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Nat Genet 2021 Jul 01;537:1075-1087. doi: 10.1038/s41588-021-00878-z.
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Three-dimensional folding dynamics of the Xenopus tropicalis genome.

Niu L , Shen W , Shi Z , Tan Y , He N , Wan J , Sun J , Zhang Y , Huang Y , Wang W , Fang C , Li J , Zheng P , Cheung E , Chen Y , Li L , Hou C .

Animal interphase chromosomes are organized into topologically associating domains (TADs). How TADs are formed is not fully understood. Here, we combined high-throughput chromosome conformation capture and gene silencing to obtain insights into TAD dynamics in Xenopus tropicalis embryos. First, TAD establishment in X. tropicalis is similar to that in mice and flies and does not depend on zygotic genome transcriptional activation. This process is followed by further refinements in active and repressive chromatin compartments and the appearance of loops and stripes. Second, within TADs, higher self-interaction frequencies at one end of the boundary are associated with higher DNA occupancy of the architectural proteins CTCF and Rad21. Third, the chromatin remodeling factor ISWI is required for de novo TAD formation. Finally, TAD structures are variable in different tissues. Our work shows that X. tropicalis is a powerful model for chromosome architecture analysis and suggests that chromatin remodeling plays an essential role in de novo TAD establishment.

PubMed ID: 34099928
PMC ID: PMC8270788
Article link: Nat Genet
Grant support: [+]

Species referenced: Xenopus tropicalis
Genes referenced: crebbp ctcf ctrl psmd6 rad21 smarca5

Article Images: [+] show captions
References [+] :
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