ArticleGenome research2017
Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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85 citing papers in PubMed, 152 citations in OpenAlex.
- A Human Accelerated Region Drives Opposing Heterochronic Changes in Craniofacial and Limb Development.bioRxiv : the preprint server for biology · 2026Article
- Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding.Nature genetics · 2026Article
- Temporal constraints on enhancer usage shape the regulation of limb gene transcription.Nature communications · 2026Article
- Initiators counteract Polycomb repression and stimulate long-range contacts between enhancers and theOpen biology · 2025Article
- Deciphering chromatin domain, domain community and chromunity for 3D genome maps with Mactop.Communications biology · 2025Article
- Wnt signaling activation induces CTCF binding and loop formation atGenome research · 2025Article
- Article
- CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation.Nature structural & molecular biology · 2025Article
- Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes.Nature genetics · 2025Article
- WNT signaling coordinately controls mouse limb bud outgrowth and establishment of the digit-interdigit pattern.Development (Cambridge, England) · 2025Article
- Epigenomic signatures of cis-regulatory elements in the developing mouse and pig forelimb.Scientific data · 2025Article
- Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues.Nature structural & molecular biology · 2025Article
- A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival.Nature communications · 2024Article
- Pre-hypertrophic chondrogenic enhancer landscape of limb and axial skeleton development.Nature communications · 2024Article
- Enhancer contacts during embryonic development show diverse interaction modes and modest yet significant increases upon gene activation.Nature genetics · 2024Article
- Increased enhancer-promoter interactions during developmental enhancer activation in mammals.Nature genetics · 2024Article
- Enhancer-promoter interactions become more instructive in the transition from cell-fate specification to tissue differentiation.Nature genetics · 2024Article
- MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops.Nucleic acids research · 2024Article
- Atlas of cardiac endothelial cell enhancer elements linking the mineralocorticoid receptor to pathological gene expression.Science advances · 2024Article
- Epigenetic regulatory layers in the 3D nucleus.Molecular cell · 2024Review
25 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Complex regulatory landscapes control the pleiotropic transcriptional activities of developmental genes. For most genes, the number, location, and dynamics of their associated regulatory elements are unknown. In this work, we characterized the three-dimensional chromatin microarchitecture and regulatory landscape of 446 limb-associated gene loci in mouse using Capture-C, ChIP-seq, and RNA-seq in forelimb, hindlimb at three developmental stages, and midbrain. The fine mapping of chromatin interactions revealed a strong preference for functional genomic regions such as repressed or active domains. By combining chromatin marks and interaction peaks, we annotated more than 1000 putative limb enhancers and their associated genes. Moreover, the analysis of chromatin interactions revealed two regimes of chromatin folding, one producing interactions stable across tissues and stages and another one associated with tissue and/or stage-specific interactions. Whereas stable interactions associate strongly with CTCF/RAD21 binding, the intensity of variable interactions correlates with changes in underlying chromatin modifications, specifically at the viewpoint and at the interaction site. In conclusion, this comprehensive data set provides a resource for the characterization of hundreds of limb-associated regulatory landscapes and a framework to interpret the chromatin folding dynamics observed during embryogenesis.
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