SRA

Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate's evolution. Further, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture. Overall design: To comprehensively explore the evolutionary principles governing 3D genome architecture and to assess the contributions of genome architecture to transcriptional regulation across species, we performed comparative analyses of high-throughput chromosome conformation capture (Hi-C) in fibroblast cells of 12 vertebrates, including two representative mammalian lineages: euarchontoglires including humans, rhesus macaques, mice, rats, and rabbits; boreoeutheria including dogs, cats, pigs, sheep, and cows; as well as two non-mammals including birds (chickens) and fish (zebrafish). We performed the Hi-C experiments in 25 fibroblasts from 11 vertebrates with 1 to 5 biological replicates (distinct cell lines or primary cells derived from different individuals) for each species, produced a total of ~ 5.75-billion uniquely aligned contacts with an average depth of ~230 million (M) contacts per library (range from ~102 M for zebrafish with a relatively small genome size of ~ 1.23 Gb to ~442 M for mouse with a genome size of ~2.73 Gb). We also combined the resulting datasets with those previously generated by us for four pig fibroblasts (pig_DB-2, pig_DB-3, pig_RC-7, and pig_RC-8) (X Tian et al.,2020) and two mouse fibroblasts (mouse_3T6 and mouse_MEF) (M He et al.,2018) using the same experimental protocol. Among these, ~ 63.03% are intra-chromosomal contacts, of which ~74.40% were occurred within 10 Mb. After KR-normalization and quantile-normalization, we generated 31 intra-chromosomal contact maps at 20-kb resolution for each of 31 libraries. With the bin size at 20-kb, there are about 83.12% of bins have at least 1,000 intra-chromosomal contacts. TAD and compartment A/B were also identified by using the 20-kb matrix.