Nuclear Cartography: Techniques for mapping chromosome conformation

ENCODE

RESEARCHER: Job Dekker, Professor and Co-Director, Program in Systems Biology, University of Massachusetts Medical School, Worcester

PROJECT: Mapping long-range DNA interactions as part of the ENCODE project

PROBLEM: 3C is not easily multiplexed, making its application to large genomic surveys impractical.

SOLUTION: 3C is sometimes called a one vs. one technique because it is used to measure individual interactions between selected pairs of genomic segments. In the technique, cellular chromatin structure is frozen in place with a crosslinker such as formaldehyde. Restriction enzymes cut the DNA and the resulting ends are then ligated together to physically link the two previously separate strands. The crosslink is then reversed to release the now-connected DNA fragments. Finally, researchers probe for specific physical interactions by using PCR to amplify across their ligation junctions.

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