#25 · Epigenomics

Physical polymer models connect 3D genome organization to regulatory output

The common thread is explicit physical simulation of DNA and chromatin organization. A haplotype-resolved polymer model of the Drosophila embryo genome reports that specific pairing buttons yield pairing-induced domains. An experimentally informed polymer model combines low-resolution contact data with MNase nucleosome positioning to reconstruct locus organization at high resolution. TORCphysics, a one-dimensional simulation, computes supercoiling-mediated expression profiles from genome architecture. The first two address structural organization, while TORCphysics addresses regulatory output, so scope is not uniform across the set. What is new here is the attempt to tie structural features of genome organization to predicted regulatory outcomes within one physical framework.