ArticleNucleic acids research2024
The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Article
- Epigenetic conditioning improves sequence-based modeling of gene regulation across cell types and alleles.bioRxiv : the preprint server for biology · 2026Article
- CLASH (Chromatin Loop Across-sample Score Harmonizer) quantifies the relative contributions of genetic variation, methylation, and CTCF occupancy on chromatin loop strength across individuals.bioRxiv : the preprint server for biology · 2026Article
- Epigenetic Perspectives on Maternal Gut Microbiota's Impact on Embryonic and Fetal Development.Comprehensive Physiology · 2026Review
- Epigenetic remodeling during early embryonic development.Frontiers in cell and developmental biology · 2026Review
- Structural variants in the 3D genome as drivers of disease.Nature reviews. Genetics · 2025Review
- Article
- Modulating immune cell fate and inflammation through CRISPR-mediated DNA methylation editing.Science advances · 2025Article
- Temporally discordant chromatin accessibility and DNA demethylation define short- and long-term enhancer regulation during cell fate specification.Cell reports · 2025Article
- Molecular regulation of whole genome DNA methylation in heat stress response of dairy cows.BMC genomics · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
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. 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.