Fig. 1.

Mesoscale model and HOXC system setup. (A) The repeating unit of the mesoscale model consists of a rigid nucleosome core with wrapped DNA represented by 300 point charges and beads for linker DNA, LH, and the flexible histone tails. See details in ref. 8. NCP, nucleosome core particle. (B) A rendering of the HOXC gene cluster model demonstrates gene positions and epigenetic elements in a 3D model. Acetylated tails are red, and WT tails are blue. Intron DNA is drawn in dark blue, exon DNA is colored light blue, and intergenic DNA is dark red. (C) DNA linker lengths used in the HOXC model are plotted against the nucleosome index, along with annotated gene locations and epigenetic features, with acetylation islands in red, LH in teal, and NFRs in green.