HiC-DC+ Enables Systematic 3D Interaction Calls and Differential Analysis for Hi-C and HiChIP

Overview

Journal Nat Commun

Specialty Biology

Date 2021 Jun 8

PMID 34099725

Citations 22

Authors

Merve Sahin

Wilfred Wong

Yingqian Zhan

Kinsey Van Deynze

Richard Koche

Christina S Leslie

Affiliations

Soon will be listed here.

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.

Citing Articles

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