Fig. 6: Variant IDRs have diverse effects on Abf1 function.
a, Schematic of MNase-seq mapping. b, In vitro genome-wide nucleosome positioning assay at Abf1 sites (n = 379; class I + II sites69) revealed that Abf1 IDRs were not required for nucleosome positioning barrier function. The lines compare the indicated purified Abf1 variants in combination with ATP, reconstituted nucleosomes (salt gradient dialysis (SGD) chromatin) and the yeast chromatin remodeller INO80. The grey area reflects the experiment with wild-type Abf1, but in the absence of INO80. c, The anchor-away technique enables ad hoc depletion of wild-type Abf1 from the nucleus. The wild-type copy of Abf1 is genetically fused to FRB, whereas the ribosomal protein Rpl13A, which transits through the nucleus during ribosome assembly, is fused to the double FKBP12 tag (2×FKBP). After adding rapamycin, FRB and FKBP bind and nuclear Abf1 is sequestered at cytosolic ribosomes, leading to ad hoc nuclear depletion. d, Schematic of ODM-seq chromatin mapping. A change from black to yellow represents DNA methylation. e, Abf1 IDR variants did not increase occupancy in NFRs relative to wild-type Abf1 and did not grossly alter nucleosome organization around Abf1 sites. The composite plots show ODM-seq data for the indicated Abf1 IDR variants aligned at n = 380 responder sites (classes I and II69; see also Extended Data Fig. 5d,e). f, Inviable Abf1 IDR variants or conditions lacking Abf1 affected +1 nucleosome positioning at essential genes differently than viable Abf1 IDR variants (growth rates in parentheses). PCA results are shown for all essential genes of ODM-seq data in the upstream flank of the in vivo +1 nucleosome (Extended Data Fig. 7g) averaged over two biological and two technical replicates (Extended Data Fig. 8a) each for the indicated Abf1 conditions. g, The Gal4 transactivation domain in the Gal4768–881 construct allowed growth even under fully GAL-inducing conditions with galactose as the sole carbon source. Shown is a spot dilution assay after two days of incubation. h, Whereas a classical view might delineate IDRs into motifs and non-motifs, our work here—and that of others—supports an emerging model in which motif function is licensed by a permissive context and in which chemical specificity contributes additional interactions that can even compensate for the loss of a motif. aro. clust., aromatic clusters.
