PUBLICATION
Demarcation of Topologically Associating Domains Is Uncoupled from Enriched CTCF Binding in Developing Zebrafish
- Authors
- Pérez-Rico, Y.A., Barillot, E., Shkumatava, A.
- ID
- ZDB-PUB-200426-30
- Date
- 2020
- Source
- iScience 23: 101046 (Journal)
- Registered Authors
- Shkumatava, Alena
- Keywords
- Biological Sciences, Chromosome Organization, Molecular Biology
- Datasets
- GEO:GSE133437
- MeSH Terms
- none
- PubMed
- 32334414 Full text @ iScience
Citation
Pérez-Rico, Y.A., Barillot, E., Shkumatava, A. (2020) Demarcation of Topologically Associating Domains Is Uncoupled from Enriched CTCF Binding in Developing Zebrafish. iScience. 23:101046.
Abstract
CCCTC-binding factor (CTCF) is a conserved architectural protein that plays crucial roles in gene regulation and three-dimensional (3D) chromatin organization. To better understand mechanisms and evolution of vertebrate genome organization, we analyzed genome occupancy of CTCF in zebrafish utilizing an endogenously epitope-tagged CTCF knock-in allele. Zebrafish CTCF shares similar facets with its mammalian counterparts, including binding to enhancers, active promoters and repeat elements, and bipartite sequence motifs of its binding sites. However, we found that in vivo CTCF binding is not enriched at boundaries of topologically associating domains (TADs) in developing zebrafish, whereas TAD demarcation by chromatin marks did not differ from mammals. Our data suggest that general mechanisms underlying 3D chromatin organization, and in particular the involvement of CTCF in this process, differ between distant vertebrate species.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping