Extracting Multi-way Chromatin Contacts from Hi-C Data

Overview

Journal PLoS Comput Biol

Specialty Biology

Date 2021 Dec 6

PMID 34871311

Citations 8

Authors

Lei Liu

Bokai Zhang

Changbong Hyeon

Affiliations

Soon will be listed here.

Abstract

There is a growing realization that multi-way chromatin contacts formed in chromosome structures are fundamental units of gene regulation. However, due to the paucity and complexity of such contacts, it is challenging to detect and identify them using experiments. Based on an assumption that chromosome structures can be mapped onto a network of Gaussian polymer, here we derive analytic expressions for n-body contact probabilities (n > 2) among chromatin loci based on pairwise genomic contact frequencies available in Hi-C, and show that multi-way contact probability maps can in principle be extracted from Hi-C. The three-body (triplet) contact probabilities, calculated from our theory, are in good correlation with those from measurements including Tri-C, MC-4C and SPRITE. Maps of multi-way chromatin contacts calculated from our analytic expressions can not only complement experimental measurements, but also can offer better understanding of the related issues, such as cell-line dependent assemblies of multiple genes and enhancers to chromatin hubs, competition between long-range and short-range multi-way contacts, and condensates of multiple CTCF anchors.

Citing Articles

Hi-C-guided many-polymer model to decipher 3D genome organization.

Shi C, Liu L, Hyeon C Biophys J. 2024; 123(16):2574-2583.

PMID: 38932457 PMC: 11365109. DOI: 10.1016/j.bpj.2024.06.023.

Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.

Schuette G, Ding X, Zhang B Biophys J. 2023; 122(17):3425-3438.

PMID: 37496267 PMC: 10502442. DOI: 10.1016/j.bpj.2023.07.017.

Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.

Schuette G, Ding X, Zhang B bioRxiv. 2023; .

PMID: 36993500 PMC: 10055272. DOI: 10.1101/2023.03.17.533194.

A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants.

Shi G, Thirumalai D Nat Commun. 2023; 14(1):1150.

PMID: 36854665 PMC: 9974990. DOI: 10.1038/s41467-023-36412-4.

Dissecting the cosegregation probability from genome architecture mapping.

Liu L, Cao X, Zhang B, Hyeon C Biophys J. 2022; 121(20):3774-3784.

PMID: 36146938 PMC: 9674989. DOI: 10.1016/j.bpj.2022.09.018.

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