TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function
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Abstract
Topological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. We find 14% of all human TAD boundaries to be shared among all eight species (ultraconserved), while 15% are human-specific. Ultraconserved TAD boundaries have stronger insulation strength, CTCF binding, and enrichment of older retrotransposons compared to species-specific boundaries. CRISPR-Cas9 knockouts of an ultraconserved boundary in a mouse model lead to tissue-specific gene expression changes and morphological phenotypes. Deletion of a human-specific boundary near the autism-related AUTS2 gene results in the upregulation of this gene in neurons. Overall, our study provides pertinent TAD boundary evolutionary conservation annotations and showcases the functional importance of TAD evolution.
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TADs are crucial for organizing transcriptional networks during neurodevelopment.
“TADs are crucial for organizing transcriptional networks during neurodevelopment (Okhovat et al., 2023).”
From Biological hierarchy from genotype to phenotype in syndromic and non-syndromic autism spectrum disorder (2026) · cites this paper as Okhovat et al., 2023
The Introduction (page unavailable) describes TADs as domains that shape regulatory interactions, and the Results (page unavailable) show that deleting one TAD boundary changes AUTS2 expression in human neurons. But the Results identify AUTS2—not TADs—as a regulator of transcriptional networks in neurodevelopment. The paper does not establish that TADs broadly organize those networks during neurodevelopment. (LLM, conf=0.84)
Experimental — accuracy not yet measuredMany higher-order chromosomal features, including TADs, lamina-associated domains, chromatin loops, and nuclear compartments, are conserved across distantly related species.
“Many such features are conserved across distantly related species.”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [126]
The Discussion reports that 14% of human and 15% of mouse TAD boundaries were conserved across the eight primate and rodent species studied. It also says these proportions challenge the notion that TAD organization is highly conserved across species. Our copy does not establish cross-species conservation of lamina-associated domains, chromatin loops, or nuclear compartments. (LLM, conf=0.88)
Experimental — accuracy not yet measuredTAD and lamina-associated domain boundaries are often conserved between species and correspond with breaks of synteny between species, implying that chromosomal inversions that break TADs are selected against.
“For example, TAD and lamina-associated domain (120) boundaries are often conserved between species and correspond with breaks of synteny between species (124–126), implying that chromosomal inversions that break TADs are selected against.”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [126]
The Introduction reports shared TAD boundaries between species, and the Results report that evolutionary breaks of synteny are enriched at TAD boundaries. The paper says selection to preserve TAD integrity is an interpretation of that pattern, but its Discussion also finds species-specific boundaries at breaks and proposes that some rearrangements may help establish new boundaries. It does not establish that inversions breaking TADs are selected against; the lamina-associated-domain point has a separate citation in the citing sentence. (LLM, conf=0.84)
Experimental — accuracy not yet measuredOverall genome topology, including TAD organization, shows conservation across distant lineages but does degrade over macroevolutionary time.
“Preliminary studies suggest that overall genome topology, including TAD organization, shows conservation across distant lineages (124–126) but does degrade over macroevolutionary time (121, 132, 133).”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [126]
The Results section reports that TAD boundaries were shared more often among closely related species and that evolutionary distance shaped cross-species TAD organization. The Discussion reports that only 14% of human and 15% of mouse TAD boundaries were conserved across all eight species. These findings support evolutionary divergence in TAD organization, but the paper does not establish that overall genome topology degrades over macroevolutionary time. (LLM, conf=0.83)
Experimental — accuracy not yet measured
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Topological Approaches in Animal Comparative Genomics
Schultz, D. T., & Simakov, O. (2026) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-030424-084541 · Cited by 1 · see citing works
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“TADs are crucial for organizing transcriptional networks during neurodevelopment (Okhovat et al., 2023).”
- Authors
- Okhovat, M., VanCampen, J., Nevonen, K. A., Harshman, L., Li, W., Layman, C. E., Ward, S., Herrera, J., Wells, J., Sheng, R. R., Mao, Y., Ndjamen, B., Lima, A. C., Vigh-Conrad, K. A., Stendahl, A. M., Yang, R., Fedorov, L., Matthews, I. R., Easow, S. A., Chan, D. K., Jan, T. A., Eichler, E. E., Rugonyi, S., Conrad, D. F., Ahituv, N., & Carbone, L.
- Affiliations
- Oregon Health & Science University (US)
- University of California, San Francisco (US)
- Shanghai Jiao Tong University (CN)
- Gladstone Institutes (US)
- Oregon National Primate Research Center (US)
- Vanderbilt University Medical Center (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Okhovat, Mariam
- Ahituv, Nadav
- Carbone, Lucia
- ORCID
- Venue
- Nature Communications
- Published
- 2023-12-07
- Volume
- 14
- Issue
- 1
- Pages
- 8111-8111
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC10703881
- OpenAlex
- W4389428478
- Cited by
- 68
- References
- 9
- Citations by year
- 2026: 21 · 2025: 31 · 2024: 14 · 2023: 2
- FWCI
- 6.06
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- PubMed Central (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (R01HG010333, R01HG002385)
- U.S. Department of Health & Human Services | NIH | NIH Office of the Director (P51 OD011092)
- Howard Hughes Medical Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- topologically associating domains, TAD boundaries, chromatin organization, evolutionary conservation, CTCF binding, chromatin insulation, retrotransposons, CRISPR/Cas9 knockout, AUTS2, autism spectrum disorder, gene expression regulation, tissue-specific gene expression
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