Conservation of chromatin conformation in carnivores

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 sp...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2022-03, Vol.119 (9), p.1
Main Authors: Corbo, Marco, Damas, Joana, Bursell, Madeline G, Lewin, Harris A
Format: Article
Language:English
Subjects:
Animals
Biological evolution
Biological Sciences
Canidae
Carnivora - genetics
Carnivores
Chromatin
Chromatin - genetics
Chromosomes
Conformation
Eigenvectors
Evolution
Evolution, Molecular
Felidae
Gene mapping
Genomes
Karyotypes
Leukocytes
Pattern analysis
Physical mapping
Scaffolds
Species
Ursidae
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Summary: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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.2120555119