Hi-C as a molecular rangefinder to examine genomic rearrangements

Kyukwang Kim, Mooyoung Kim, Yubin Kim, Dongsung Lee, Inkyung Jung

Research output: Contribution to journalReview articlepeer-review

7 Scopus citations


The mammalian genome is highly packed into the nucleus. Over the past decade, the development of Hi-C has contributed significantly to our understanding of the three-dimensional (3D) chromatin structure, uncovering the principles and functions of higher-order chromatin organizations. Recent studies have repositioned its property in spatial proximity measurement to address challenging problems in genome analyses including genome assembly, haplotype phasing, and the detection of genomic rearrangements. In particular, the power of Hi-C in detecting large-scale structural variations (SVs) in the cancer genome has been demonstrated, which is challenging to be addressed solely with short-read-based whole-genome sequencing analyses. In this review, we first provide a comprehensive view of Hi-C as an intuitive and effective SV detection tool. Then, we introduce recently developed bioinformatics tools utilizing Hi-C to investigate genomic rearrangements. Finally, we discuss the potential application of single-cell Hi-C to address the heterogeneity of genomic rearrangements and sub-population identification in the cancer genome.

Original languageEnglish
Pages (from-to)161-170
Number of pages10
JournalSeminars in Cell and Developmental Biology
StatePublished - Jan 2022


  • 3D chromatin structure
  • Hi-C
  • Single-cell Hi-C
  • Structural variations


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