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The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation

GSE246984 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 28 samples Submitted 2024/07/23 Platform GPL19057Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 28 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
28 samples: 12 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
The impact of the embryonic DNA methylation program on CTCF-mediated genome regulationNucleic acids research · 2024
Summary (written by the submitters)
During mammalian embryogenesis, both the 5-cytosine DNA methylation (5meC) landscape and three dimensional (3D) chromatin architecture are profoundly remodeled during a process known as 'epigenetic reprogramming.' An understudied aspect of epigenetic reprogramming is how the 5meC flux, per se, affects the 3D genome. This is pertinent given the 5meC-sensitivity of DNA binding for a key regulator of chromosome folding: CTCF.
Read the full summary ↓
We profiled the CTCF binding landscape using a mouse embryonic stem cell (ESC) differentiation protocol that models embryonic 5meC dynamics. Mouse ESCs lacking DNA methylation machinery are able to exit naive pluripotency, thus allowing for dissection of subtle effects of CTCF on gene expression. We performed CTCF HiChIP in both wild-type and mutant conditions to assess gained CTCF-CTCF contacts in the absence of 5meC. We performed H3K27ac HiChIP to determine the impact that ectopic CTCF binding has on cis-regulatory contacts. Using 5meC epigenome editing, we demonstrated that the methyl-mark is able to impair CTCF binding at select loci. Finally, a detailed dissection of the imprinted Zdbf2 locus showed how 5meC-antagonism of CTCF allows for proper gene regulation during differentiation. This work provides a comprehensive overview of how 5meC impacts the 3D genome in a relevant model for early embryonic events.
Published in
The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation
Monteagudo-Sánchez A, Richard Albert J, Scarpa M et al. · Nucleic acids research 2024 · PMID 39180406 · doi:10.1093/nar/gkae724
This dataset
Open GSE246984 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 GSE246984_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 PRJNA1035481 and SRA study SRP470110. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39180406) ↗
Study design
12 conditions, mostly in duplicate
D0_WT_CTCF_CUTnRUN ×2 D0_TKO_CTCF_CUTnRUN ×2 D4_WT_CTCF_CUTnRUN ×2 D4_TKO_CTCF_CUTnRUN ×2 D0_WT_CTCF_HiChIP ×2 D0_TKO_CTCF_HiChIP ×2 D4_WT_CTCF_HiChIP ×2 D4_TKO_CTCF_HiChIP ×2 +8 more

Supports a between-group comparison across 24 samples.

How we read this: 12 replicated groups read from 28 sample titles; they account for 24 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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