The Hi-C you might remember from childhood was a delicious fruit punch drink with a mix of flavors. But as a recent Methods article points out, there’s a new Hi-C method on the scene. It’s not a juice beverage, but it is a tasty combination of techniques to analyze chromatin interactions that epigenetics researchers will love.
Hi–C is the latest method based on chromosome conformation capture (3C), only taking the extra step of connecting it with next generation sequencing (NGS) to give it a whole new kick. Job Dekker and his team at UMass say that Hi–C enables analyses of chromatin interactions as never before. Basically, Hi–C works by labeling all genomic fragments with biotin before ligation, marking the ligation junctions. Magnetic beads then purify those junctions, creating a library of ligation products that are fed into NGS. The resulting chromatin interaction data is highly useful for studying genome organization at high resolution.
Other 3C-based techniques only look at certain loci, which as the scientists say “ enables ‘one-versus-some’ (basic 3C and ChIP-loop), ‘one-versus-all’ (4C), or ‘many-versus-many’ (5C) explorations of the conformation of chromosomal regions of interest.” In contrast, Hi–C enables what they call an ‘‘all-versus-all’’ interaction profile, which covers overall genome structure, biophysical chromatin properties and long distance contacts of genomic elements.
From the genome-wide interaction maps that Hi–C delivers it’s now easier to study nuclear organization and chromosome architecture that may generate new insights into gene regulation, nuclear partitioning, or chromatin dynamics. The authors think that Hi-C provides the “ultimate connectivity between the genomic sequence and spatial conformation.”
Learn all about the Hi-C technique at Methods, June 2012
For additional reading about chromosome conformation capture methods, check out this article on Hi-C and related methods from our friends at Active Motif.