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

Author

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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)

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.

Suggested Citation

  • Qi Wang & Qiu Sun & Daniel M. Czajkowsky & Zhifeng Shao, 2018. "Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-017-02526-9
    DOI: 10.1038/s41467-017-02526-9
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    Cited by:

    1. Varvara Lukyanchikova & Miroslav Nuriddinov & Polina Belokopytova & Alena Taskina & Jiangtao Liang & Maarten J. M. F. Reijnders & Livio Ruzzante & Romain Feron & Robert M. Waterhouse & Yang Wu & Chunh, 2022. "Anopheles mosquitoes reveal new principles of 3D genome organization in insects," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
    2. Botong Zhou & Ping Hu & Guichun Liu & Zhou Chang & Zhiwei Dong & Zihe Li & Yuan Yin & Zunzhe Tian & Ge Han & Wen Wang & Xueyan Li, 2024. "Evolutionary patterns and functional effects of 3D chromatin structures in butterflies with extensive genome rearrangements," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    3. Olivier Messina & Flavien Raynal & Julian Gurgo & Jean-Bernard Fiche & Vera Pancaldi & Marcelo Nollmann, 2023. "3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. Yi Liao & Juntao Wang & Zhangsheng Zhu & Yuanlong Liu & Jinfeng Chen & Yongfeng Zhou & Feng Liu & Jianjun Lei & Brandon S. Gaut & Bihao Cao & J. J. Emerson & Changming Chen, 2022. "The 3D architecture of the pepper genome and its relationship to function and evolution," Nature Communications, Nature, vol. 13(1), pages 1-18, December.

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