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CFP1 promotes germinal center affinity maturation and restrains and memory B cell differentiation through H3K4me3 modulation

GSE288059 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 12 samples Submitted 2025/08/02 Platform GPL28330
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
12 samples: 3 × RNA_GCB cells, Cfp1fl/fl vs 3 × RNA_GCB cells, Cfp1fl/flAcidaCre vs 3 × H3K4me3_GCB cells, Cfp1fl/fl vs 3 × H3K4me3_GCB cells, Cfp1fl/flAcidaCreGroups 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 promotes germinal center affinity maturation and restrains memory B cell differentiation through H3K4me3 modulationNature communications · 2025
Summary (written by the submitters)
Affinity maturation and differentiation of B cells in the germinal center (GC) are tightly controlled by epigenetically regulated transcription programs but the underlying mechanisms are only partially understood. Here we show that CFP1, an integral component of the histone methyltransferase complex Set1A/B, is critically required for GC responses.
Read the full summary ↓
CFP1 deficiency in activated B cells greatly impairs GC formation with diminished proliferation, somatic hypermutation and affinity maturation. Mechanistically, CFP1 deletion reduces H3K4me3 marks at a subset of cell cycle and GC-related genes and impairs their transcription. Importantly, CFP1 promotes the expression of transcription factors MEF2B and OCA-B and the Bcl6 enhancer-promoter looping for its efficient induction. Accordingly, CFP1-deficient GCB cells upregulate IRF4 and preferentially differentiate into plasmablasts. Furthermore, CFP1 ablation upregulates a panel of pre-memory genes with elevated H3K4me3 and leads to markedly expanded memory B populations. In summary, our study reveals that CFP1-safeguarded epigenetic regulation ensures proper dynamics of GCB cells for affinity maturation and prevents the pre-mature exit from GC as memory cells.
Published in
CFP1 promotes germinal center affinity maturation and restrains memory B cell differentiation through H3K4me3 modulation
Zhao Y, Gong S, Yang Y et al. · Nature communications 2025 · PMID 40866336 · doi:10.1038/s41467-025-63291-8
This dataset
Open GSE288059 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 GSE288059_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 PRJNA1186388 and SRA study SRP545816. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40866336) ↗
Study design
3 × RNA_GCB cells, Cfp1fl/fl vs 3 × RNA_GCB cells, Cfp1fl/flAcidaCre vs 3 × H3K4me3_GCB cells, Cfp1fl/fl vs 3 × H3K4me3_GCB cells, Cfp1fl/flAcidaCre

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 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
Datasets on a similar topic

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