ArticleNature communications2023
A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it, 18 citations in OpenAlex.
- Research progress on exosomes in the otology field: a systematic review.Stem cell research & therapy · 2025Pooled it
- Hox/Meis-dependent gene-regulatory transition underlies cardiopharyngeal neural crest diversification.The EMBO journal · 2026Article
- Atlas of cell types and regulatory elements underlying human facial diversity.Nature genetics · 2026Article
- A Human Accelerated Region Drives Opposing Heterochronic Changes in Craniofacial and Limb Development.bioRxiv : the preprint server for biology · 2026Article
- The cardiac 4D nucleome: nuclear and chromatin dynamics across development, disease and ageing.Nature reviews. Cardiology · 2026Review
- Retinoic Acid Informs the Positional Identity of Frontonasal Neural Crest Cells Through Alx Family of Transcription Factors.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- Functional and Genetic Analyses Unveil the Implication ofJournal of developmental biology · 2026Article
- Polycomb chromatin topology enables long-range enhancer recruitment during craniofacial development.Nature communications · 2026Article
- The inner nuclear membrane protein LEMD3 organizes the 3D chromatin architecture to maintain vascular smooth muscle cell identity.Nature communications · 2025Article
- The Biological Function of Genome Organization.International journal of molecular sciences · 2025Review
- Klf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity.Nature communications · 2025Article
- Unbiased profiling of multipotency landscapes reveals spatial modulators of clonal fate biases.bioRxiv : the preprint server for biology · 2025Article
- Auricular malformations are driven by copy number variations in a hierarchical enhancer cluster and a dominant enhancer recapitulates human pathogenesis.Nature communications · 2025Article
- Genetic factors mediating long-range enhancer-promoter communication in mammalian development.Current opinion in genetics & development · 2025Review
- Machine learning tools for deciphering the regulatory logic of enhancers in health and disease.Frontiers in genetics · 2025Review
- A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival.Nature communications · 2024Article
- A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development.Nature communications · 2024Article
- TFAP2 paralogs regulate midfacial development in part through a conserved ALX genetic pathway.Development (Cambridge, England) · 2024Article
- Topology regulatory elements: From shaping genome architecture to gene regulation.Current opinion in structural biology · 2023Review
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Enhancer-promoter interactions preferentially occur within boundary-insulated topologically associating domains (TADs), limiting inter-TAD interactions. Enhancer clusters in linear proximity, termed super-enhancers (SEs), ensure high target gene expression levels. Little is known about SE topological regulatory impact during craniofacial development. Here, we identify 2232 genome-wide putative SEs in mouse cranial neural crest cells (CNCCs), 147 of which target genes establishing CNCC positional identity during face formation. In second pharyngeal arch (PA2) CNCCs, a multiple SE-containing region, partitioned into Hoxa Inter-TAD Regulatory Element 1 and 2 (HIRE1 and HIRE2), establishes long-range inter-TAD interactions selectively with Hoxa2, that is required for external and middle ear structures. HIRE2 deletion in a Hoxa2 haploinsufficient background results in microtia. HIRE1 deletion phenocopies the full homeotic Hoxa2 knockout phenotype and induces PA3 and PA4 CNCC abnormalities correlating with Hoxa2 and Hoxa3 transcriptional downregulation. Thus, SEs can overcome TAD insulation and regulate anterior Hoxa gene collinear expression in a CNCC subpopulation-specific manner during craniofacial development.
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