The genetic landscape of a physical interaction
- Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Spain
- Universitat Pompeu Fabra, Spain
- Institució Catalana de Recerca i Estudis Avançats, Spain
Figures
Figure 1 with 1 supplement
deepPCA.
(A) Leucine zipper domains (colored) and heptad positions of human Fos and Jun. (B) Overview of the assay. Single amino acid variants of Fos and Jun were constructed by overlap-extension PCR using …
Figure 1—figure supplement 1
Quality control of the PPI scores measured by deepPCA.
(A) Density plots showing the high correlation between PPI scores calculated from sequencing data filtered at different quality cut-offs. (B) Density plot showing the relationship between PPI scores …
Figure 2 with 1 supplement
Effects of single mutants.
(A) Heatmap of single mutant PPI scores averaged between the three replicates. Letters inside the heatmap represent the wild-type amino acid. White represents missing data. (B) Distribution of PPI …
Figure 2—figure supplement 1
Single mutant effects.
(A) Distribution of single mutants effects. (B) Proportion of single mutants that strongly decrease PPI strength (FDR < 0.05, one sample t-test with mu = 1) at different PPI score thresholds. (C) …
Figure 3 with 2 supplements
A thermodynamic model predicts double mutant outcomes.
(A) Distribution of double mutants PPI scores compared to Fos and Jun single mutants. (B) Observed double mutants PPI scores against the scores predicted by a multiplicative model. (C) Pie chart …
Figure 3—figure supplement 1
Correlations between genetic interaction scores from the three biological replicates of the trans library selection.
Genetic interactions calculated using the multiplicative model.
Figure 3—figure supplement 2
Fitting the thermodynamic model on the trans library data.
(A) Parameter search. Proportion of variance explained as a function of the three parameters of the thermodynamic model. The third parameter (b/ABWT) is represented as surfaces of different colors. …
Figure 4 with 3 supplements
Structural genetic interactions.
(A) Heatmap (top) and distribution (bottom) of percentage of significantly (absolute genetic interaction score > 0.1, FDR < 0.2) positive (left) or negative (right) genetic interactions per pairs of …
Figure 4—figure supplement 1
Distribution of number of significant genetic interactions for Fos or Jun single mutants at different magnitude thresholds.
Each row of the heatmap is the distribution of the number of interactions at that magnitude threshold. FDR < 0.2.
Figure 4—figure supplement 2
Robustness of enrichments in position pairs for significant (FDR < 0.2) genetic interactions at different magnitude thresholds.
Pairs of positions presented as significantly enriched in Figure 4C (magnitude threshold of 0.1). Enrichments and their corresponding FDRs were calculated at all 1024 pairs of positions, for each …
Figure 4—figure supplement 3
Robustness of enrichments in structural features for significant (FDR < 0.2) genetic interactions at different magnitude thresholds.
(A) Enrichments for different position types. Enrichments and their corresponding FDRs were calculated for each magnitude threshold independently. (B) Enrichments for pairs of mutations at …
Figure 5 with 9 supplements
Comparison of double mutant mutation outcome and genetic interactions in cis and trans.
(A) Cartoon illustrating how the cis library differs from the trans one. NNS, whole codon substitution. Asterisk, point mutation. (B) Scatter plot between Average PPI scores of identical pairs of …
Figure 5—figure supplement 1
PPI scores for the cis library.
(A) Correlation between PPI scores from the three biological replicates of the cis mutation library selection. Contains both single (n = 190) and double (n = 17,290) mutations. Variants with less …
Figure 5—figure supplement 2
Proportion of cis and trans double mutants classified as strengthening, intermediate effect or severely detrimental using different score thresholds.
The libraries where sub-sampled to match the distribution of the single mutant PPI scores as described in the method section. (A) Distribution of single mutants PPI scores before (solid lines) after …
Figure 5—figure supplement 3
Fitting the thermodynamic model on both the trans and cis data.
(A) Proportion of total variance explained in both datasets when fitting the model on either the trans or the cis data only. The models were fitted on the pooled replicates. Percentage of variance …
Figure 5—figure supplement 4
Significant structural genetic interactions in cis and trans.
(A) Correlation of structural genetic interaction scores between the three replicates of each library. Genetic interaction scores are from the thermodynamic model fitted on the two original …
Figure 5—figure supplement 5
Comparisons of the patterns of structural genetic interactions in cis and trans.
(A–B) Enrichment (Fisher’s exact test) for strong positive (green) or negative (purple) genetic interactions at different distance thresholds between the two mutated positions (A) and between …
Figure 5—figure supplement 6
Comparisons of the pairs of positions enriched in cis and trans.
(A) Pairs of positions significantly enriched in positive (green) or negative (purple) genetic interactions (Fisher’s exact test, FDR = 10%). Each pair of positions is also classified according to …
Figure 5—figure supplement 7
Robustness of the enrichments in structural features when sub-sampling to match single mutant effects.
Enrichments calculated from one of the sub-samples picked randomly. (A–B) Enrichment (Fisher’s exact test) for strong positive (green) or negative (purple) genetic interactions at different distance …
Figure 5—figure supplement 8
Robustness of enrichments in significant (FDR < 0.2) genetic interactions at different magnitude thresholds in the cis and trans libraries.
(A) Pairs of positions presented as significantly enriched in Figure 5—figure supplement 6A (magnitude threshold of 0.1). Enrichments and their corresponding FDRs were calculated at all 1024 pairs …
Figure 5—figure supplement 9
Comparisons of the extent of structural genetic interactions in cis and trans.
(A–B) Proportion of true positive (A) or negative (B) genetic interactions in the original (solid lines) or sub-sampled (open circles) libraries at different p-value cut-offs, showing that the …
Additional files
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Supplementary file 1
Data from the full trans library.
- https://doi.org/10.7554/eLife.32472.024
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Supplementary file 2
Variance explained by physico-chemical amino acid features.
- https://doi.org/10.7554/eLife.32472.025
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Supplementary file 3
Data from the restricted trans library.
- https://doi.org/10.7554/eLife.32472.026
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Supplementary file 4
Data from the cis library.
- https://doi.org/10.7554/eLife.32472.027
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Supplementary file 5
Primer sequences
- https://doi.org/10.7554/eLife.32472.028
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Transparent reporting form
- https://doi.org/10.7554/eLife.32472.029
