Biophysical Society Thematic Meeting| Santa Cruz 2018

Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes

Poster Abstracts

8-POS Board 8 Establishment of the Three-dimensional Chromatin Architectures in Medaka Embryogenesis Ryohei Nakamura 1 ; Yuichi Motai 2 ; Masahiko Kumagai 4 ; Haruyo Nishiyama 1 ; Neva C Durand 3 ; Erez L Aiden 3 ; Shinichi Morishita 2 ; Hiroyuki Takeda 1 1 The University of Tokyo, Department of Biological Sciences, Bunkyo-ku, Tokyo, Japan 2 The University of Tokyo, Department of Computational Biology and Medical Sciences, Kashiwa, Chiba, Japan 3 Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, Texas, United States 4 National Agriculture and Food Research Organization, , Tsukuba, Ibaraki, Japan Mammalian genomes have two distinct three-dimensional (3D) architectures in nuclei; compartments and loop domains, while fruit fly genome exhibits compartments but no loop domains. This difference sheds light on the conservation of the 3D features of chromatin across species, motivating us to understand the 3D structural differences in vertebrates. We generated the loop-resolution Hi-C contact maps in medaka (Japanese killfish) fibroblast cells, and observed both of the two structures in medaka like mammals, indicating that the principal mechanisms underlying chromatin architecture in mammals have been conserved since the emergence of bony fish. Similar to other epigenetic features, the 3D genome architectures are also reprogrammed in early embryogenesis. According to the study of mouse embryo, both compartments and loop domains emerge during zygotic genome activation (ZGA). ZGA occurs at the one- to two-cell stage in mouse; however, in fishes and amphibians, ZGA takes place at the mid-blastula stage (256 to 1024-cell stage). Due to such extensive variability in the timing and duration of ZGA, the order of ZGA and the reprogramming of 3D chromatin structures remains uncertain. Here, using medaka, we generated loop-resolution Hi-C maps at 12 time points spanning embryogenesis. As the mammalian studies, we find the small contact domains and compartmentalization appears during ZGA simultaneously with the emergence of chromatin accessibility variation for each locus.

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