Hi-C: A comprehensive technique to capture the conformation of genomes

By Jon-Matthew Belton, R. McCord, J. Gibcus, N. Naumova, Y. Zhan, Job Dekker. Methods, 2012

1,147 citations recorded by the source corpus.

We describe a method, Hi-C, to comprehensively detect chromatin interactions in the mammalian nucleus. This method is based on Chromosome Conformation Capture, in that chromatin is crosslinked with formaldehyde, then digested, and re-ligated in such a way that only DNA fragments that are covalently linked together form ligation products. The ligation products contain the information of not only where they originated from in the genomic sequence but also where they reside, physically, in the 3D organization of the genome. In Hi-C, a biotin-labeled nucleotide is incorporated at the ligation junction, making it possible to enrich for chimeric DNA ligation junctions when modifying the DNA molecules for deep sequencing. The compatibility of Hi-C with next generation sequencing platforms makes it possible to detect chromatin interactions on an unprecedented scale. This advance gives Hi-C the power to both explore the chromatin biophysics as well as the implications of chromatin structure in the biological functions of the nucleus. A massively parallel survey of chromatin interaction provides the previously missing dimension of spatial context to other genomic studies. This spatial context will provide a new perspective to studies of chromatin and its role in genome regulation in normal conditions and in disease.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/09f75fbe0e49b90d1f9209157aae73c96b03a831

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Citations in the corpus

Structural variant calling: the long and the short of it (2019, methodology): “In this section, we provide a brief overview of these technologies and the associated software packages and refer the interested reader to other reviews for more details [95, 100 – 102].”
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies (2017, methodology): “The Hi-C method was developed to comprehensively detect chromatin interactions in the cell nucleus using proximity ligation and shotgun sequencing of the ligation products (Belton et al. 2012).”
HiCUP: pipeline for mapping and processing Hi-C data (2015, background): “For example, a high proportion of circularised di-tags suggests inadequate cross-linking, whereas a high proportion of dangling ends implies the chewback step to remove biotin from unligated restriction fragments was inefficient 13 .”
Dilated Convolutions for Modeling Long-Distance Genomic Dependencies (2017, methodology): “Next, we intend to incorporate more DNA structural information, such as Hi-C data that measures DNA conformation (Belton et al., 2012).”