Practical Analysis of Hi-C Data: Generating A/B Compartment Profiles

Methods in Molecular Biology
Hisashi MiuraIchiro Hiratani

Abstract

Recent advances in next-generation sequencing (NGS) and chromosome conformation capture (3C) analysis have led to the development of Hi-C, a genome-wide version of the 3C method. Hi-C has identified new levels of chromosome organization such as A/B compartments, topologically associating domains (TADs) as well as large megadomains on the inactive X chromosome, while allowing the identification of chromatin loops at the genome scale. Despite its powerfulness, Hi-C data analysis is much more involved compared to conventional NGS applications such as RNA-seq or ChIP-seq and requires many more steps. This presents a significant hurdle for those who wish to implement Hi-C technology into their laboratory. On the other hand, genomics data repository sites sometimes contain processed Hi-C data sets, allowing researchers to perform further analysis without the need for high-spec workstations and servers. In this chapter, we provide a detailed description on how to calculate A/B compartment profiles from processed Hi-C data on the autosomes and the active/inactive X chromosomes.

Citations

Dec 21, 2018·Biophysics Reviews·Koustav PalFrancesco Ferrari
May 17, 2019·Clinical Epigenetics·Ignacio Pacheco-BernalLorena Aguilar-Arnal
Aug 24, 2019·Nature Communications·Mohamed Osama Ali AbdallaNoriko Saitoh
Jan 26, 2021·Development, Growth & Differentiation·Rawin Poonperm, Ichiro Hiratani

Related Concepts

Metazoa
Chromatin
DNA, Double-Stranded
DNA Conformation
Computer Programs and Programming
Sequence Determinations, DNA
Computational Molecular Biology
Genomics
Mouse, Swiss
High-Throughput Nucleotide Sequencing

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