Extracting multi-way chromatin contacts from Hi-C data

• Main Authors: Hyeon, C. (Author), Liu, L. (Author), Zhang, B. (Author)
• Format: Article
• Language: English
• Published: Public Library of Science 2021
• Subjects: animal cell; Article; binding site; cell differentiation; chemistry; chromatin; Chromatin; chromosomal mapping; Chromosome Mapping; chromosome structure; controlled study; data analysis; DNA; DNA sequencing; Enhancer Elements, Genetic; enhancer region; erythroid cell; fluorescence in situ hybridization; gene; gene expression regulation; Gene Expression Regulation; gene locus; Genes; genetic database; genetic distance; genetics; genomics; Genomics; hemoglobin alpha chain; high throughput sequencing; High-Throughput Nucleotide Sequencing; human; Humans; mathematical computing; metabolism; monomer; mouse; nonhuman; prediction; procedures; transcription factor CTCF
• Online Access: View Fulltext in Publisher

 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. Copyright: © 2021 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.