Differential Crosslinking and Contractile Motors Drive Nuclear Chromatin Compaction

Abstract

During interphase, a typical cell nucleus features spatial compartmentalization of transcriptionally active euchromatin and repressed heterochromatin domains. In conventional nuclear organization, euchromatin predominantly occupies the nuclear interior, while heterochromatin, which is approximately 50% more dense than euchromatin, is positioned near the nuclear periphery. Peripheral chromatin organization can be further modulated by the nuclear lamina, which is itself a deformable structure. While a number of biophysical mechanisms for compartmentalization within rigid nuclei have been explored, we study a chromatin model consisting of an active, crosslinked polymer tethered to a deformable, polymeric lamina shell. Contractile motors, the deformability of the shell, and the spatial distribution of crosslinks all play pivotal roles in this compartmentalization. We find that a radial crosslink density distribution, even with a small linear differential of higher crosslinking density at the edge of the nucleus, combined with contractile motor activity, drives genomic segregation, in agreement with experimental observations. This arises from contractile motors preferentially drawing crosslinks into their vicinity at the nuclear periphery, forming high-density domains that promote heterochromatin formation. We also find an increased stiffness of nuclear wrinkles given the preferential heterochromatin compaction below the lamina shell, which is consistent with instantaneous nuclear stiffening under applied nanoindentation. We conclude with the potential for experimental validation of our model predictions.

Fig. 1:. 3D computational model of chromatin in a deformable nucleus.

(a) A two-dimensional schematic of the model. (b) A schematic illustrating the two types of motors acting on the chromatin. (c) A Simulation snapshot. The chromatin polymer consists of linearly connected monomers, depicted in red, while the active chromatin subunits are shown in cyan. The lamina is made up of lamin subunits, represented in grey. (d) The radial distribution of crosslink density (ρ_c) as a function of nuclear radius R_s. All quantities are reported in simulation units (s. u.), where 1 s. u. of length = 1 μm.

Fig. 2:. Radial chromatin density shaped by motors and crosslink profiles.

Chromatin density, ${\varphi }_c$, as a function of ${\mathrm{R}}_s$. (a) Initial chromatin density at $t=0$, and final chromatin density for (b) passive, (c) extensile, and (d) contractile motors, for different crosslink density profiles. The rescaled chromatin density, $\frac{{\varphi }_c^{f_m\ne 0}}{{\varphi }_c^{f_m=0}}$, is shown in the insets of panels (c) and (d), highlighting motor-induced changes relative to the passive case. Each case corresponds to $N_c=2000$ crosslinks and $N_L=600$ chromatin-lamina linkages. All quantities are reported in simulation units (s. u.), where $1\mathrm{s}.\mathrm{u}.$ of length $=1\mu m$ and $1\mathrm{s}.\mathrm{u}.\text{of time}=0.5\mathrm{s}$.

Fig. 3:. Influence of motor activity and number of crosslinks on chromatin distribution.

Chromatin density, ${\varphi }_c$, as a function of ${\mathrm{R}}_s$ for (a) passive, (b) extensile, and (c) contractile motors, shown for different numbers of crosslinks $\left(N_c\right)$ with a linear crosslink density profile. Results correspond to $N_L=600$ chromatin crosslinks. All quantities are reported in simulation units (s. u.), where $1\mathrm{s}.\mathrm{u}.$ of length $=1\mu m$ and $1\mathrm{s}.\mathrm{u}.\text{of time}=0.5\mathrm{s}$.

Fig. 4:. Contractile motor-induced organization of euchromatin and heterochromatin.

(a) Schematic illustrating the categorization of chromatin monomers into euchromatin (EuCh) and heterochromatin (HetCh) based on a local density cutoff (${\varphi }_{\mathit{loc}}^{i/j}$). (b) Density of EuCh and HetCh as a function of ${\mathrm{R}}_s$ and (c) average local density ($⟨{\varphi }_c^{\text{local}}⟩$) of EuCh and HetCh for a contractile motor with a linear crosslink density profile. The results shown correspond to $N_c=2000$ crosslinks and $N_L=600$ chromatin-lamina linkages. All quantities are reported in simulation units (s. u.), where $1\mathrm{s}.\mathrm{u}.$ of length $=1\mu m$ and $1\mathrm{s}.\mathrm{u}.\text{of time}=0.5\mathrm{s}$.

Fig. 5:. Distribution of motor density and motor–crosslink associations for linear and inverted crosslink profiles.

Radial distribution of (i) motor density (${\rho }_m$) and (ii) the average number of crosslinks per motor. Density color map of the number of crosslinks per motor ($N_c^m$) as a function of ${\mathrm{R}}_s$ for (iii) extensile and (iv) contractile motors. (a) Linear and (b) inverted crosslink profiles, each with subpanels (i–iv). The results shown correspond to $N_c=2000$ crosslinks and $N_L=600$ chromatin-lamina linkages. All quantities are reported in simulation units (s. u.), where 1 s. u. of length $=1\mu m$ and $1\mathrm{s}.\mathrm{u}.\text{of time}=0.5\mathrm{s}$.

Fig. 6:. Motor–crosslink coupling modulates local chromatin density for linear and inverted crosslink profiles.

Colormap of local chromatin density (${\varphi }_{\mathit{loc}}^c$) as a function of nuclear radius ($R_s$) and number of crosslinks per motor $\left(N_c^m\right)$ for extensile and contractile motors for linear (top row: a, b) and inverted (bottom row: d, e) crosslink profiles. The color bar represents the normalized local chromatin density. Panels (c) and (f) show the local neighborhoods of an extensile motor (i, ii) and a contractile motor (iii, iv), with maximum and minimum crosslinks, respectively, for linear (top row) and reverse (bottom row) profiles. Magenta/green: contractile/extensile motors; blue: crosslinked chromatin; red: chromatin monomers. All quantities are reported in simulation units (s. u.), where $1\mathrm{s}.\mathrm{u}.$ of length $=1\mu m$ and $1\mathrm{s}.\mathrm{u}.\text{of time}=0.5\mathrm{s}$.

Fig. 7:. Temporal profile of nuclear deformations and local properties of bulges and wrinkles with motor activity for a linear crosslink profile.

Time evolution of (a) the number of bulges/wrinkles ($N_{def}$) for (i) extensile and (ii) contractile motors, (b) chromatin density (${\varphi }_p$) at bulges/wrinkles, and (c) local fluctuations (${\delta }_{\mathit{local}}$) characterizing bulges and wrinkle regions, all for a linear crosslink density profile. The results shown correspond to $N_c=2000$ crosslinks and $N_L=600$ chromatin-lamina linkages. All quantities are reported in simulation units (s. u.), where 1 s. u. of length $=1\mu m$ and $1\mathrm{s}.\mathrm{u}.\text{of time}=0.5\mathrm{s}$.