Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University
Mengnan He
Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University
Qianzi Tang
Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University
Shilin Tian
Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University
Jiaman Zhang
Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University
Yan Li
Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University
Danyang Wang
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation
Long Jin
Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University
Chunyou Ning
Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University
Wei Zhu
Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University
Silu Hu
Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University
Keren Long
Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University
Jideng Ma
Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University
Jing Liu
University of Chinese Academy of Sciences
Zhihua Zhang
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation
Mingzhou Li
Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University
Abstract Background The three-dimensional (3D) architecture of the genome has a highly ordered and hierarchical nature, which influences the regulation of essential nuclear processes at the basis of gene expression, such as gene transcription. While the hierarchical organization of heterochromatin and euchromatin can underlie differences in gene expression that determine evolutionary differences among species, the way 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. Results This analysis shows a correlation between genome size and chromosome length that affects chromosome territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through the evolution of vertebrates. Furthermore, 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. Conclusions Our analysis uncovers organizational features that appear to determine the conservation and transcriptional regulation of functional genes across species. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.
