Hi-C in Budding Yeast

UMMS Affiliation

Program in Systems Biology; Department of Biochemistry and Molecular Pharmacology



Document Type



Biochemistry, Biophysics, and Structural Biology | Genetics and Genomics | Laboratory and Basic Science Research | Systems Biology


Hi-C enables simultaneous detection of interaction frequencies between all possible pairs of restriction fragments in the genome. The Hi-C method is based on chromosome conformation capture (3C), which uses formaldehyde cross-linking to fix chromatin regions that interact in three-dimensional space, irrespective of their genomic locations. In the Hi-C protocol described here, cross-linked chromatin is digested with HindIII and the ends are filled in with a nucleotide mix containing biotinylated dCTP. These fragments are ligated together, and the resulting chimeric molecules are purified and sheared to reduce length. Finally, biotinylated ligation junctions are pulled down with streptavidin-coated beads, linked to high-throughput sequencing adaptors, and amplified via polymerase chain reaction (PCR). The resolution of the Hi-C data set will depend on the depth of sequencing and choice of restriction enzyme. When sufficient sequence reads are obtained, information on chromatin interactions and chromosome conformation can be derived at single restriction fragment resolution for complete genomes.

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Citation: Cold Spring Harb Protoc. 2015 Jul 1;2015(7):pdb.prot085209. doi: 10.1101/pdb.prot085209. Link to article on publisher's site

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Link to Article in PubMed

Journal Title

Cold Spring Harbor protocols

PubMed ID