Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools

• Published in: Nature protocols Vol. 16; no. 9; pp. 4144 - 4176
• Main Authors: Freire-Pritchett, Paula, Ray-Jones, Helen, Della Rosa, Monica, Eijsbouts, Chris Q., Orchard, William R., Wingett, Steven W., Wallace, Chris, Cairns, Jonathan, Spivakov, Mikhail, Malysheva, Valeriya
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.09.2021; Nature Publishing Group
• Subjects: 631/114/2415; 631/1647/48; 631/1647/794; 631/337/100/101; Analytical Chemistry; Biological Techniques; Biomedical and Life Sciences; Chromatin - chemistry; Chromosomes; Chromosomes - physiology; Computational Biology/Bioinformatics; Computer applications; Conformation; Enzymes; Genes; Genomes; Genomic analysis; Genomics; Laboratories; Life Sciences; Mathematical models; Methods; Microarrays; Models, Statistical; Molecular biology; Noise; Organic Chemistry; Preprocessing; Protocol; Signal detection; Software; Statistical models; Structure; Testing procedures; Workflow; United Kingdom
• ISSN: 1754-2189; 1750-2799; 1750-2799
• DOI: 10.1038/s41596-021-00567-5

Capture Hi-C is widely used to obtain high-resolution profiles of chromosomal interactions involving, at least on one end, regions of interest such as gene promoters. Signal detection in Capture Hi-C data is challenging and cannot be adequately accomplished with tools developed for other chromosome conformation capture methods, including standard Hi-C. Capture Hi-C Analysis of Genomic Organization (CHiCAGO) is a computational pipeline developed specifically for Capture Hi-C analysis. It implements a statistical model accounting for biological and technical background components, as well as bespoke normalization and multiple testing procedures for this data type. Here we provide a step-by-step guide to the CHiCAGO workflow that is aimed at users with basic experience of the command line and R. We also describe more advanced strategies for tuning the key parameters for custom experiments and provide guidance on data preprocessing and downstream analysis using companion tools. In a typical experiment, CHiCAGO takes ~2–3 h to run, although pre- and postprocessing steps may take much longer. This protocol describes a complete workflow for detecting significant contacts in Capture Hi-C data, including preprocessing, interaction calling and downstream analyses, based on the CHiCAGO pipeline and companion tools.