Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells

Qi Wang, Qiu Sun, Daniel M. Czajkowsky () and Zhifeng Shao ()
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Qi Wang: Shanghai Jiao Tong University
Qiu Sun: Shanghai Jiao Tong University
Daniel M. Czajkowsky: Shanghai Jiao Tong University
Zhifeng Shao: Shanghai Jiao Tong University

Nature Communications, 2018, vol. 9, issue 1, 1-8

Abstract: Abstract Topologically associating domains (TADs) are fundamental elements of the eukaryotic genomic structure. However, recent studies suggest that the insulating complexes, CTCF/cohesin, present at TAD borders in mammals are absent from those in Drosophila melanogaster, raising the possibility that border elements are not conserved among metazoans. Using in situ Hi-C with sub-kb resolution, here we show that the D. melanogaster genome is almost completely partitioned into >4000 TADs, nearly sevenfold more than previously identified. The overwhelming majority of these TADs are demarcated by the insulator complexes, BEAF-32/CP190, or BEAF-32/Chromator, indicating that these proteins may play an analogous role in flies as that of CTCF/cohesin in mammals. Moreover, extended regions previously thought to be unstructured are shown to consist of small contiguous TADs, a property also observed in mammals upon re-examination. Altogether, our work demonstrates that fundamental features associated with the higher-order folding of the genome are conserved from insects to mammals.

Date: 2018
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DOI: 10.1038/s41467-017-02526-9

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