Fig 1.
A data-driven model for a 18-μm HeLa cell: A) the cytoplasmic components are: ER, mitochondria and Golgi (not included in the figure for clarity); and B) a nucleus containing nuclear pore complexes, Cajal bodies and nuclear speckles.
The cytosol, nuclear pore complexes, nuclear speckles, and Cajal bodies are directly involved in RNA splicing processes, whereas ER, mitochondria and Golgi apparatus provide excluded volume effects.
Table 1.
The cellular components of the constructed HeLa model.
Fig 2.
A) The reaction scheme describing the formation of U1 and U2 splicing particles mapped on a cross-section of our in-silico HeLa cell [38, 39]. The four spherically-shaped regions in cyan color are Cajal bodies. B) Splicing reactions as implemented in our simulations. The reactions together with their corresponding rate constants are presented in Tables 2 and 3. Abbreviations are: Pol II (RNA polymerase II), Ex1 and 2 (Exon 1 and 2).
Table 2.
Reactions describing U1 (u1snRNP) and U2 (U2snRNP) splicing particles formation together with their associated rates.
Abbreviations are: DNA(D), Gemin 5(G5), five already-assembled Sm proteins (Sm5), the remaining Sm proteins (Sm2), diffusion-limited (D.L.), model assumption (M), nucleus (N), NPC (P), Cajal bodies (J) and cytoplasm (C).
Table 3.
Spliceosome assembly and splicing reaction.
Abbreviations are: DNA (D), U1snRNP (U1), U2snRNP (U2), U4/U6⋅ U5snRNP (tri⋅ U), model assumption (M), diffusion-limited (D.L.), nuclear speckles (S) and nucleus (N).
Fig 3.
Spliceosomal particle formation depends on NPC count.
Increase (pink) or decrease (blue) in the number NPCs by 20% results in a corresponding change in the number of U1 (A) and U2 (B) particles formed. The effect is consistent for different nuclear sizes. P-values for U1 results are: 1.8 × 10−2 (3.7 μm), 6.8 × 10−3 (4.7 μm), 4 × 10−3 (5.3 μm); and for U2 results are: 3.9 × 10−12 (3.7 μm), 6.4 × 10−6 (4.7 μm), 8.5 × 10−5 (5.3 μm). Error bars represent the standard deviations. For each condition, 20 simulation replicates for duration of 30 seconds were performed.
Fig 4.
Splicing efficiency increases in the presence of speckles in the cells: A) The higher the probability for the splicing particles to transition from the cell nucleus to the speckles, relative to the reverse transition, the higher the localization of splicing particles in speckles. Schematically, the randomly distributed splicing particles (yellow dots) in the cell nucleus (colored in purple), localize in nucleus speckles (blue shaded regions) as the probability imbalance increases (the splicing particles concentration is 1 nM). B) As the percentage of splicing particles located in speckles increases, the number of spliced mRNA also increases. C) This enhancement in mRNA production is highly sensitive to the localization of splicing particles in speckles; with only a 10% localization of splicing particles in speckles, the splicing reaction is enhanced ∼ 250-fold relative to the case with no speckles. D) Noise estimated as coefficient of variation (CV), decreases as a greater percentage of splicing particles are localized in speckles. Splicing particle concentration affects the functional advantage of speckles: E) Enhancement in mRNA production due to the presence of speckles, depends on the U1 splicing particle concentration; F) Effect of the U1 splicing particle concentration on the mRNA production noise. Note that for cells with 0.1 nM U1, below 25% splicing particle localization, the CV is not defined due to lack of mRNA production. For each condition, 20 simulation replicates were performed. For simulation details see Methods.
Fig 5.
A) Increasing the number of nuclear speckles, results in an increase of the surface area (magenta curve) and decrease of the speckles diameter (blue curve); B) mRNA production increases as the number of speckles increases till about 50 speckles beyond which the production plateaus.
Error bars represent the standard deviations. For each condition, 20 simulation replicates were performed.
Fig 6.
Our model predicts that the mRNA production decreases by a factor of two, above 0.05 μm.
An schematics shows a nuclear speckle in red and the distance of active genes on chromatin (curved line in grey) from the speckle periphery (d). Error bars represent the standard deviations. For each condition, 20 simulation replicates were performed.
Fig 7.
Formation of speckles in our simulations: A) splicing particles (U1 and U2 colored in yellow and orange, respectively) diffusing freely in the nucleus without speckle, B) Introduction of an imbalance on transition probabilities of splicing particles from the nucleus to speckles results in the localization of the splicing particles in the speckles shown as red-shaded regions.