Unraveling the 3D genome: genomics tools for multiscale exploration

• In vivo nucleosome–nucleosome packing interactions are poorly understood due to a dearth of methods.
• The megabase-scale 3D organization of the genome is being uncovered by high-resolution Hi-C methods.
• Genomics is transitioning to hypothesis-driven science with new tools for perturbing chromatin.

A decade of rapid method development has begun to yield exciting insights into the 3D architecture of the metazoan genome and the roles it may play in regulating transcription. Here we review core methods and new tools in the modern genomicist's toolbox at three length scales, ranging from single base pairs to megabase-scale chromosomal domains, and discuss the emerging picture of the 3D genome that these tools have revealed. Blind spots remain, especially at intermediate length scales spanning a few nucleosomes, but thanks in part to new technologies that permit targeted alteration of chromatin states and time-resolved studies, the next decade holds great promise for hypothesis-driven research into the mechanisms that drive genome architecture and transcriptional regulation.