3D genomic organization in cancers

Abstract

Background: The hierarchical three-dimensional (3D) architectures of chromatin play an important role in fundamental biological processes, such as cell differentiation, cellular senescence, and transcriptional regulation. Aberrant chromatin 3D structural alterations often present in human diseases and even cancers, but their underlying mechanisms remain unclear.

Results: 3D chromatin structures (chromatin compartment A/B, topologically associated domains, and enhancer-promoter interactions) play key roles in cancer development, metastasis, and drug resistance. Bioinformatics techniques based on machine learning and deep learning have shown great potential in the study of 3D cancer genome.

Conclusion: Current advances in the study of the 3D cancer genome have expanded our understanding of the mechanisms underlying tumorigenesis and development. It will provide new insights into precise diagnosis and personalized treatment for cancers.

Author summary

This review focuses on the role of 3D chromatin structures in cancer development. We also summarized common bioinformatics techniques, especially machine learning and deep learning methods for studying 3D cancer genome, and introduced their limitations.

Graphical abstract

Keywords

the three-dimensional (3D) genome / chromatin compartment / topologically associated domain (TAD) / loop / cancer

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ACKNOWLEDGEMENTS

We thank Prof. Cheng Li for the helpful discussion. This work was supported by the Beijing Nova Program of Science and Technology (No. 20220484198 to HC) and the National Natural Science Foundation of China (Nos. 62173338, 61873276 and 31900488 to HC, XB, and HL, respectively).

COMPLIANCE WITH ETHICS GUIDELINES

The authors Junting Wang, Huan Tao, Hao Li, Xiaochen Bo and Hebing Chen declare that they have no conflict of interest or financial conflicts to disclose.

This article is a review article and does not contain any studies with human or animal materials performed by any of the authors.

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