Chromatin fiber polymorphism triggered by variations of DNA linker lengths

Abstract

Deciphering the factors that control chromatin fiber structure is key to understanding fundamental chromosomal processes. Although details remain unknown, it is becoming clear that chromatin is polymorphic depending on internal and external factors. In particular, different lengths of the linker DNAs joining successive nucleosomes (measured in nucleosome-repeat lengths or NRLs) that characterize different cell types and cell cycle stages produce different structures. NRL is also nonuniform within single fibers, but how this diversity affects chromatin fiber structure is not clear. Here we perform Monte Carlo simulations of a coarse-grained oligonucleosome model to help interpret fiber structure subject to intrafiber NRL variations, as relevant to proliferating cells of interphase chromatin, fibers subject to remodeling factors, and regulatory DNA sequences. We find that intrafiber NRL variations have a profound impact on chromatin structure, with a wide range of different architectures emerging (highly bent narrow forms, canonical and irregular zigzag fibers, and polymorphic conformations), depending on the NRLs mixed. This stabilization of a wide range of fiber forms might allow NRL variations to regulate both fiber compaction and selective DNA exposure. The polymorphic forms spanning canonical to sharply bent structures, like hairpins and loops, arise from large NRL variations and are surprisingly more compact than uniform NRL structures. They are distinguished by tail-mediated far-nucleosome interactions, in addition to the near-nucleosome interactions of canonical 30-nm fibers. Polymorphism is consistent with chromatin's diverse biological functions and heterogeneous constituents. Intrafiber NRL variations, in particular, may contribute to fiber bending and looping and thus to distant communication in associated regulatory processes.

Keywords: chromatin bending and looping; chromatin polymorphism; coarse-grained modeling; nonuniform NRL.

Fig. 1.

Representation of the integrated coarse-grained oligonucleosome model with nonuniform NRLs (NRL₁ = 200 bp and NRL₂ = 227 bp) in regular alternation. (A) Nucleosome (with DNA wrapped around) with its irregular surface in gray. (A, Inset) The histone tail beads are in green (H4), blue (H3), magenta (H2B), yellow (H2A₁, N-termini), and orange (H2A₂, C-termini); the LH beads are in turquoise; and the linker DNA beads are in red. (B) Space-filling view without tails with alternating DNA shown in red and dark red, successive nucleosomes in blue and white, LHs in turquoise, and fiber axis in yellow. (C) Extended conformation illustrating regular alternation of NRLs (NRL₁–NRL₂–…).

Fig. 2.

Representative equilibrium snapshots for nonuniform NRL chromatin fibers. The snapshots are space-filling models (for color code, see Fig. 1). (A) Three bent-ladder conformations observed in the equilibrium ensembles of fibers with one short NRL (fibers 1–3 in Table 1). These snapshots are termed “bent,” “loop,” and “hairpin-like” simply to aid visualization and exemplify the narrow and highly bent conformations adopted by nonuniform NRL chromatin with one short NRL. The snapshot inside the dashed box is used to illustrate far-neighbor nucleosome contacts in Fig. 3. A nucleosome triplet (consecutive nucleosomes are numbered) is also shown to illustrate the lack of DNA stem formation due to the short linker DNA involved, and the occurrence of some DNA bending. (B) Representative canonical zigzag configuration for fibers combining medium-to-long NRLs with a moderate NRL variation. Only one snapshot is shown because canonical fibers are homogeneous. They exhibit full DNA stems with straight DNA linkers. Fibers combining long NRLs form additional stems with some DNA bending (see triplets in C). (C) Four observed polymorphic equilibrium snapshots for fibers combining two medium-to-long NRLs with a large NRL variation. The structures represent the compact and diverse forms adopted, including a canonical (irregular/heteromorphic zigzag) fiber, a slightly bent form, a sharply bent (hairpin-like) structure, and a compact chromatin loop. Polymorphic fibers form full DNA stems, and exhibit both straight and bent DNA linkers, as illustrated in the two nucleosome triples on the right.

Fig. 3.

Chromatin fiber structure as characterized through the frequency of near- and far-neighbor interactions. (A) Internucleosome interaction patterns (equilibrium ensemble average and SD) categorized by fiber types (bent ladder, canonical, and polymorphic). For each fiber type, a section of the fiber is shown to exemplify common interactions (selected nucleosomes are numbered) among neighbors separated by k DNA linker segments. Bent ladders have strong $i\pm 1$, $i\pm 2$, and $i\pm 3$ contacts, typical of ladder-like structures. Canonical fibers are characterized by $i\pm 2$, $i\pm 3$, and $i\pm 5$ zigzag contacts. Contrary to the other fiber types, polymorphic structures have internucleosome interaction patterns that do not overlap with that of the uniform NRL fiber; larger error bars and a wide range of strong contacts present highlight the structural diversity. (B) Ensemble average and SD of the percentage of conformations with far-neighbor interactions (i.e., conformations with at least one contact between nucleosomes separated by more than nine linker DNA segments) for the three fiber types identified, and the reference uniform fibers (26). Polymorphic fibers, followed by the bent ladders, have the highest occurrence of far-neighbor interactions. One snapshot illustrating the nature of far-neighbor interactions (selected nucleosomes are numbered) is shown (for the color version, see Fig. 2).

Fig. 4.

Fiber compaction as a function of the average NRL per fiber, from equilibrium ensemble averages and SD. Compaction is assessed through the nucleosome linear packing ratio measured as the number of nucleosomes per 11 nm of fiber axis length. Selected simulation snapshots (space-filling models) illustrate differences in compaction (for a description of space-filling model, see the color code in Fig. 1). Data for nonuniform NRL fibers are classified into three types (Table 1): bent ladder (purple), canonical (green), and polymorphic (orange) fibers. The black dashed lines represent the uniform NRL fibers (26). Fiber numbers correspond to those in Table 1. Polymorphic fibers are the most compact.