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Jk DNA GAGA MOTIFS ARE REQUIRED FOR LOCAL NUCLEOSOME REMODELING AND Vk-Jk RECOMBINATION [ATAC-Seq]

GSE288585 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 27 samples Submitted 2026/01/14 Platform GPL34328Platform GPL19057
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 27 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
27 samples: 9 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.
Paper
Jk Dna Gaga Motifs Are Required for Local Nucleosome Remodeling and Vk-jk RecombinationResearch square · 2025
Summary (written by the submitters)
Immunoreceptor gene recombination requires complementary 12 bp and 23 bp recombination signal sequences (RSSs). In addition, the RSSs that assemble the RAG proteins, recombination centers, must be accessible yet flanked by a 5’ nucleosome decorated with H3K4me3. In Drosophila, DNA GAGA motifs play an important role in nucleosome positioning.
Read the full summary ↓
Herein, we report that 5’ to each functional Jk RSS is a DNA GAGA motif conserved across mammalian species. In mice, the GAGA motif 5’ to Jk1 regulated local RSS accessibility and 5’ nucleosome placement. Furthermore, it was required for Vk-Jk1 recombination. Murine Jk3 is nonfunctional, having mutations in both RSS and GAGA motifs. Restoring both GAGA and RSS motifs rescued Vk-Jk3 recombination. In contrast, restoring the RSS alone did not. Genome-wide, strong cryptic 23 RSSs were preferentially bound to nucleosomes. Furthermore, evolutionary selection against cRSS only occurred in the A Compartment of B lymphocytes, not embryonic stem cells. These data indicate that in developing B cells, nucleosome positioning both enables and restricts recombination to Jk. Furthermore, our data suggest an expanded definition of recombination center-associated RSSs to include a 5’ GAGA sequence that dictates the local epigenetic state required for gene recombination.
Published in
Jk Dna Gaga Motifs Are Required for Local Nucleosome Remodeling and Vk-jk Recombination
Clark M, Veselits M, McLean K et al. · Research square 2025 · PMID 41502567 · doi:10.21203/rs.3.rs-8340154/v1
This dataset
Open GSE288585 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 GSE288585_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 PRJNA1218635 and SRA study SRP561222. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41502567) ↗
Study design
9 conditions, mostly in duplicate
mm_atac_spreb_Jk3-GAGArepai ×5 mm_atac_spreb_Jk3-RSS_only ×5 mm_atac_spreb_WT ×3 mm_atac_spreb ×2 mm_atac_spreb_jk1-del40 ×2 mm_atac_spreb_jk1-del57 ×2 mm_atac_spreb_jk1-GAGA-del ×2 mm_atac_spreb_Jk1-GAGAmut ×2 +3 more

Supports a between-group comparison across 25 samples.

How we read this: 9 replicated groups read from 27 sample titles; they account for 25 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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