Figure 4. Genetic interaction analyses.

Libraries in panels B, C, E and G are displayed in the same order as in Figure 1C. (A) Comparison of the number of transposons inserted in each of the 6603 yeast CDSs in the wild-type (x-axis) and mmm1Δ VPS13(D716H) (y-axis) libraries. (B) Transposon coverage of genes encoding ERMES components is increased in libraries from strains bearing the VPS13(D716H) allele. (C) Examples of genes showing synthetic sick/lethal interaction with mmm1Δ VPS13(D716H). (D) Comparison of the number of transposons inserted in each of the 6603 yeast CDSs in the wild-type (x-axis) and dpl1Δ (y-axis) libraries. (E) Transposon coverage of the HIP1 locus in the dpl1Δ his3Δ library and in all the other libraries (HIS3). (F) Comparison of the number of transposons inserted in each of the 6603 yeast CDSs in the dpl1Δ (x-axis) and dpl1Δ psd2Δ (y-axis) libraries. (G) Transposon coverage of the PSD1 locus in the dpl1Δ psd2Δ and in all other libraries.

DOI: http://dx.doi.org/10.7554/eLife.23570.015

Figure 4—figure supplement 1. Volcano plots comparing libraries or combinations of libraries as indicated.

The calculated fold-change in transposon density between the two sets of libraries is plotted in log₂ scale on the x-axis. The -log₁₀(p-value) (computed using the Student’s t-test) is plotted on the y-axis. ⁽¹⁾The VPS13(D716H) and the mmm1Δ VPS13(D716H) strains were generated in a MET17 background while all other libraries where generated in a met17Δ background. As a result MET17 and the overlapping ORF YLR302C appear as transposon free in the reference set. MET6 is more targeted by transposons in met17Δ libraries, likely because Met17 produces homocysteine, which needs to be converted to methionine by Met6, or might otherwise accumulate to toxic levels. ⁽²⁾The VPS13(D716H) and mmm1Δ VPS13(D716H) strains were generated in a Matα background, while the others were generated in a Mata background. ⁽³⁾YGR190C overlaps with HIP1. ⁽⁴⁾GPP1 shows synthetic lethality with a recessive Mendelian variant present in the psd2Δ dpl1Δ strain. However, this variant is neither linked to DPL1 nor to PSD2 (data not shown). ⁽⁵⁾ERMES component genes scores very high with respect to fold change, because two of the five libraries in the reference set bear the VPS13(D716H) allele. The p-value, by contrast, is not significant.

DOI: http://dx.doi.org/10.7554/eLife.23570.016