Work

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

Year: 2018

Type: article

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.

Source: Cell Reports

DOI: 10.1016/j.celrep.2018.06.003

Authors: Lucas J.T. Kaaij, Robin H. van der Weide, René F. Ketting, Elzo de Wit

Institutions: Institute of Molecular Biology, The Netherlands Cancer Institute, Oncode Institute

Language: English

Topic: Genomics and Chromatin Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $5,620

Funders: Marie Curie, Nederlandse Organisatie voor Wetenschappelijk Onderzoek, KWF Kankerbestrijding, European Research Council