ArticleProceedings of the National Academy of Sciences of the United States of America2022
Conservation of chromatin conformation in carnivores.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 29 citations in OpenAlex.
- Deciphering the 3D genome organization across species from Hi-C data.Nucleic acids research · 2026Article
- Identification of a complex chromosomal insertion using the chromosome conformation based karyotyping technique for the implementation of PGT-SR.BMC genomics · 2026Article
- Evolution of chromosomes and nuclear architectures of amniotes.Nature communications · 2025Article
- Coexisting With Humans: Genomic and Behavioral Consequences in a Small and Isolated Bear Population.Molecular biology and evolution · 2025Article
- Leveraging Hi-C Data to Detect Chromosomal Reorganizations.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Patterns of chromosome evolution in ruminants.Molecular ecology · 2024Article
- Comparative genomics of Metarhizium brunneum strains V275 and ARSEF 4556: unraveling intraspecies diversity.G3 (Bethesda, Md.) · 2024Article
- The Ruminant Telomere-to-Telomere (RT2T) Consortium.Nature genetics · 2024Review
- Strong association between genomic 3D structure and CRISPR cleavage efficiency.PLoS computational biology · 2024Article
- Hi-C sequencing unravels dynamic three-dimensional chromatin interactions in muntjac lineage: insights from chromosome fusions in Fea's muntjac genome.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2023Article
- Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA.Briefings in bioinformatics · 2023Article
- Genomic rearrangements and evolutionary changes in 3D chromatin topologies in the cotton tribe (Gossypieae).BMC biology · 2023Article
- Genome report: chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris).G3 (Bethesda, Md.) · 2022Article
- Evolution of the ancestral mammalian karyotype and syntenic regions.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
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4 authors at 3 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
High throughput chromatin conformation capture (Hi-C) of leukocyte DNA was used to investigate the evolutionary stability of chromatin conformation at the chromosomal level in 11 species from three carnivore families: Felidae, Canidae, and Ursidae. Chromosome-scale scaffolds (C-scaffolds) of each species were initially used for whole-genome alignment to a reference genome within each family. This approach established putative orthologous relationships between C-scaffolds among the different species. Hi-C contact maps for all C-scaffolds were then visually compared and found to be distinct for a given reference chromosome or C-scaffold within a species and indistinguishable for orthologous C-scaffolds having a 1:1 relationship within a family. The visual patterns within families were strongly supported by eigenvectors from the Hi-C contact maps. Analysis of Hi-C contact maps and eigenvectors across the three carnivore families revealed that most cross-family orthologous subchromosomal fragments have a conserved three-dimensional (3D) chromatin structure and thus have been under strong evolutionary constraint for ∼54 My of carnivore evolution. The most pronounced differences in chromatin conformation were observed for the X chromosome and the red fox genome, whose chromosomes have undergone extensive rearrangements relative to other canids. We also demonstrate that Hi-C contact map pattern analysis can be used to accurately identify orthologous relationships between C-scaffolds and chromosomes, a method we termed "3D comparative scaffotyping." This method provides a powerful means for estimating karyotypes in de novo sequenced species that have unknown karyotype and no physical mapping information.
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