ArticleNature communications2021
Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 69 citations in OpenAlex.
- Foundation model reveals the shared organization of transcription and topologically associating domains.Cell systems · 2026Article
- Mechanisms and functional implications of long-range enhancer-dependent gene regulation.Nature genetics · 2026Review
- Non-coding genome in nail-patella syndrome: Genetic diagnosis as a guide for personalized follow-up.European journal of human genetics : EJHG · 2026Article
- Convergence of external and internal stressors on a stress-responsive enhancer of theProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Enhancer Trajectories in Lineage Commitment: Regulatory Logic of States and Cooperation.Biomolecules · 2026Review
- Bystander activation across a TAD boundary supports a cohesin-dependent transcription cluster model for enhancer function.Genes & development · 2025Article
- Advances in large-scale DNA engineering with the CRISPR system.Experimental & molecular medicine · 2025Review
- MIA-Jet: Multi-scale Identification Algorithm of Chromatin Jets.bioRxiv : the preprint server for biology · 2025Article
- Direction and modality of transcription changes caused by TAD boundary disruption in Slc29a3/Unc5b locus depends on tissue-specific epigenetic context.Epigenetics & chromatin · 2025Article
- Article
- Two unrelated distal genes activated by a shared enhancer benefit from localizing inside the same small topological domain.Genes & development · 2025Article
- Genetic factors mediating long-range enhancer-promoter communication in mammalian development.Current opinion in genetics & development · 2025Review
- Common variants increase risk for congenital diaphragmatic hernia within the context of de novo variants.American journal of human genetics · 2024Article
- A dominant missense variant within LMBR1 related to equine polydactyly.Communications biology · 2024Article
- TAD boundary deletion causes PITX2-related cardiac electrical and structural defects.Nature communications · 2024Article
- Enhancer-promoter specificity in gene transcription: molecular mechanisms and disease associations.Experimental & molecular medicine · 2024Review
- Association of genetic variation ineLife · 2024Article
- Topology regulatory elements: From shaping genome architecture to gene regulation.Current opinion in structural biology · 2023Review
- Allelic chromatin structure precedes imprinted expression ofGenes & development · 2023Article
- Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers.Nucleic acids research · 2023Article
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Authors and funding
15 authors at 5 institutions in 5 countries.
Funding
Abstract
Acheiropodia, congenital limb truncation, is associated with homozygous deletions in the LMBR1 gene around ZRS, an enhancer regulating SHH during limb development. How these deletions lead to this phenotype is unknown. Using whole-genome sequencing, we fine-mapped the acheiropodia-associated region to 12 kb and show that it does not function as an enhancer. CTCF and RAD21 ChIP-seq together with 4C-seq and DNA FISH identify three CTCF sites within the acheiropodia-deleted region that mediate the interaction between the ZRS and the SHH promoter. This interaction is substituted with other CTCF sites centromeric to the ZRS in the disease state. Mouse knockouts of the orthologous 12 kb sequence have no apparent abnormalities, showcasing the challenges in modelling CTCF alterations in animal models due to inherent motif differences between species. Our results show that alterations in CTCF motifs can lead to a Mendelian condition due to altered enhancer-promoter interactions.
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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.