How does the genome fold in vivo at the kilobase length-scale?

New methods based on high-throughput sequencing have begun to reveal the genome-wide architecture of chromosomes at the level of single nucleosomes and at the much larger scale of megabase-sized chromosome loops. Between those two size regimes lies chromatin structure on the scale of several nucleosomes, which plays an important role in regulating processes that are essential to normal cell function and development: transcription, DNA replication, and DNA repair. A significant gap remains in our understanding of this level of chromatin organization spanning tens of nucleosomes and a few kilobases of DNA, which we are calling the secondary structure of chromatin. Decades of work on chromatin's secondary structure has provided conflicting evidence regarding the presence of a “30-nm fiber,” a compacted fiber-like structure comprising an organizational level just above the “beads-on-a-string” of individual nucleosomes. The specific topology of this structure – or indeed the very existence of 30-nm structure in vivo – is still hotly debated, and almost nothing is known about the variability of these putative structures as a function of genome position. We are working to develop a clearer picture of this scale of chromatin organization by integrating both the physical and biochemical views of the nucleus. This work will impact diverse questions such as the regulation of gene expression during normal human development and differentiation, the emergence of cancer and aneuploidy, and the mechanisms of epigenome regulation and maintenance.