GEO series

Molecular Mechanisms of the MLL4 Complex in H3K4 Methylation and p53-Dependent Transcription Activation [ChIP-Seq]

GSE308469 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 20 samples Submitted 2026/05/26 Platform GPL34284

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 20 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: Homo sapiens (human)
Samples: 20 samples: 6 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)

MLL4 is a mammalian H3K4 mono-methyltransferase that plays a critical role in enhancer-regulated gene activation and tissue-specific gene expression during development. Here, we utilized a reconstituted MLL4 complex (MLL4C) containing a truncated MLL4 “fusion” protein (MLL4F) that retains its catalytic SET domain and N-terminal functional regions for comprehensive structural and functional analyses.

Read the full summary ↓

In vitro H3K4 methyltransferase assays demonstrated that MLL4 catalytic activity is notably stimulated by p53 and CBP/p300. Cryo-electron microscopy (cryo-EM) analysis revealed that the MLL4 fusion core complex engages the nucleosome in three major distinct conformational states, providing mechanistic insights into the regulation of MLL4 and other MLL family methyltransferases by two structurally rigid modules: the SET–ASH2L–DPY30 module and the RBBP5–WDR5 module. In addition, we delineated a third structurally rigid module within the functional region upstream of MLL4 SET domain, encompassing the tandem PHD4–6, PHD7, and FYR domains, which is essential for MLL4- and p53-dependent transcription. Comparative structural analyses reveal that this third module is evolutionarily conserved across MLL1 to MLL4. Furthermore, we employed crosslinking mass spectrometry and integrative modeling to generate a complete model of the nine-subunit MLL4FC complex and elucidated its functional interactions with p53. Finally, genomic studies in the human colon cancer cell line HCT116 revealed that MLL4 colocalizes with p53 at active enhancers of p53 target genes. MLL4 knockout led to significant downregulation of p53-regulated genes, coupled with the reduction of p53 binding at active enhancers. These findings provide molecular insights into the catalytic and transcriptional functions of the MLL4 complex in establishing active enhancers and facilitating p53-dependent transcription activation.

This dataset

Open GSE308469 in finder → Find more human 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 GSE308469_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 PRJNA1330720 and SRA study SRP621857. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in duplicate

H3K4me3_MLL4WT ×2 H3K4me3_MLL4KO ×2 H3K27ac_MLL4WT ×2 H3K27ac_MLL4KO ×2 p53_MLL4WT ×2 p53_MLL4KO ×2 H3K4me1_MLL4WT ×1 H3K4me1_MLL4KO ×1 +6 more

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 20 sample titles; they account for 12 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

GSM9246356 H3K4me1_MLL4WT
GSM9246357 H3K4me1_MLL4KO
GSM9246358 H3K4me3_MLL4WT_rep1 H3K4me3_MLL4WT
GSM9246359 H3K4me3_MLL4KO_rep1 H3K4me3_MLL4KO
GSM9246360 H3K27ac_MLL4WT_rep1 H3K27ac_MLL4WT
GSM9246361 H3K27ac_MLL4KO_rep1 H3K27ac_MLL4KO
GSM9246362 MLL4_MLL4WT
GSM9246363 MLL4_MLL4KO
GSM9246364 p53_MLL4WT_rep1 p53_MLL4WT
GSM9246365 p53_MLL4KO_rep1 p53_MLL4KO
GSM9246366 H3K4me3_MLL4WT_rep2 H3K4me3_MLL4WT
GSM9246367 H3K4me3_MLL4KO_rep2 H3K4me3_MLL4KO
GSM9246368 MLL1_MLL4WT
GSM9246369 MLL1_MLL4KO
GSM9246370 Input_MLL4WT
GSM9246371 Input_MLL4KO
GSM9246372 p53_MLL4WT_rep2 p53_MLL4WT
GSM9246373 p53_MLL4KO_rep2 p53_MLL4KO
GSM9246374 H3K27ac_MLL4WT_rep2 H3K27ac_MLL4WT
GSM9246375 H3K27ac_MLL4KO_rep2 H3K27ac_MLL4KO

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