TY - JOUR
T1 - Hi-C as a molecular rangefinder to examine genomic rearrangements
AU - Kim, Kyukwang
AU - Kim, Mooyoung
AU - Kim, Yubin
AU - Lee, Dongsung
AU - Jung, Inkyung
N1 - Publisher Copyright:
© 2021 Elsevier Ltd
PY - 2022/1
Y1 - 2022/1
N2 - 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.
AB - 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.
KW - 3D chromatin structure
KW - Hi-C
KW - Single-cell Hi-C
KW - Structural variations
UR - http://www.scopus.com/inward/record.url?scp=85105732285&partnerID=8YFLogxK
U2 - 10.1016/j.semcdb.2021.04.024
DO - 10.1016/j.semcdb.2021.04.024
M3 - Review article
C2 - 33992531
AN - SCOPUS:85105732285
SN - 1084-9521
VL - 121
SP - 161
EP - 170
JO - Seminars in Cell and Developmental Biology
JF - Seminars in Cell and Developmental Biology
ER -