Mesoscale phase separation of chromatin in the nucleus
- Weizmann Institute of Science, Israel
Figures
Figure 1 with 1 supplement
Snapshots of the simulated system from different views.
This representation is generated by drawing the surfaces around the beads that represent the lamin and chromatin. The same set of pictures shown here are depicted in a different graphical …
Figure 1—figure supplement 1
Snapshots of the simulated system visualized in terms of beads.
Outside view: The spherical volume representing the nucleus is surrounded by lamin beads (green). Within the sphere, the chromatin chain of N = 37,333 beads comprises two types beads: LAD (yellow) …
Figure 2
Variation of the chromatin concentration profile as a function of the intra-chromatin attractive interactions.
Left panel: Chromatin concentrations are shown for different intra-chromatin attraction strengths () with a volume fraction of chromatin and maximal LAD-lamina interactions (). For smaller …
Figure 3 with 1 supplement
Variation of the chromatin concentration profile as a function of the fraction of LAD domains bound to the lamina.
Left panel: Variation in the fraction ψ of LAD beads that can bond to the lamin, associated domains relative to its maximal value of , where 48% of the chromatin consists of LAD domains that can …
Figure 3—figure supplement 1
Transition from peripheral to central chromatin localization.
Here we show the transition from peripheral to central chromatin localization for small chromatin volume fraction as the fraction of chromatin that can bind to the lamin is varied from to . L…
Figure 4
Variation of the chromatin concentration profile as a function of the chromatin volume fraction.
Left panel: Chromatin concentrations are shown for different volume fractions of chromatin, . Right panel: The local volume fraction profiles show peripheral organization for and but not for …
Figure 5
State diagrams showing the transition from peripheral to uniform to central localization of chromatin.
(a) For a fixed value of (maximally bonded LAD), we calculated the local volume fraction obtained from simulations with different pairs (24 pairs) of the chromatin volume fraction and …
Figure 6
Angular separation of LAD and non-LAD chromatin.
(a) Simulation snapshot for parameter values , , and , shows peripheral organization with LAD near lamina and non-LADs separated from LADs in the radial direction. (b) Simulation snapshot for …
Appendix 1—figure 1
Comparison of the simulations with the experimental images.
(a) Snapshots of simulations for chromatin-chromatin attractions . For relatively small volume fraction of chromatin () and relatively high chromatin-lamina binding interactions (), the …
Appendix 2—figure 1
Scaling behavior of unconfined chromatin chains in good and poor solvent.
(a) LJ potential as a function of the distance between two beads, with snapshot of simulations of chromatin chain having 500 beads. Snapshots show unconfined, self-avoiding chromatin in good solvent …
Appendix 3—figure 1
Analysis of LADs sequence data of Drosophila.
(a) Mean cluster length of LAD for different chromosomes of Drosophila (Ho et al., 2014). (b) Length distribution of LAD for different Drosophila chromosomes. In both subfigures (a) and (b), the …
Appendix 4—figure 1
Alternate simulations for random LAD sequences.
(a) Schematic diagram describing our coarse-grained model of chromatin-lamina interactions. Two cases for LAD binding to lamin: (i) Randomly distributed as single beads, (ii) Exponentially …
Appendix 4—figure 2
Local volume fraction profiles of LAD, non-LAD, and lamin beads.
For , the local volume fraction profiles of LAD, non-LAD and lamin beads are shown. The graph shows the location of each of these bead types in the spherical volume where is the sphere center …
Appendix 5—figure 1
Wetting droplet and central chromatin organization for relatively weak LAD-lamina interactions.
(a) 3D snapshots of simulations showing central organization of chromatin with/without ‘arms’ as well as the wetting droplet. (b) Experiments also suggest central organization of chromatin …
Appendix 6—figure 1
Comparison of chromatin contacts in peripheral, central, and conventional organization.
(a,b) Contact maps from simulations, of different 50-kbp bins, for different chromatin organization. The color scheme varies from black to white, representing high to low contact counts (). (a) …
Appendix 7—figure 1
Phase separation of euchromatin-like and heterochromatin-like regions in conventional chromatin.
(a) Snapshots of simulations for different ψ are shown. In figure, LAD beads (yellow) are self attractive chain whereas non-LAD beads (red) are self-avoiding. This modeling results in a stronger …
Tables
Table 1
Parameter values used in the simulations.
| Parameter | Description | Reduced unit | SI unit |
|---|---|---|---|
| Thermal energy | 1.0 | 4.1 × 10−21J | |
| Bead mass | 1.0 | 10−21 kg | |
| σ | LJ size parameter | 1.0 | 10 nm |
| LJ energy parameter | 4.1 × 10−21J | ||
| rc | Contact distance | 25 nm | |
| ks | Spring constant | 0.41 Jm−2 | |
| lp | Persistence length | 20 nm | |
| kb | Bending stiffness | 8.2 × 10−21J | |
| τ | Damping time | 2 µs | |
| Time step | 20 ns |
