CTCF looping is established during gastrulation in medaka embryos
| Autor: | Neva C. Durand, Ryohei Nakamura, Takashi Kondo, Candice L. Wike, Erez Lieberman Aiden, Hiroyuki Takeda, Shinichi Morishita, Tatsuya Tsukahara, Kaori Kondo, Yuichi Motai, Yoichiro Nakatani, Masahiko Kumagai, Haruyo Nishiyama, Bradley R. Cairns, Atsuko Shimada |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
CCCTC-Binding Factor
Oryzias Cellular differentiation Cell Cycle Proteins Insulator (genetics) 03 medical and health sciences Mice 0302 clinical medicine Genetics Animals Zebrafish Genetics (clinical) 030304 developmental biology 0303 health sciences biology Research Gastrulation biology.organism_classification Chromatin Cell biology CTCF Maternal to zygotic transition 030217 neurology & neurosurgery |
| Zdroj: | Genome Res |
| Popis: | Chromatin looping plays an important role in genome regulation. However, because ChIP-seq and loop-resolution Hi-C (DNA-DNA proximity ligation) are extremely challenging in mammalian early embryos, the developmental stage at which cohesin-mediated loops form remains unknown. Here, we study early development in medaka (the Japanese killifish, Oryzias latipes) at 12 time points before, during, and after gastrulation (the onset of cell differentiation) and characterize transcription, protein binding, and genome architecture. We find that gastrulation is associated with drastic changes in genome architecture, including the formation of the first loops between sites bound by the insulator protein CTCF and a large increase in the size of contact domains. In contrast, the binding of the CTCF is fixed throughout embryogenesis. Loops form long after genome-wide transcriptional activation, and long after domain formation seen in mouse embryos. These results suggest that, although loops may play a role in differentiation, they are not required for zygotic transcription. When we repeated our experiments in zebrafish, loops did not emerge until gastrulation, that is, well after zygotic genome activation. We observe that loop positions are highly conserved in synteny blocks of medaka and zebrafish, indicating that the 3D genome architecture has been maintained for >110–200 million years of evolution. |
| Databáze: | OpenAIRE |
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