Work

Methods for comparative ChIA-PET and Hi-C data analysis

Year: 2019

Type: review

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.

Source: Methods

DOI: 10.1016/j.ymeth.2019.09.019

Authors: Dan Capurso, Zhonghui Tang, Yijun Ruan

Institutions: The Jackson Laboratory for Genomic Medicine, UConn Health

Language: English

Topic: Genomics and Chromatin Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $3,300

Funders: Jackson Laboratory, National Human Genome Research Institute, National Institute of Diabetes and Digestive and Kidney Diseases