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Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes [bullk ATAC-seq]

GSE281967 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 21 samples Submitted 2025/09/05 Platform GPL19057
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 21 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
21 samples: 15 distinct titles, 4 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
Functional Mapping of Epigenomic Regulators Uncovers Coordinated Tumor Suppression by the HBO1 and MLL1 ComplexesCancer discovery · 2025
Summary (written by the submitters)
Epigenetic dysregulation is widespread in cancer. However, the specific epigenetic regulators and the processes they control to drive cancer phenotypes are poorly understood. We employed a novel, scalable and high-throughput in vivo method to perform iterative functional screens of >250 epigenetic regulators within autochthonous oncogenic KRAS-driven lung tumors.
Read the full summary ↓
We identified many previously unappreciated epigenetic tumor-suppressor and tumor-dependency genes. We show that a specific HBO1 complex and MLL1 complex are the most impactful tumor suppressive epigenetic regulators in lung cancer. Histone modifications generated by HBO1 complex are frequently reduced in human lung adenocarcinomas. HBO1 and MLL1 complexes regulate chromatin accessibility at shared genomic regions, lineage fidelity and expression of canonical tumor suppressor genes. The HBO1 and MLL1 complexes are epistatic during lung tumorigenesis, and their functional correlation is conserved in human cancer cell lines. Together, these results provide a phenotypic roadmap of epigenetic regulators in lung tumorigenesis in vivo.
Published in
Functional Mapping of Epigenomic Regulators Uncovers Coordinated Tumor Suppression by the HBO1 and MLL1 Complexes
Tang YJ, Xu H, Hughes NW et al. · Cancer discovery 2025 · PMID 40997327 · doi:10.1158/2159-8290.CD-24-1565
This dataset
Open GSE281967 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 GSE281967_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 PRJNA1186336 and SRA study SRP545355. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40997327) ↗
Study design
15 distinct titles, 4 of them repeated
sgPsip1 mouse_ID LA ×3 sgKat7 mouse ID MT ×3 sgMeaf6 mouse_ID MT ×2 sgKmt2a mouse_ID MT ×2

How we read this: Read from 21 sample titles: 15 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
Datasets on a similar topic

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