| Accession | PRJCA004418 | ||||||||
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| Title | Comparative 3D Genome Architecture in Vertebrates | ||||||||
| Relevance | Evolution | ||||||||
| Data types |
Transcriptome or Gene expression
Raw sequence reads Hi-C |
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| Organisms |
Mus musculus
Oryctolagus cuniculus Ovis aries Canis lupus familiaris Danio rerio Rattus norvegicus Homo sapiens Macaca mulatta Bos taurus Sus scrofa Felis catus Gallus gallus |
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| Description | The 3D genome is essential to key nuclear processes, such as the gene expression. However, the evolutionary pattern of 3D genome in vertebrates remains unclear. Here, we reported a comprehensive comparison on the 3D genomes with fine resolution Hi-C data in fibroblasts cells from the fish, chicken and 10 mammals. We found that the genome size and chromosome lengths govern the overall features of 3D genome architecture, e.g., the layout of chromosome territories (CT), while the local features, e.g., the activity or insulation of genome fragments, were evolved with the speciation. Further, we found that the conservation pattern of topologically associating domains (TADs) is strongly associated with the modularity of the expression profile over the species. Last, we showed that the LINE and SINE family of the transposable elements may have distinct contributions, i.e., reshaping the heterochromatin and euchromatin, respectively, in the evolution of genome architecture. The data we generated and the correlations we reported here provides a new base for further exploration of genome evolution. | ||||||||
| Sample scope | Multispecies | ||||||||
| Release date | 2022-04-20 | ||||||||
| Grants |
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| Submitter | Li Diyan (diyanli@sicau.edu.cn) | ||||||||
| Organization | Sichuan Agricultural University | ||||||||
| Submission date | 2021-02-02 |