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An agent-based model for mRNA export through the nuclear pore complex.

Azimi M, Bulat E, Weis K, Mofrad MR - Mol. Biol. Cell (2014)

Bottom Line: On running the model, we observed that mRNA export is sensitive to the number and distribution of transport receptors coating the mRNA and that there is a rate-limiting step in the nuclear basket that is potentially associated with the mRNA reconfiguring itself to thread into the central channel.Of note, our results also suggest that using a single location-monitoring mRNA label may be insufficient to correctly capture the time regime of mRNA threading through the pore and subsequent transport.This has implications for future experimental design to study mRNA transport dynamics.

View Article: PubMed Central - PubMed

Affiliation: Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, Graduate Program in Chemical Biology, Berkeley, Berkeley, CA 94720.

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Distribution, by affinity, of mRNA residence times in the nuclear basket for successful export events as calculated using a single, randomly placed hrp36 probe, compared with using two probes that are placed at both 5′ and 3′ ends of the mRNA. The x-axis is on a log10 scale. Larger points indicate higher frequency of the specified measurement. The p values on the right correspond to a nonparametric (Wilcoxon rank sum) test of significance in the difference between the residence-time distributions obtained with each probe method.
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Figure 4: Distribution, by affinity, of mRNA residence times in the nuclear basket for successful export events as calculated using a single, randomly placed hrp36 probe, compared with using two probes that are placed at both 5′ and 3′ ends of the mRNA. The x-axis is on a log10 scale. Larger points indicate higher frequency of the specified measurement. The p values on the right correspond to a nonparametric (Wilcoxon rank sum) test of significance in the difference between the residence-time distributions obtained with each probe method.

Mentions: More-granular representations of single-tag and double-tag mRNA residence times are shown in Figure 4 for the nuclear basket and Figure 5 for the central channel. A nonparametric Wilcoxon rank-sum test comparing residence times obtained using the two different mRNA- tracking approaches confirmed that residence times were significantly different for all affinities, with the exception of 120 μM for the nuclear basket and 160 μM for the central channel. We suspect that there was a lack of significance at those affinities partly due to sparse sampling of successful transport events.


An agent-based model for mRNA export through the nuclear pore complex.

Azimi M, Bulat E, Weis K, Mofrad MR - Mol. Biol. Cell (2014)

Distribution, by affinity, of mRNA residence times in the nuclear basket for successful export events as calculated using a single, randomly placed hrp36 probe, compared with using two probes that are placed at both 5′ and 3′ ends of the mRNA. The x-axis is on a log10 scale. Larger points indicate higher frequency of the specified measurement. The p values on the right correspond to a nonparametric (Wilcoxon rank sum) test of significance in the difference between the residence-time distributions obtained with each probe method.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4230623&req=5

Figure 4: Distribution, by affinity, of mRNA residence times in the nuclear basket for successful export events as calculated using a single, randomly placed hrp36 probe, compared with using two probes that are placed at both 5′ and 3′ ends of the mRNA. The x-axis is on a log10 scale. Larger points indicate higher frequency of the specified measurement. The p values on the right correspond to a nonparametric (Wilcoxon rank sum) test of significance in the difference between the residence-time distributions obtained with each probe method.
Mentions: More-granular representations of single-tag and double-tag mRNA residence times are shown in Figure 4 for the nuclear basket and Figure 5 for the central channel. A nonparametric Wilcoxon rank-sum test comparing residence times obtained using the two different mRNA- tracking approaches confirmed that residence times were significantly different for all affinities, with the exception of 120 μM for the nuclear basket and 160 μM for the central channel. We suspect that there was a lack of significance at those affinities partly due to sparse sampling of successful transport events.

Bottom Line: On running the model, we observed that mRNA export is sensitive to the number and distribution of transport receptors coating the mRNA and that there is a rate-limiting step in the nuclear basket that is potentially associated with the mRNA reconfiguring itself to thread into the central channel.Of note, our results also suggest that using a single location-monitoring mRNA label may be insufficient to correctly capture the time regime of mRNA threading through the pore and subsequent transport.This has implications for future experimental design to study mRNA transport dynamics.

View Article: PubMed Central - PubMed

Affiliation: Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, Graduate Program in Chemical Biology, Berkeley, Berkeley, CA 94720.

Show MeSH
Related in: MedlinePlus