Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D

	Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D
	Chen, Y; Lin, ZB; Wang, SK; Wu, B; Niu, LJ; Zhong, JY; Sun, YM; Zheng, ZX; Bai, X; Liu, LR; Xie, W; Chi, W; Ye, TTT; Luo, RB; Hou, CH; Luo, F; Xiao, CL
	2025
发表期刊	NAT STRUCT MOL BIOL
ISSN	1545-9993
摘要	Differential high-order chromatin interactions between homologous chromosomes affect many biological processes. Traditional chromatin conformation capture genome analysis methods mainly identify two-way interactions and cannot provide comprehensive haplotype information, especially for low-heterozygosity organisms such as human. Here, we present a pipeline of methods to delineate diploid high-order chromatin interactions from noisy Pore-C outputs. We trained a previously published single-nucleotide variant (SNV)-calling deep learning model, Clair3, on Pore-C data to achieve superior SNV calling, applied a filtering strategy to tag reads for haplotypes and established a haplotype imputation strategy for high-order concatemers. Learning the haplotype characteristics of high-order concatemers from high-heterozygosity mouse allowed us to devise a progressive haplotype imputation strategy, which improved the haplotype-informative Pore-C contact rate 14.1-fold to 76% in the HG001 cell line. Overall, the diploid three-dimensional (3D) genome interactions we derived using Dip3D surpassed conventional methods in noise reduction and contact distribution uniformity, with better haplotype-informative contact density and genomic coverage rates. Dip3D identified previously unresolved haplotype high-order interactions, in addition to an understanding of their relationship with allele-specific expression, such as in X-chromosome inactivation. These results lead us to conclude that Dip3D is a robust pipeline for the high-quality reconstruction of diploid high-order 3D genome interactions.
收录类别	SCI
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/14464
专题	科研部门_进化发育与四维基因调控（候春晖）
推荐引用方式 GB/T 7714	Chen, Y,Lin, ZB,Wang, SK,et al. Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D[J]. NAT STRUCT MOL BIOL,2025.
APA	Chen, Y.,Lin, ZB.,Wang, SK.,Wu, B.,Niu, LJ.,...&Xiao, CL.(2025).Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D.NAT STRUCT MOL BIOL.
MLA	Chen, Y,et al."Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D".NAT STRUCT MOL BIOL (2025).

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