Figure 2.

Hierarchical looping at the fiber level. (a) Our mesoscale model treats the various chromatin constituents separately. DNA is modeled as a modified worm-like chain, with 9 bp per bead. LHs are coarse-grained from all-atom molecular dynamics simulations so that six beads represent the globular head and 22 beads represent the C-terminal domain. The histone tails are coarse-grained from united-atom representations similarly, so that 5 amino acids define a tail bead. Nucleosome cores, without tails, are treated as rigid bodies with 300 Debye-Hückel pseudo-charges placed on the irregular nucleosome surface using our program DiSCO (92), so that the electrostatic field is reasonably reproduced as a function of the monovalent salt concentration. These DNA, LH, and histone tail beads are combined with the nucleosome to form our mesoscale chromatin model. (b–d) Sample 96-nucleosome configurations are shown for LH-deficient (−LH) (b), partially LH-saturated (one LH per two nucleosomes, or ½LH) (c), and LH-saturated (one LH per nucleosome, or +LH) (d) fibers. Internucleosome contact matrices are calculated from each mesoscale configuration by measuring the distance between any two core, tail, or linker DNA beads belonging to separate nucleosomes, where any distance measured <2 Å is considered a contact. In these matrices, local contacts are highlighted in red, whereas medium-range contacts are highlighted in green, and long-range contacts are colored in blue. To help visualize the three types of internucleosome contacts, we mark specific nucleosome interactions in the contact matrices with an x symbol, and indicate the corresponding pair of nucleosomes in the configurations above. We also sketch, at each bottom-right corner of the matrix, a simple polymer view to illustrate the evolution of flaking. At bottom, EMANIC contact probabilities for metaphase and interphase chromatin were derived by cross linking native HeLa cell contacts in vivo, before relaxing the structures and imaging via EM (9). When compared to contact probabilities derived from mesoscale models (black and dashed lines) of varying LH concentrations, the patterns of −LH fibers show good agreement with metaphase chromatin, whereas ½LH fibers correspond well to interphase chromatin. LHs can modulate both local and global compaction: more compact fibers with saturated LH content have less self-association and thus are globally less compact, whereas ½LH or −LH fibers are locally less compact, but globally more compact due to enhanced long-range (i ± ≥7) contacts. To see this figure in color, go online.