TASEP modelling provides a parsimonious explanation for the ability of a single uORF to derepress translation during the integrated stress response
- University College Cork, Ireland
- Lomonosov Moscow State University, Russia
- The University of Texas at Dallas, United States
Figures
Figure 1
ICIER model.
(A) Parameters of the model. The lattice is shown as a black line with the positions of start and stop codons separated by L sites (codons). Scanning ribosomes are blue and elongating are red in …
Figure 2
uORF length (L) influences how the flux of scanning ribosomes changes downstream (rout) in response to lowered ribosome load (rin) due to stress.
Other parameters in the simulations: tε>σ=0; tσ>ε=0.8; mσ=mε=0.3. (A, B) Relative (rout[rin]/rout[rin=0.1]) (A) and absolute (B) changes in the density of ribosomes downstream of a uORF for a range …
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Figure 2—source data 1
Source data for Figure 2A.
- https://doi.org/10.7554/eLife.32563.004
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Figure 2—source data 2
Source data for Figure 2B.
- https://doi.org/10.7554/eLife.32563.005
Figure 3
The effect the movement rates (mε) for elongating ribosomes on stress resistance.
Other parameters of the simulations tε>σ=0; tσ>ε=0.8; L=100; mσ=0.3. (A, B) Relative (rout[rin]/rout[rin=0.1]) (A) and absolute (B) changes in the density of ribosomes downstream of the uORF for a …
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Figure 3—source data 1
Source data for Figure 3A.
- https://doi.org/10.7554/eLife.32563.007
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Figure 3—source data 2
Source data for Figure 3B.
- https://doi.org/10.7554/eLife.32563.008
Figure 4
The effect of uORF initiation efficiency (tσ>ε) on stress resistance.
Other parameters of the simulations tε>σ=0; L=100; mσ=0.3; mε=0.3. (A, B) Relative (rout[rin]/rout[rin=0.1]) (A) and absolute (B) changes in the density of ribosomes downstream of a uORF for a range …
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Figure 4—source data 1
Source data for Figure 4A.
- https://doi.org/10.7554/eLife.32563.010
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Figure 4—source data 2
Source data for Figure 4B.
- https://doi.org/10.7554/eLife.32563.011
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Figure 4—source data 3
Source data for Figure 4E.
- https://doi.org/10.7554/eLife.32563.012
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Figure 4—source data 4
Source data for Figure 4F.
- https://doi.org/10.7554/eLife.32563.013
Figure 5
The effect of reinitiation downstream of the uORF on stress resistance.
Other parameters of the simulations tε>σ=0; tσ>ε=0.8; L=100; mσ=0.3; mε=0.3. (A, B) Relative (rout[rin]/rout[rin=0.1]) (A) and absolute (B) changes in the density of ribosomes downstream of a uORF …
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Figure 5—source data 1
Source data for Figure 5A.
- https://doi.org/10.7554/eLife.32563.015
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Figure 5—source data 2
Source data for Figure 5B.
- https://doi.org/10.7554/eLife.32563.016
Figure 6
The effect of the size of scanning ribosomes (Dσ) and probability of spontaneous ribosome dissociation (Pσ) on stress resistance.
Other parameters of the simulations; tσ>ε=0.8; L=100; mσ=0.3; mε=0.3. (A, B) Absolute changes in the density of ribosomes downstream of a uORF under a scenario in which scanning (A) or elongating (B)…
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Figure 6—source data 1
Source data for Figure 6A.
- https://doi.org/10.7554/eLife.32563.018
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Figure 6—source data 2
Source data for Figure 6B.
- https://doi.org/10.7554/eLife.32563.019
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Figure 6—source data 3
Source data for Figure 6C.
- https://doi.org/10.7554/eLife.32563.020
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Figure 6—source data 4
Source data for Figure 6D.
- https://doi.org/10.7554/eLife.32563.021
Figure 7
Correlations between translational stress resistance of mRNAs and features in the 5’ leaders of uOFRs for three studies.
(A) uORF length. (B) uORF translation initiation measured as uORF translation efficiency. (C) Ribosome pausing estimated with pause score. Pearson correlation coefficients (r) and Spearman rank …
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Figure 7—source data 1
- https://doi.org/10.7554/eLife.32563.023
Additional files
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Supplementary file 1
The parameters of the computer simulations.
- https://doi.org/10.7554/eLife.32563.024
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Supplementary file 2
The coordinates of the uORFs.
- https://doi.org/10.7554/eLife.32563.025
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Transparent reporting form
- https://doi.org/10.7554/eLife.32563.026
