PUBLICATION

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

Authors
Kaaij, L.J.T., van der Weide, R.H., Ketting, R.F., de Wit, E.
ID
ZDB-PUB-180705-3
Date
2018
Source
Cell Reports   24: 1-10.e4 (Journal)
Registered Authors
Ketting, René
Keywords
none
Datasets
GEO:GSE105013, GEO:GSE105015, GEO:GSE105014
MeSH Terms
  • Animals
  • Chromatin/metabolism*
  • Embryonic Development/genetics*
  • Enhancer Elements, Genetic/genetics
  • Epigenomics
  • Genome
  • Histone Code
  • Zebrafish/embryology*
  • Zebrafish/genetics*
PubMed
29972771 Full text @ Cell Rep.
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.
Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping