Genomics / chromosome conformation capture · BEGINNER LESSON
Hi-C
Hi-C is a genome-wide chromosome conformation capture method that measures which DNA regions were close together inside a cell nucleus. It does this by preserving nearby DNA contacts, joining them into chimeric fragments, and sequencing those fragments to infer 3D genome organization.
What Hi-C measures
Hi-C measures physical proximity between DNA regions in the nucleus, not direct chemical bonding or gene activity itself. The result is a contact map: a genome-wide record of which genomic fragments were often near each other when cells were fixed, cut, joined, and sequenced. This makes Hi-C useful for studying 3D genome architecture and chromatin organization. Acronym note: Hi-C stands for high-throughput chromosome conformation capture; 3C means chromosome conformation capture. [1][2][3]
[1] CiFi: accurate long-read chromosome conformation capture with low-input requirements [2] Protocol for the generation of low-input Hi-C sequencing libraries of ... [3] Hi-C informed kernel association test: integrating 3-dimensional genome structure into variant-set association for whole-genome sequencing data
How the method works
First, cells are crosslinked, usually with formaldehyde, so DNA regions that were close in space stay linked. The DNA is then cut with a restriction enzyme, and nearby ends are ligated, creating hybrid DNA fragments that represent a physical contact. Those fragments are sequenced, and the read pairs are mapped back to the genome to show which loci were near one another. In some protocols, the cut ends are filled in with biotinylated nucleotides before library preparation. [1][2][3]
[2] Protocol for the generation of low-input Hi-C sequencing libraries of ... [3] Hi-C informed kernel association test: integrating 3-dimensional genome structure into variant-set association for whole-genome sequencing data
What scientists use it for
Hi-C helps researchers study promoter-enhancer relationships. A promoter is a DNA region near a gene’s start site where transcription begins, and an enhancer is a regulatory DNA region that can influence a gene from farther away. Hi-C also supports haplotype phasing, which is sorting variants into parental copies of chromosomes, and genome assembly, where separate contigs are ordered and oriented into larger scaffolds. [0][2]
[1] CiFi: accurate long-read chromosome conformation capture with low-input requirements [3] Hi-C informed kernel association test: integrating 3-dimensional genome structure into variant-set association for whole-genome sequencing data
Limitations and caveats
Hi-C often needs many cells and deep sequencing, which can make experiments costly and difficult for rare samples. Low-input protocols exist, but they can still produce duplicate-rich, low-complexity libraries. Short-read Hi-C can miss unique mapping in repetitive DNA, and restriction enzymes can bias which regions are sampled because sites are not evenly distributed. Contact maps can also be noisy or sparse, especially for long-range contacts. [0][1][2]
[1] CiFi: accurate long-read chromosome conformation capture with low-input requirements [2] Protocol for the generation of low-input Hi-C sequencing libraries of ... [3] Hi-C informed kernel association test: integrating 3-dimensional genome structure into variant-set association for whole-genome sequencing data
SEE THE IDEA
How Hi-C turns 3D proximity into sequence data
Fix DNA regions that were close together in the nucleus.
Restriction enzymes break chromatin at selected sites.
Nearby fragments join into chimeric DNA contacts.
Read pairs are aligned to locate interacting genomic regions.
Each step preserves or reveals spatial proximity, so the final sequence data can be used to infer 3D genome contacts.
Hi-C converts close nuclear neighbors into sequenced DNA pairs that stand in for physical contacts. [1][2][3]
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Sources and further reading
This general lesson was generated from public source material. It explains a concept; it does not interpret a private paper or provide medical advice.
- CiFi: accurate long-read chromosome conformation capture with low-input requirements
- Protocol for the generation of low-input Hi-C sequencing libraries of ...
- Hi-C informed kernel association test: integrating 3-dimensional genome structure into variant-set association for whole-genome sequencing data