Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

Key Points Mining increasingly comprehensive chromatin interaction maps for chromosomal domains and complete genomes requires novel computational methods and modelling tools. Looping interactions between specific genomic elements — for example, gene promoters and regulatory elements — can be identified from chromatin interaction data by detecting interaction frequencies that are significantly higher than empirically estimated background levels. Looping interactions appear to be very abundant: most promoters interact with several other genomic elements. Statistical analysis of Hi-C data identifies multiple scales of domain organization: larger (1–10 Mb) chromosomal compartments and smaller (