Schematic representation of the conversion process from SRRW to SR-EV.

The SRRW configurational motif hides the overlap of several beads in a molecule that has the structure of a branching polymer. By the introduction of excluded volume in SR-EV, the overlapping beads separate to form a cluster and a linear molecule.

Example SRRW and SR-EV configurations.

The top row are for the SRRW case, and bottom row corresponds to the associated SR-EV configuration. (A) and (E) represent the bonds of the full configurations and show that while SR-EV looks denser than the SRRW case the overall structure is preserved upon removal of the original overlaps. (B) and (F) correspond to the same small portion of the conformation and shows SR-EV having many more beads than SRRW due to the excluded volume between beads. The red circles explicitly highlight a structural motif that in SRRW is a central bead with 7 bonds branching out (a sequence of seven consecutive jump and returns steps) that transform to 15 linearly connecting beads forming a cluster. (C) and (G) display the chromatin conformations wrapped by a tight mesh suggesting the separation between a chromatin rich and a chromatin depleted regions, the latter being the space that free crowders could easily occupy. (D) and (H) show the bare interface between the two regions that resembles the interface dividing two bi-continuous phases and also clearly expose the difference between SRRW and SR-EV.

Packing domains and nucleosome accessibility.

Same SR-EV configuration displayed on Figure 2, but colored by the coordination number of each nucleosome. A) Full configuration reveals the spacial dispersity of packing domains in red, consistent with heterochromatic region, intercalated with low coordinated, accesible regions. B) 50 nm slab cut at the center of the configuration displaying details of the system heterogeneity and transition from packing domains to the intermediate, low coordinated, region. Note the white nucleosomes (CN ~ 6) at the periphery of the packing domains.

Linker DNA mean value for the twelve ϕ, α studied combinations.

The folding parameter α controls the return rules, Eqs. (1) and (2). N is the total number of nucleosomes represented in the model, which is related to the overall volume fraction ϕ = N(rº/Rc)3 with rº representing the radius of the nucleosomes and Rc the global spherical cutoff. The average number of DNA base pairs per model nucleosome, including the linker DNA, is 186.6.

Slab images:

A) representation of a 100 nm slab cut at the center of a SR-VE conformation obtained with ϕ = 0. 16 and α = 1.10. B) 2D chromatin density corresponding to coordinates of panel A). C) ChromSTEM 2D chromatin density obtained from a 100 nm slab ofa A549 cell. The 2D density color scale is the same for B) and C), and the density is normalized to its highest value in each image.

Theoretical and experimental polymeric properties of chromatin:

SR-EV ensemble average of (A) end-to-end distance and (B) contact probability a as a function of the genomic distance for all simulated conditions. The crossover between short distance intra-domain and long distance inter-domain regimes is explicitly indicated, as well as the confinement effect at longer distances. Notice that on these two panels there are four lines per α value, while α ∈ {1.10, 1.15, 1.20}. (C) Experimental (Hi-C) contact probability for chromosome 1 of HCT-116 cells showing quantitative agreement with the theoretical results.

Chromatin Volume Concentration for A) ϕ = 0.08, B) ϕ = 0.12, C) ϕ = 0. 16 and A) ϕ = 0.20 and α e {1.10, 1.15, 1.20}. The results for ϕ = 0.20, ϕ = 1.15 are the closest to the experimental findings of Ref (Ou et al., 2017). ϕ = 0.08 produce CVC distributions with a much larger contribution of low density regions, and ϕ = 0.20, ϕ = 1.10 over enhance the high density regions.

Chromatin packing domains:

(A) Distributions of domain radii Rd,i for all combinations of SR-EV parameters α and ϕ, as labeled in the figure. (B) Mean value 〈Rd〉 of the domain radii distributions. (C) In green, experimental distribution of domain radii obtained with ChromSTEM on A549 cell line, and the closest approximation from SR-EV that corresponds to α = 1.15 and ϕ = 0.16.

Packing coefficient D:

(A) Ensemble average cumulative pair correlation function 〈G(r)〉 for ϕ = 0. 16 and the three studied values of α. The vertical black lines mark the boundaries used to perform a power law regression to calculate D. (B) Packing coefficient 〈D〉 as a function of ϕ and α. (C) Distribution of packing coefficient Di for all the individual configurations for the twelve simulated conditions and, for comparison, we inserted the experimental PWS D results for U2OS cells that agrees very well with the SR-EV results for ϕ = 0.12 and α = 1.15.

Local correlation between packing parameter and chromatin volume concentration:

Relation between the calculated Di with the average local volume fraction 〈ϕi〉. Both quantities are calculated for the same configuration and in the same spherical region of 240 nm in radius. The figure includes one point for each one of the 12,000 configurations of the twelve simulated ensembles.

Effect of degrading Rad21 on the relation between packing parameter and chromatin volume concentration:

The small open symbols are the SR-EV results for ϕ = 0.12, α = 1.10 and 1.15. The filled symbols represent the experimental values obtained with ChromSTEM (Li et al., 2024) for the control sample (blue) and the Rad21 degrade sample (red)

Example of domain and domain’s center determination from SR-EV slabs. The left image shows the collapse SR-EV density from a 100 nm slab. The right image shows the identified domains cores in black and their geometric centers in yellow. Three different domains are identified with the numbers.

Example of the determination of the density profiles of domains and their effective radii. The three cases correspond to the large, medium and small domains denoted by 1, 2 and 3 in Figure S1. The profiles are calculated from the domain center using the coordinates from the configurations and assuming cylindrical symmetry. The radius of a domain corresponds to the first minimum in the density profile.

Example of cumulative distribution functions, Gi(r), for five different SR-EV configurations. Each Gi(r) is fitted with a power law between 40 and 120 nm to determine the packing coefficient Di corresponding to that configuration.