Discovering genome regulation with 3C and 3C-related technologies

It has been known for some time that eukaryotic genomic DNA is packaged in the form of highly organized chromatin in vivo. This organization is important not only to reduce the length of chromosomes during interphase but also because it represents a type of higher-order genome regulation mechanism. Indeed, spatial chromatin architecture is known to be important for transcription, DNA replication and repair. Chromosome structure can be observed at different scales and studied with a variety of complementary techniques. For example, microscopy can provide single cell information while technologies such as the chromosome conformation capture (3C) method and its derivatives can yield higher-resolution data from cell populations. In this review, we report on the biological questions addressed with 3C and 3C-related techniques and what has been uncovered to date. We also explore what these methods may further reveal about the regulation of genomic DNA activities.

► This review describes how 3C technologies can probe functional genome organization. ► 3C and 3C-related techniques map physical chromatin contacts in vivo. ► Physical chromatin contacts regulate transcription, DNA replication and repair. ► Functional genome organization relies on physical chromatin contacts.