Deciphering single-cell 3D chromatin structure using scCTG.

Autor:	Jiang R; Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China., Xue Y; Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China., Huang Y; Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.; Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China.; Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 528107, China., Gao YQ; Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.; Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China.; Changping Laboratory, Beijing 102206, China.
Jazyk:	angličtina
Zdroj:	The Journal of chemical physics [J Chem Phys] 2024 Dec 28; Vol. 161 (24).
DOI:	10.1063/5.0241334
Abstrakt:	Sequencing-based Hi-C technology has been widely used to study the three-dimensional structure of chromatin. More recently, the development of single-cell Hi-C technology has enabled the study of chromatin structural variations between individual cells. However, single-cell Hi-C data are often highly sparse, necessitating the use of imputation algorithms to address insufficient sampling. Current methods encounter challenges such as significant discrepancies from real structural features, limited reproducibility, slower computational speeds, or reliance on large amounts of training data, which hinder their broader applicability. In this study, we improved the previously published CTG (Hi-C To Geometry) algorithm to introduce the single-cell CTG (scCTG) algorithm, which combines convolution and diffusion processes to yield the spatial distance matrix for various types of single-cell chromatin structure data. scCTG algorithm shows a good performance in terms of computational efficiency, robustness, and correlation with physical spatial distances. The scCTG algorithm can be applied to effectively identify compartments and insulation strength for each locus, providing deeper insights into the relationship between chromatin structure and gene expression at the single-cell level. (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)
Databáze:	MEDLINE
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