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CFP1-mediated H3K4me3 broad domains control early B cell lineage fate determination [ChIP-Seq]

GSE289599 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 13 samples Submitted 2026/02/08 Platform GPL28330
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 13 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
13 samples: 4 × CFP1 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol vs 2 × RAG2 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol vs 2 × RAG2 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biolGroups 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
CFP1-mediated H3K4me3 broad domains control early B cell lineage fate determinationNucleic acids research · 2026
Summary (written by the submitters)
Histone H3K4me3 broad domain (BD) is a unique epigenetic feature to mark cell identity-associated genes, but its physiological role in lineage differentiation remains unclear. Here we show that CFP1, an integral component of the Setd1A/B methyltransferase complex, is critically required for functional H3K4me3-BD installation and B cell fate determination.
Read the full summary ↓
Cfp1 deletion impairs H3K4me3-BDs on a subset of B-lineage genes and redistributes H3K4me3 from active genes to bivalent promoters. Transcription of subsets of H3K4me3-BD-bound gene is diminished in part due to reduced RNA Pol II at the promoter and gene body. Specifically, CFP1 ablation abolishes H3K4me3-BD at the recombination center and distal PAIR elements in the immunoglobulin heavy chain (IgH) gene, severely compromises its locus contraction for efficient V-to-DJ recombination and consequently arrests cells at the pro-B stage. Moreover, Cfp1-deficient pro-B cells upregulate a panel of progenitor and myeloid-specific genes with elevated H3K4me3 marks and can trans-differentiate into various myeloid cell types. Therefore, our study reveals pivotal roles for CFP1-mediated H3K4me3-BDs in the transcriptional regulation of cell lineage fate specification and commitment.
Published in
CFP1-mediated H3K4me3 broad domains control early B cell lineage fate determination
Bai W, Yang Y, Zhao Y et al. · Nucleic acids research 2026 · PMID 41728956 · doi:10.1093/nar/gkag125
This dataset
Open GSE289599 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 GSE289599_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 PRJNA1223130 and SRA study SRP563719. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41728956) ↗
Study design
4 × CFP1 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol vs 2 × RAG2 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol vs 2 × RAG2 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol

Supports a between-group comparison across 8 samples.

How we read this: 3 replicated groups read from 13 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
Datasets on a similar topic

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