ArticleGenome biology2019
CTCF modulates allele-specific sub-TAD organization and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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62 citing papers in PubMed, 95 citations in OpenAlex.
- Allele-specific chromatin architecture shapes imprinted domains and coordinates a distal enhancer and antisense transcription at the mouse Mest-Copg2 domain.Nature communications · 2026Article
- Metamorphosis and lncRNAs: A Close Relationship.Genesis (New York, N.Y. : 2000) · 2026Review
- DNA methylation and lncRNA control asynchronous DNA replication at specific imprinted gene domains.Nature communications · 2026Article
- The superpowers of imprinting control regions.Genome research · 2026Review
- Unraveling the interplay of DNA methylation and chromosome organization.Biochemical Society transactions · 2025Review
- Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs.bioRxiv : the preprint server for biology · 2025Article
- Igf2 adult-specific skeletal muscle enhancer activity revealed in mice with intergenic CTCF boundary deletion.PLoS genetics · 2025Article
- Sequence and parent-of-origin dependent mThe EMBO journal · 2025Article
- Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D.Nature structural & molecular biology · 2025Article
- Non-disruptive 3D profiling of combinations of epigenetic marks in single cells.bioRxiv : the preprint server for biology · 2025Article
- BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries.Genome research · 2025Article
- A biallelically active embryonic enhancer dictates GNAS imprinting through allele-specific conformations.Nature communications · 2025Article
- An EED/PRC2-H19 Loop Regulates Cerebellar Development.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Virus Infection Induces Immune Gene Activation with CTCF-anchored Enhancers and Chromatin Interactions in Pig Genome.Genomics, proteomics & bioinformatics · 2024Article
- Identification of responsible sequences which mutations cause maternal H19-ICR hypermethylation with Beckwith-Wiedemann syndrome-like overgrowth.Communications biology · 2024Article
- The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation.Nucleic acids research · 2024Article
- Integration of CTCF loops, methylome, and transcriptome in differentiating LUHMES as a model for imprinting dynamics of the 15q11-q13 locus in human neurons.Human molecular genetics · 2024Article
- The structure of the TH/INS locus and the parental allele expressed are not conserved between mammals.Heredity · 2024Article
- Differential 3D genome architecture and imprinted gene expression: cause or consequence?Biochemical Society transactions · 2024Review
- The long non-coding RNA Meg3 mediates imprinted gene expression during stem cell differentiation.Nucleic acids research · 2024Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundGenomic imprinting is essential for mammalian development and provides a unique paradigm to explore intra-cellular differences in chromatin configuration. So far, the detailed allele-specific chromatin organization of imprinted gene domains has mostly been lacking. Here, we explored the chromatin structure of the two conserved imprinted domains controlled by paternal DNA methylation imprints-the Igf2-H19 and Dlk1-Dio3 domains-and assessed the involvement of the insulator protein CTCF in mouse cells.
resultsBoth imprinted domains are located within overarching topologically associating domains (TADs) that are similar on both parental chromosomes. At each domain, a single differentially methylated region is bound by CTCF on the maternal chromosome only, in addition to multiple instances of bi-allelic CTCF binding. Combinations of allelic 4C-seq and DNA-FISH revealed that bi-allelic CTCF binding alone, on the paternal chromosome, correlates with a first level of sub-TAD structure. On the maternal chromosome, additional CTCF binding at the differentially methylated region adds a further layer of sub-TAD organization, which essentially hijacks the existing paternal-specific sub-TAD organization. Perturbation of maternal-specific CTCF binding site at the Dlk1-Dio3 locus, using genome editing, results in perturbed sub-TAD organization and bi-allelic Dlk1 activation during differentiation.
conclusionsMaternal allele-specific CTCF binding at the imprinted Igf2-H19 and the Dlk1-Dio3 domains adds an additional layer of sub-TAD organization, on top of an existing three-dimensional configuration and prior to imprinted activation of protein-coding genes. We speculate that this allele-specific sub-TAD organization provides an instructive or permissive context for imprinted gene activation during development.
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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.