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Cell Rep. 2018 Jul 3;24(1):1-10.e4. doi: 10.1016/j.celrep.2018.06.003.

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development.

Author information

1
Institute of Molecular Biology, 55128 Mainz, Germany.
2
Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
3
Institute of Molecular Biology, 55128 Mainz, Germany. Electronic address: r.ketting@imb-mainz.de.
4
Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands. Electronic address: e.d.wit@nki.nl.

Abstract

The spatial organization of chromosomes is critical in establishing gene expression programs. We generated in situ Hi-C maps throughout zebrafish development to gain insight into higher-order chromatin organization and dynamics. Zebrafish chromosomes segregate in active and inactive chromatin (A/B compartments), which are further organized into topologically associating domains (TADs). Zebrafish A/B compartments and TADs have genomic features similar to those of their mammalian counterparts, including evolutionary conservation and enrichment of CTCF binding sites at TAD borders. At the earliest time point, when there is no zygotic transcription, the genome is highly structured. After zygotic genome activation (ZGA), the genome loses structural features, which are re-established throughout early development. Despite the absence of structural features, we see clustering of super-enhancers in the 3D genome. Our results provide insight into vertebrate genome organization and demonstrate that the developing zebrafish embryo is a powerful model system to study the dynamics of nuclear organization.

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