Contributions of Local Structural and Energetic Features of DNA to Large-scale Genomic Organization

The three-dimensional architecture of the genome is intimately tied to fundamental biological processes. How the primary sequence of DNA base pairs leads to the complex folding and dynamics of a full chromosome is an open question. Here we present a picture of chromatin folding that is emerging from the combination of fine structural data with novel experimental measurements and increasingly coarse grained, interconnected levels of DNA modeling. We draw attention to the role of DNA twist in the spacing of nucleosomes and the effects of nucleosome spacing and the surprising influence of nucleosomal twist on the expansion and compression of short simulated chromatin arrays. We also discuss the connection between base-pair and nucleosome-level treatments of DNA and the direct connection between protein and DNA fine structure, with investigations of chromatin looping based on these treatments.