Related Experiment Video
Updated: Nov 5, 2025
06:05
Visualization and Quantitative Analysis of Embryonic Angiogenesis in Xenopus tropicalis
Published on: May 25, 2017
8.7K
CTCF looping is established during gastrulation in medaka embryos
Ryohei Nakamura1, Yuichi Motai2, Masahiko Kumagai3
1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033 Japan.
Genome Research
|May 19, 2021
Summary
Chromatin loops form during gastrulation in fish embryos, after genome activation and domain formation. These loops, mediated by CTCF binding, are crucial for differentiation but not initial transcription.
Area of Science:
- Developmental Biology
- Genomics
- Epigenetics
Background:
- Chromatin looping is vital for genome regulation.
- The timing of cohesin-mediated loop formation in early development is unknown due to technical challenges in mammalian embryos.
Purpose of the Study:
- Investigate the developmental timing of chromatin loop formation.
- Characterize genome architecture changes during early embryogenesis in medaka.
- Determine the relationship between loop formation, transcription, and protein binding.
Main Methods:
- Studied medaka (Oryzias latipes) development across 12 time points.
- Utilized ChIP-seq and loop-resolution Hi-C (DNA-DNA proximity ligation).
- Analyzed transcription, CTCF binding, and 3D genome architecture.
Main Results:
- Gastrulation is linked to significant genome architecture changes, including the first CTCF-bound loops and expanded contact domains.
- CTCF binding is constant throughout medaka embryogenesis.
- Loop formation occurs after genome-wide transcription and domain formation, and after zygotic genome activation in zebrafish.
Conclusions:
- Chromatin loops are not required for zygotic transcription but may be involved in cell differentiation.
- Loop positions are evolutionarily conserved between medaka and zebrafish, indicating ancient 3D genome architecture maintenance.
