FIGURE 5.

Chromatin organization: ideal and deduced models for relaxed chromatin and stretched chromatin fibers. A–C, solenoid, zigzag, and heteromorphic models, respectively. A, ideal model (parallel and perpendicular views) for a 48-core 209-bp one-start solenoid fiber with six nucleosomes/turn in which DNA linkers (DNA segments shown in red connecting nucleosomes) are bent and neighboring nucleosomes (i±1 interactions (int.)) are in the closest contact. B, ideal two-start zigzag model (parallel and perpendicular views) for a 48-core 209-bp fiber in which DNA linkers are straight and i±2 nucleosomes are in the closest contact. C, heteromorphic architecture predicted by modeling and Monte Carlo simulations of 48-core 209-bp arrays with LH at room temperature (293 K), 0.15 m NaCl, and low concentration of magnesium ions and confirmed by cross-linking experiments (29). DNA linkers are shown in red, alternate nucleosomes are shown in white and blue, and LHs are shown as turquoise spheres. The view parallel to the fiber axis (left) and two enlarged nucleosome triplets are shown. Both straight and bent DNA linkers occur. In all views, connecting DNA linkers and DNA wrapped around the nucleosomes are colored in red; odd and even nucleosomes are white and blue, respectively; and LHs are shown in turquoise. The close-ups of trinucleosomes show both intra- and internucleosome interactions. The core histone tails are colored yellow (H2A), red (H2B), blue (H3), and green (H4). D, effect of NRL (173, 209, and 218 bp) and LH on the structure of the chromatin fiber as predicted from Monte Carlo simulations of 48-core arrays at 0.15 m monovalent ions (72). The center images also show the individual histone tail beads. Color coding is as described above. E, effect of various dynamic LH binding mechanisms on the chromatin unfolding mechanism for 24-core 209-bp fibers as revealed from stretching simulations mimicking single-molecule pulling experiments at monovalent salt conditions of 0.15 m (43). Panel 1, resulting force extension curves for fibers with one LH rigidly fixed to each core (blue curve) versus LHs that bind/unbind dynamically (average concentration of 0.8 LH/core; red curve) with added divalent cations. Dynamic LH binding/unbinding dramatically decreases the fiber stiffness and the forces needed for unfolding with respect to fibers with fixed LH, improving the agreement with experiments (33) significantly. pN, piconewtons. Panel 2, images representing unfolding intermediates at different forces along the dynamic LH curve in panel 1. Intermediates reveal “superbead-on-a-string” structures in which compact clusters coexist with extended fiber regions. Panel 3, effect of fast and slow dynamic LH binding/unbinding during chromatin fiber unfolding without divalent ions (43). The slow-rebinding LH molecules cause a more dramatic softening effect than a pool of fast-rebinding LH, whereas fast LH rebinding promotes formation of superbead-on-a-string conformations with compact clusters. Together, fast- and slow-binding LH pools provide facile fiber unfolding through heteromorphic superbead conformations.