HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP Journal Article
| Authors: | Sahin, M.; Wong, W.; Zhan, Y.; Van Deynze, K.; Koche, R.; Leslie, C. S. |
| Article Title: | HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP |
| Abstract: | Recent genome-wide chromosome conformation capture assays such as Hi-C and HiChIP have vastly expanded the resolution and throughput with which we can study 3D genomic architecture and function. Here, we present HiC-DC+, a software tool for Hi-C/HiChIP interaction calling and differential analysis using an efficient implementation of the HiC-DC statistical framework. HiC-DC+ integrates with popular preprocessing and visualization tools and includes topologically associating domain (TAD) and A/B compartment callers. We found that HiC-DC+ can more accurately identify enhancer-promoter interactions in H3K27ac HiChIP, as validated by CRISPRi-FlowFISH experiments, compared to existing methods. Differential HiC-DC+ analyses of published HiChIP and Hi-C data sets in settings of cellular differentiation and cohesin perturbation systematically and quantitatively recovers biological findings, including enhancer hubs, TAD aggregation, and the relationship between promoter-enhancer loop dynamics and gene expression changes. HiC-DC+ therefore provides a principled statistical analysis tool to empower genome-wide studies of 3D chromatin architecture and function. © 2021, The Author(s). |
| Keywords: | chromosome; gene expression; statistical analysis; software; visualization; topology; model validation; three-dimensional modeling |
| Journal Title: | Nature Communications |
| Volume: | 12 |
| ISSN: | 2041-1723 |
| Publisher: | Nature Publishing Group |
| Date Published: | 2021-06-07 |
| Start Page: | 3366 |
| Language: | English |
| DOI: | 10.1038/s41467-021-23749-x |
| PUBMED: | 34099725 |
| PROVIDER: | scopus |
| PMCID: | PMC8184932 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 1 July 2021 -- Source: Scopus |
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