GEO series
H3K27 and H3K9 Methylation Mask Potential CTCF Binding Sites to Maintain 3D Genome Integrity
GSE293581
Mus musculus (mouse)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
40 samples
Submitted 2025/07/17
Platform GPL21273
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 40 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
- 40 samples: 20 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
- H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrityGenome research · 2025
Summary (written by the submitters)
The three-dimensional (3D) genome structure is essential for gene regulation and various genomic functions. CTCF plays a key role in organizing Topologically Associated Domains (TADs) and promoter-enhancer loops, contributing to proper cell differentiation and development. Although CTCF binds the genome with high sequence specificity, its binding sites are dynamically regulated during development, and aberrant CTCF binding is linked to diseases such as cancer and neurological disorders, and aging.
Read the full summary ↓
However, the mechanisms controlling CTCF binding remain unclear. Here, we investigated the role of repressive chromatin modifications in CTCF binding using H3K9 methyltransferase-deficient immortalized mouse embryonic fibroblasts (iMEFs) and H3K27 methyltransferase EZH1/2 inhibitor. We found that H3K9 and H3K27 methylation regulate CTCF binding at distinct genomic regions, and their simultaneous loss induces drastic changes in CTCF binding. These changes were associated with alterations in 3D genome architecture and gene expression, suggesting that repressive chromatin modifications preserve proper chromatin organization by preventing aberrant CTCF binding. Additionally, while CTCF binding sites repressed by H3K9 methylation were bound by CTCF in early mouse embryos, those repressed by both H3K9 and H3K27 methylation remained inaccessible, with early embryonic-specific H3K27 methylation forming at these sites. These findings implicate that H3K27 methylation prevents abnormal CTCF binding in early embryos, ensuring proper genome organization during development.
Published in
Fukuda K, Shimura C, Shinkai Y
· Genome research 2025
· PMID 40764058
· doi:10.1101/gr.280732.125
This dataset
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.
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 GSE293581_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1245290 and SRA study SRP576141. Searching any of these in the dataset finder brings you back here.
Study design
20 conditions, mostly in duplicate
CTCF ChIP-seq in WT+DS ×2
CTCF ChIP-seq in 5KOcln14+DS ×2
CTCF ChIP-seq in 5KOcln55+DS ×2
CTCF ChIP-seq in Setdb1KO+DS ×2
CTCF ChIP-seq in TKO+DS ×2
Input ChIP-seq in WT+DS ×2
Input ChIP-seq in 5KOcln14+DS ×2
Input ChIP-seq in 5KOcln55+DS ×2
+12 more
Supports a between-group comparison across 40 samples.
How we read this: 20 replicated groups read from 40 sample titles; they account for 40 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
- GSM8885805 CTCF ChIP-seq in WT+DS rep1 CTCF ChIP-seq in WT+DS
- GSM8885806 CTCF ChIP-seq in WT+DS rep2 CTCF ChIP-seq in WT+DS
- GSM8885807 CTCF ChIP-seq in 5KOcln14+DS rep1 CTCF ChIP-seq in 5KOcln…
- GSM8885808 CTCF ChIP-seq in 5KOcln14+DS rep2 CTCF ChIP-seq in 5KOcln…
- GSM8885809 CTCF ChIP-seq in 5KOcln55+DS rep1 CTCF ChIP-seq in 5KOcln…
- GSM8885810 CTCF ChIP-seq in 5KOcln55+DS rep2 CTCF ChIP-seq in 5KOcln…
- GSM8885811 CTCF ChIP-seq in Setdb1KO+DS rep1 CTCF ChIP-seq in Setdb1…
- GSM8885812 CTCF ChIP-seq in Setdb1KO+DS rep2 CTCF ChIP-seq in Setdb1…
- GSM8885813 CTCF ChIP-seq in TKO+DS rep1 CTCF ChIP-seq in TKO+DS
- GSM8885814 CTCF ChIP-seq in TKO+DS rep2 CTCF ChIP-seq in TKO+DS
- GSM8885815 Input ChIP-seq in WT+DS rep1 Input ChIP-seq in WT+DS
- GSM8885816 Input ChIP-seq in WT+DS rep2 Input ChIP-seq in WT+DS
- GSM8885817 Input ChIP-seq in 5KOcln14+DS rep1 Input ChIP-seq in 5KOcl…
- GSM8885818 Input ChIP-seq in 5KOcln14+DS rep2 Input ChIP-seq in 5KOcl…
- GSM8885819 Input ChIP-seq in 5KOcln55+DS rep1 Input ChIP-seq in 5KOcl…
- GSM8885820 Input ChIP-seq in 5KOcln55+DS rep2 Input ChIP-seq in 5KOcl…
- GSM8885821 Input ChIP-seq in Setdb1KO+DS rep1 Input ChIP-seq in Setdb…
- GSM8885822 Input ChIP-seq in Setdb1KO+DS rep2 Input ChIP-seq in Setdb…
- GSM8885823 Input ChIP-seq in TKO+DS rep1 Input ChIP-seq in TKO+DS
- GSM8885824 Input ChIP-seq in TKO+DS rep2 Input ChIP-seq in TKO+DS
- GSM8885825 CTCF ChIP-seq in WT rep1 CTCF ChIP-seq in WT
- GSM8885826 CTCF ChIP-seq in WT rep2 CTCF ChIP-seq in WT
- GSM8885827 CTCF ChIP-seq in 5KOcln14 rep1 CTCF ChIP-seq in 5KOcln…
- GSM8885828 CTCF ChIP-seq in 5KOcln14 rep2 CTCF ChIP-seq in 5KOcln…
- GSM8885829 CTCF ChIP-seq in 5KOcln55 rep1 CTCF ChIP-seq in 5KOcln…
- GSM8885830 CTCF ChIP-seq in 5KOcln55 rep2 CTCF ChIP-seq in 5KOcln…
- GSM8885831 CTCF ChIP-seq in Setdb1KO rep1 CTCF ChIP-seq in Setdb1…
- GSM8885832 CTCF ChIP-seq in Setdb1KO rep2 CTCF ChIP-seq in Setdb1…
- GSM8885833 CTCF ChIP-seq in TKO rep1 CTCF ChIP-seq in TKO
- GSM8885834 CTCF ChIP-seq in TKO rep2 CTCF ChIP-seq in TKO
- GSM8885835 Input ChIP-seq in WT rep1 Input ChIP-seq in WT
- GSM8885836 Input ChIP-seq in WT rep2 Input ChIP-seq in WT
- GSM8885837 Input ChIP-seq in 5KOcln14 rep1 Input ChIP-seq in 5KOcl…
- GSM8885838 Input ChIP-seq in 5KOcln14 rep2 Input ChIP-seq in 5KOcl…
- GSM8885839 Input ChIP-seq in 5KOcln55 rep1 Input ChIP-seq in 5KOcl…
- GSM8885840 Input ChIP-seq in 5KOcln55 rep2 Input ChIP-seq in 5KOcl…
- GSM8885841 Input ChIP-seq in Setdb1KO rep1 Input ChIP-seq in Setdb…
- GSM8885842 Input ChIP-seq in Setdb1KO rep2 Input ChIP-seq in Setdb…
- GSM8885843 Input ChIP-seq in TKO rep1 Input ChIP-seq in TKO
- GSM8885844 Input ChIP-seq in TKO rep2 Input ChIP-seq in TKO
Datasets on a similar topic
- GSE262936 H3K9me3 and H3K27me3 genomic occupancy on neonatal mouse cardiomyocytes (CMs) treated with PBS/phenylephrine (PE) and lincRNA-p21 WT/knockdown 20 samples shares h3k27, h3k9
- GSE266317 RNA-seq and ChIP-seq analysis of H3K27ac, H3K27me3, H3K9me2, and JMJD1A in 3T3-L1 cells and ChIP-seq analysis of NFIC in imSVF cells. 14 samples shares h3k27, h3k9
- GSE297574 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [spike-in ChIP-seq of mESC] 64 samples shares h3k9, methylation
- GSE278338 ChIP-seq to measure binding of NIPBL/MAU2, RAD21, and CTCF in mouse embryonic stem cells and neural progenitor cells 50 samples shares ctcf, binding
- GSE296991 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [CATCH-seq of early embryo] 23 samples shares h3k9, methylation
- GSE233039 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [ATAC-Seq] 18 samples shares h3k9, integrity
- GSE72539 CTCF binding polarity determines chromatin looping [4C] 504 samples shares ctcf, binding
- GSE296994 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation 174 samples shares h3k9, methylation
Share this dataset
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.