE336091 KMT2C catalytic activity regulates enhancer H3K4me1 and synaptic gene expression in cortical excitatory neurons [CUT&Tag] 48 samples shares kmt2c, enhancer
GSE290849 Acute intervention reveals critical roles of BAF, KMT2D and p300 in MyoD binding on enhancers 143 samples shares kmt2d, enhancer
GSE335970 KMT2C catalytic activity regulates enhancer H3K4me1 and synaptic gene expression in cortical excitatory neurons [RNA-Seq] 39 samples shares kmt2c, enhancer
GSE245647 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [ChIP-seq] 62 samples shares activation, enhancer
GSE245646 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [ATAC-seq_muscle] 22 samples shares activation, enhancer
GSE244812 Multi-omics profiling of retinal pigment epithelium reveals enhancer-driven activation of RANK-NFATc1 signaling in traumatic proliferative vitreoretinopathy. 54 samples shares activation, enhancer

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