ArticleCell2022
Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes.
Article in Cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 51 citations in OpenAlex.
- Integrative characterization of tissue-specific 3D genome organization and associated transcriptional regulation in pig liver and muscle.Functional & integrative genomics · 2026Article
- Remodeling ofScience advances · 2026Article
- Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus.Nature structural & molecular biology · 2025Article
- Conserved noncoding cis elements associated with hibernation modulate metabolic and behavioral adaptations in mice.Science (New York, N.Y.) · 2025Article
- Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes.Nature genetics · 2025Article
- Bridging spatial and temporal scales of developmental gene regulation.Current opinion in genetics & development · 2025Review
- Conservation of regulatory elements with highly diverged sequences across large evolutionary distances.Nature genetics · 2025Article
- Polymer models of chromatin organization in virally infected cells.Biochemical Society transactions · 2025Review
- Genetic factors mediating long-range enhancer-promoter communication in mammalian development.Current opinion in genetics & development · 2025Review
- Article
- Widespread 3D genome reorganization precedes programmed DNA rearrangement inbioRxiv : the preprint server for biology · 2025Article
- Evolution and function of chromatin domains across the tree of life.Nature structural & molecular biology · 2024Review
- Review
- Cooperative insulation of regulatory domains by CTCF-dependent physical insulation and promoter competition.Nature communications · 2024Article
- TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene.Nature communications · 2024Article
- Genomic context sensitizes regulatory elements to genetic disruption.Molecular cell · 2024Article
- Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells.Nature communications · 2024Article
- Increased enhancer-promoter interactions during developmental enhancer activation in mammals.Nature genetics · 2024Article
- Genomic context sensitizes regulatory elements to genetic disruption.bioRxiv : the preprint server for biology · 2024Article
- Structural variants in the Epb41l4a locus: TAD disruption and Nrep gene misregulation as hypothetical drivers of neurodevelopmental outcomes.Scientific reports · 2024Article
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29 authors at 11 institutions in 6 countries.
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Abstract
Regulatory landscapes drive complex developmental gene expression, but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1's intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42's unresponsiveness. Rather, Zfp42's promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome wide, most TADs contain multiple independently expressed genes.
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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 Socratic graph.