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High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding.

Authors :
Zhong JY
Niu L
Lin ZB
Bai X
Chen Y
Luo F
Hou C
Xiao CL
Source :
Nature communications [Nat Commun] 2023 Mar 06; Vol. 14 (1), pp. 1250. Date of Electronic Publication: 2023 Mar 06.
Publication Year :
2023

Abstract

Canonical three-dimensional (3D) genome structures represent the ensemble average of pairwise chromatin interactions but not the single-allele topologies in populations of cells. Recently developed Pore-C can capture multiway chromatin contacts that reflect regional topologies of single chromosomes. By carrying out high-throughput Pore-C, we reveal extensive but regionally restricted clusters of single-allele topologies that aggregate into canonical 3D genome structures in two human cell types. We show that fragments in multi-contact reads generally coexist in the same TAD. In contrast, a concurrent significant proportion of multi-contact reads span multiple compartments of the same chromatin type over megabase distances. Synergistic chromatin looping between multiple sites in multi-contact reads is rare compared to pairwise interactions. Interestingly, the single-allele topology clusters are cell type-specific even inside highly conserved TADs in different types of cells. In summary, HiPore-C enables global characterization of single-allele topologies at an unprecedented depth to reveal elusive genome folding principles.<br /> (© 2023. The Author(s).)

Subjects

Subjects :
Humans
Alleles
Chromatin genetics

Details

Language :
English
ISSN :
2041-1723
Volume :
14
Issue :
1
Database :
MEDLINE
Journal :
Nature communications
Publication Type :
Academic Journal
Accession number :
36878904
Full Text :
https://doi.org/10.1038/s41467-023-36899-x