ArticlePLoS genetics2019
Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates.
Article in PLoS genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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55 citing papers in PubMed, 95 citations in OpenAlex.
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- Polymorphic 3D genome architecture mediated by transposable elements.bioRxiv : the preprint server for biology · 2026Article
- Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence.bioRxiv : the preprint server for biology · 2025Article
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- Topologically associating domains and the evolution of three-dimensional genome architecture in rice.The Plant journal : for cell and molecular biology · 2025Article
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- Comparing chromatin contact maps at scale: methods and insights.Nature methods · 2025Article
- Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease.bioRxiv : the preprint server for biology · 2024Article
- Sequence-Based Machine Learning Reveals 3D Genome Differences between Bonobos and Chimpanzees.Genome biology and evolution · 2024Article
- Deciphering the role of structural variation in human evolution: a functional perspective.Current opinion in genetics & development · 2024Review
- Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription.Genomics, proteomics & bioinformatics · 2024Article
- Astrocytes Drive Divergent Metabolic Gene Expression in Humans and Chimpanzees.Genome biology and evolution · 2024Article
- TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function.Nature communications · 2023Article
- Functional genomics in Spiralia.Briefings in functional genomics · 2023Article
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Authors and funding
5 authors at 1 institution in 1 country.
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Abstract
A growing body of evidence supports the notion that variation in gene regulation plays a crucial role in both speciation and adaptation. However, a comprehensive functional understanding of the mechanisms underlying regulatory evolution remains elusive. In primates, one of the crucial missing pieces of information towards a better understanding of regulatory evolution is a comparative annotation of interactions between distal regulatory elements and promoters. Chromatin conformation capture technologies have enabled genome-wide quantifications of such distal 3D interactions. However, relatively little comparative research in primates has been done using such technologies. To address this gap, we used Hi-C to characterize 3D chromatin interactions in induced pluripotent stem cells (iPSCs) from humans and chimpanzees. We also used RNA-seq to collect gene expression data from the same lines. We generally observed that lower-order, pairwise 3D genomic interactions are conserved in humans and chimpanzees, but higher order genomic structures, such as topologically associating domains (TADs), are not as conserved. Inter-species differences in 3D genomic interactions are often associated with gene expression differences between the species. To provide additional functional context to our observations, we considered previously published chromatin data from human stem cells. We found that inter-species differences in 3D genomic interactions, which are also associated with gene expression differences between the species, are enriched for both active and repressive marks. Overall, our data demonstrate that, as expected, an understanding of 3D genome reorganization is key to explaining regulatory evolution.
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