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DOT1L provides transcriptional memory through PRC1.1 antagonism [ChIP-Seq]

GSE260742 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 158 samples Submitted 2025/11/23 Platform GPL24676Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 158 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
158 samples: 142 distinct titles, 12 of them repeatedGroups 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.
Paper
Low-loss hollow-core silica/air photonic bandgap fibreNature · 2003
Summary (written by the submitters)
DOT1L and Menin are essential cofactors for the oncogenic activity of MLL-fusion proteins (MLL-FPs) in leukaemia. However, the mechanisms underpinning the therapeutic effects of their inhibitors remain unclear. Here, we identify a critical role for the non-canonical Polycomb repressive complex 1.1 (PRC1.1) in mediating the cellular responses to DOT1L and Menin inhibitors.
Read the full summary ↓
Menin inhibition induces PRC1.1-dependent deposition of H2AK119ub to silence a subset of MLL-FP targets, whereas DOT1L inhibition results in a genome-wide increase in H2AK119ub. We show that enhanced PRC1.1 activity arises specifically from the progressive loss of DOT1L-mediated H3K79 methylation, independent of MLL-FP displacement or transcriptional repression. This regulatory crosstalk is conserved across cell types and is driven by direct biochemical antagonism between H3K79 methylation and PRC1.1 activity. Together, our findings establish DOT1L as a component of transcriptional memory co-opted in leukaemia and suggest it serves as the missing link balancing the opposing forces of the MLL-Polycomb system.
Published in
Low-loss hollow-core silica/air photonic bandgap fibre
Smith CM, Venkataraman N, Gallagher MT et al. · Nature 2003 · PMID 12904788 · doi:10.1038/nature01849
This dataset
Open GSE260742 in finder → Find more 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 GSE260742_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 PRJNA1083204 and SRA study SRP493030. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 12904788) ↗
Study design
142 distinct titles, 12 of them repeated
MLLAF9 Control - DMSO H2AK119ub ×3 MLLAF9 Control - SGC0946 5uM H2AK119ub ×3 MLLAF9 Control - VTP50469 500nM H2AK119ub ×3 NTvKO Control - DMSO input ×3 MLLAF9 Control - DMSO input ×2 MLLAF9 Control - DMSO RING1B ×2 NTvKO PCGF1 KO DMSO H2AK119ub ×2 NTvKO PCGF1 KO SGC0946 5uM H2AK119ub ×2 +4 more

How we read this: Read from 158 sample titles: 142 distinct titles with little repetition. 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

+ 118 more — browse all 158 samples with per-sample file links →

Datasets on a similar topic

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