Hi-C (genomic analysis technique)

Figure 1. An overview of the Hi-C workflow and its applications in research. Figure made using BioRender

Hi-C is a high-throughput genomic and epigenomic technique to capture chromatin conformation (3C).[1] In general, Hi-C is considered as a derivative of a series of chromosome conformation capture technologies, including but not limited to 3C (chromosome conformation capture), 4C (chromosome conformation capture-on-chip/circular chromosome conformation capture), and 5C (chromosome conformation capture carbon copy).[1][2][3][4] Hi-C comprehensively detects genome-wide chromatin interactions in the cell nucleus by combining 3C and next-generation sequencing (NGS) approaches and has been considered as a qualitative leap in C-technology (chromosome conformation capture-based technologies) development and the beginning of 3D genomics.[2][3][4]

Similar to the classic 3C technique, Hi-C measures the frequency (as an average over a cell population) at which two DNA fragments physically associate in 3D space, linking chromosomal structure directly to the genomic sequence.[4] The general procedure of Hi-C involves first crosslinking chromatin material using formaldehyde.[3][4] Then, the chromatin is solubilized and fragmented, and interacting loci are re-ligated together to create a genomic library of chimeric DNA molecules.[4] The relative abundance of these chimeras, or ligation products, is correlated to the probability that the respective chromatin fragments interact in 3D space across the cell population.[4] While 3C focuses on the analysis of a set of predetermined genomic loci to offer “one-versus-some” investigations of the conformation of the chromosome regions of interest, Hi-C enables “all-versus-all” interaction profiling by labeling all fragmented chromatin with a biotinylated nucleotide before ligation.[3][4] As a result, biotin-marked ligation junctions can be purified more efficiently by streptavidin-coated magnetic beads, and chromatin interaction data can be obtained by direct sequencing of the Hi-C library.[3][4]

Analyses of Hi-C data not only reveal the overall genomic structure of mammalian chromosomes, but also offer insights into the biophysical properties of chromatin as well as more specific, long-range contacts between distant genomic elements (e.g. between genes and regulatory elements),[4][5][6] including how these change over time in response to stimuli.[7] In recent years, Hi-C has found its application in a wide variety of biological fields, including cell growth and division, transcription regulation, fate determination, development, autoimmune disease, and genome evolution.[7][5][6] By combining Hi-C data with other datasets such as genome-wide maps of chromatin modifications and gene expression profiles, the functional roles of chromatin conformation in genome regulation and stability can also be delineated.[4]

  1. ^ a b Lieberman-Aiden, E; van Berkum, NL; Williams, L; Imakaev, M; Ragoczy, T; Telling, A; Amit, I; Lajoie, BR; Sabo, PJ; Dorschner, MO; Sandstrom, R; Bernstein, B; Bender, MA; Groudine, M; Gnirke, A; Stamatoyannopoulos, J; Mirny, LA; Lander, ES; Dekker, J (9 October 2009). "Comprehensive mapping of long-range interactions reveals folding principles of the human genome". Science. 326 (5950): 289–93. Bibcode:2009Sci...326..289L. doi:10.1126/science.1181369. PMC 2858594. PMID 19815776.
  2. ^ a b Lin, Da; Hong, Ping; Zhang, Siheng; Xu, Weize; Jamal, Muhammad; Yan, Keji; Lei, Yingying; Li, Liang; Ruan, Yijun; Fu, Zhen F.; Li, Guoliang; Cao, Gang (May 2018). "Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture". Nature Genetics. 50 (5): 754–763. doi:10.1038/s41588-018-0111-2. ISSN 1546-1718. PMID 29700467. S2CID 13740808.
  3. ^ a b c d e Kong, Siyuan; Zhang, Yubo (1 February 2019). "Deciphering Hi-C: from 3D genome to function". Cell Biology and Toxicology. 35 (1): 15–32. doi:10.1007/s10565-018-09456-2. ISSN 1573-6822. PMID 30610495. S2CID 57427743.
  4. ^ a b c d e f g h i j Belton, Jon-Matthew; McCord, Rachel Patton; Gibcus, Johan; Naumova, Natalia; Zhan, Ye; Dekker, Job (November 2012). "Hi-C: A comprehensive technique to capture the conformation of genomes". Methods. 58 (3): 268–276. doi:10.1016/j.ymeth.2012.05.001. ISSN 1046-2023. PMC 3874846. PMID 22652625.
  5. ^ a b Eagen, Kyle P. (June 2018). "Principles of Chromosome Architecture Revealed by Hi-C". Trends in Biochemical Sciences. 43 (6): 469–478. doi:10.1016/j.tibs.2018.03.006. ISSN 0968-0004. PMC 6028237. PMID 29685368.
  6. ^ a b Kim, Kyukwang; Kim, Mooyoung; Kim, Yubin; Lee, Dongsung; Jung, Inkyung (1 January 2022). "Hi-C as a molecular rangefinder to examine genomic rearrangements". Seminars in Cell & Developmental Biology. 121: 161–170. doi:10.1016/j.semcdb.2021.04.024. ISSN 1084-9521. PMID 33992531. S2CID 234746398.
  7. ^ a b Burren, Oliver S.; Rubio García, Arcadio; Javierre, Biola-Maria; Rainbow, Daniel B.; Cairns, Jonathan; Cooper, Nicholas J.; Lambourne, John J.; Schofield, Ellen; Castro Dopico, Xaquin; Ferreira, Ricardo C.; Coulson, Richard; Burden, Frances; Rowlston, Sophia P.; Downes, Kate; Wingett, Steven W. (2017-09-04). "Chromosome contacts in activated T cells identify autoimmune disease candidate genes". Genome Biology. 18 (1): 165. doi:10.1186/s13059-017-1285-0. ISSN 1474-760X. PMC 5584004. PMID 28870212.