Document Type

Article

Publication Date

2020

Keywords

JGM

JAX Source

Methods 2020; 170:69-74

PMID

31629084

DOI

https://doi.org/10.1016/j.ymeth.2019.09.019

Grant

Jackson Laboratory Director's Innovation Fund, HG009409, DK107967

Abstract

The three-dimensional architecture of chromatin in the nucleus is important for genome regulation and function. Advanced high-throughput sequencing-based methods have been developed for capturing chromatin interactions (Hi-C, genome-wide chromosome conformation capture) or enriching for those involving a specific protein (ChIA-PET, chromatin interaction analysis with paired-end tag sequencing). There is widespread interest in utilizing and interpreting ChIA-PET and Hi-C. We review methods for comparative ChIA-PET and Hi-C data analysis and visualization. The topics reviewed include: downloading ChIA-PET and Hi-C data from the ENCODE and 4DN portals; processing ChIA-PET data using ChIA-PIPE; processing Hi-C data using Juicer or distiller and cooler; viewing 2D contact maps using Juicebox or Higlass; viewing peaks, loops, and domains using BASIC Browser; annotating convergent and tandem CTCF loops.

Comments

We thank Yuliang Feng and Ping Wang for previously generating the HFFc6 in situ ChIA-PET data used as demo data in this review; thank Byoungkoo Lee for previously coordinating installation of a local Juicebox.js instance; and thank members of the Ruan Lab for helpful discussions.

This article is available under the Creative Commons CC-BY-NC-ND license.

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