Three-dimensional genome architecture: from contacts to mechanisms

Three-dimensional genome architecture (3DGA) is an active, self-reinforcing system in which chromatin biochemical state and spatial organization are reciprocally coupled. Thus, 3DGA provides a physical substrate through which past regulatory events are encoded, maintained, and re-established, as a form of cellular memory. Understanding how 3DGA arises and persists requires the integration of three complementary approaches, each illuminating aspects of 3DGA that the others cannot fully capture. Chromosome conformation capture and its derivatives, culminating in Hi-C, have generated genome-wide maps of chromatin contacts revealing compartments, topologically associating domains, and loops, but report ensemble-averaged contact frequencies that obscure the variability and dynamics realized in individual nuclei. Super-resolution microscopy and chromatin tracing directly resolve the spatial geometry of chromatin in single cells, revealing that the structural features inferred from Hi-C are probabilistic and heterogeneous rather than fixed, and capturing the transient, stochastic nature of enhancer-promoter contacts. Biochemical reconstitution together with single-molecule approaches define the causal mechanisms underlying the organizational features of 3DGA, but operate on material removed from its native cellular context. We discuss how the integration of these three approaches has shifted our view of 3DGA from a passive correlate of gene expression to a dynamic memory machine.