Modeling studies of chromatin fiber structure as a function of DNA linker length

Abstract

Chromatin fibers encountered in various species and tissues are characterized by different nucleosome repeat lengths (NRLs) of the linker DNA connecting the nucleosomes. While single cellular organisms and rapidly growing cells with high protein production have short NRL ranging from 160 to 189 bp, mature cells usually have longer NRLs ranging between 190 and 220 bp. Recently, various experimental studies have examined the effect of NRL on the internal organization of chromatin fiber. Here, we investigate by mesoscale modeling of oligonucleosomes the folding patterns for different NRL, with and without linker histone (LH), under typical monovalent salt conditions using both one-start solenoid and two-start zigzag starting configurations. We find that short to medium NRL chromatin fibers (173 to 209 bp) with LH condense into zigzag structures and that solenoid-like features are viable only for longer NRLs (226 bp). We suggest that medium NRLs are more advantageous for packing and various levels of chromatin compaction throughout the cell cycle than their shortest and longest brethren; the former (short NRLs) fold into narrow fibers, while the latter (long NRLs) arrays do not easily lead to high packing ratios due to possible linker DNA bending. Moreover, we show that the LH has a small effect on the condensation of short-NRL arrays but has an important condensation effect on medium-NRL arrays, which have linker lengths similar to the LH lengths. Finally, we suggest that the medium-NRL species, with densely packed fiber arrangements, may be advantageous for epigenetic control because their histone tail modifications can have a greater effect compared to other fibers due to their more extensive nucleosome interaction network.

Figure 1

Mesoscale model of the basic chromatin building block. The nucleosome core surface with wrapped DNA without histone tails is modeled as an irregularly shaped rigid body with 300 optimized pseudo surface charges (smallest white, pink, magenta, and blue spheres). The linker DNA (large red spheres) is treated using the discrete worm like chain model. The histone tails are coarse grained as bead models (red, yellow, green, and blue medium spheres). The LH is modeled as 3 charged beads rigidly connected to the nucleosome (turquoise spheres).

Figure 2

Space filling models based on MC simulations of 48-unit oligonucleosome chains of all NRL compacted at 0.15 M monovalent salt with LH (turquoise beads). Alternating nucleosomes are colored white and navy, with corresponding wrapped DNA as red and burgundy. In the 182-bp array, nucleosomes i, i + 1 and i + 2 are colored white, navy, and light blue, with corresponding DNA as red, burgundy, and purple, to highlight the three-start structure. LH is turquoise.

Figure 3

Selected models from Figure 2 analyzed for internucleosome contacts and linker DNA bending. (a) Arrays with very short NRL (173 bp) and LH fold into a narrow structure with low linear packing ratio regardless LH presence. (b) and (c) Arrays with medium long NRL (191 and 209 bp) and linker histone fold into zigzag structures with straight linkers and DNA linker stems. (d) Arrays with longest NRL (226 bp) fold into irregular structures with both DNA stems and bent linkers. Alternating nucleosomes are colored white and navy, with correspondingly wrapped DNA as red and burgundy. LH is turquoise.

Figure 4

Internucleosomal interactions patterns at 0.15 M monovalent salt. Interaction intensities versus nucleosome position separation k for 24-core arrays: (a) Short NRL (173 and 182 bp) without LH, (b) Short NRL (173 and 182 bp) with LH, (c) Medium NRL (191, 200, and 209 bp) without LH, (d) Medium NRL (191, 200, and 209 bp) with LH, (e) Long NRL (218 and 226 bp) without LH, (f) Long NRL (218 and 226 bp) with LH. Results for trajectories started from idealized zigzag and interdigitated solenoid conformations are shown separately.

Figure 5

Chromatin fiber dimensions as a function of NRL. (a) Nucleosome linear packing ratio, (b) fiber width, and (c) sedimentation coefficients, (d) fiber volume, (e) fiber curvature, and (f) percentage of filled volume, all as functions of nucleosome repeat length for 24-core oligonucleosomes. Results shown for simulations started from zigzag configuration and modeled without LH, started from solenoid without LH, started from zigzag with LH, started from solenoid with LH at 0.15 M monovalent salt. Nucleosome packing ratios are measured as a number of nucleosomes per 11 nm of fiber axis length. The fiber width is calculated as an average distance of nucleosomes (+ nucleosome half radius) from the fiber axis (Supplemental Figure S6).

Figure 6

Geometric parameters for different NRL systems 24-core arrays: (a) dimer distances (between i ± 1 nucleosome neighbors), (b) triplet distances (between i ± 2 neighbors), (c) bending angles, (d) dihedral angles, and (e) triplet angles for 24-core arrays at 0.15 M monovalent salt. The bending angle is defined as the angle between vectors passing through first two and last two DNA linker beads. The triplet angle is an angle between the geometric centers of three consecutive nucleosomes. The dihedral angle is the angle between two planes defined by four consecutive nucleosomes. See Supplemental Figure S4.

Figure 7

Chromatin fiber measurements as a function of the salt environment for 24 oligonucleosomes: (a) Nucleosome linear packing ratio and (b) sedimentation coefficients. Ensemble averages over trajectories started from zigzag and interdigitated solenoid configurations. The three new salt environment corresponds to monovalent C_S = 0.01 M without LH (−LH), monovalent C_S = 0.2 M with LH (+LH) and moderate monovalent salt at C_S = 0.15 M with LH and divalent ions (+LH+Mg).

Figure 8

Frequency analyses and cartoon images of different tail interactions in 24-core oligonucleosomes with linker histone at 0.15 M monovalent salt: (a) nucleosome/nucleosome interactions, (b) interactions with parent linker DNA, (c) interactions with non-parent DNA linkers, and (d) interactions with parent nucleosome. H2A₁ and H2A₂ denote N-termini and C-termini, respectively, of the H2A tails.