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

  • Hisashi Miura
  • Rawin Poonperm
  • Saori Takahashi
  • Ichiro HirataniEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1861)


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.

Key words

Epigenetics Hi-C contact map 3D genome organization A/B compartments Inactive X chromosome Bioinformatics 



This work was supported by a RIKEN CDB intramural grant to I.H.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Hisashi Miura
    • 1
  • Rawin Poonperm
    • 1
  • Saori Takahashi
    • 1
  • Ichiro Hiratani
    • 1
    Email author
  1. 1.Laboratory for Developmental EpigeneticsRIKEN Center for Developmental Biology (CDB) and Center for Biosystems Dynamics Research (BDR)KobeJapan

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