Fig. 4: Global PPI dynamics under DNA replication stress reveals a role for the SAGA complex.
a, Protein complexes likely to change assembly state under DNA replication stress. Proteins with changing FLiP markers are indicated by a black circle. b, Differential abundance analysis of proteins coimmuno-precipitated with Ada3-FLAG in anti-FLAG AP–MS under HU stress compared to control. P values were calculated by a Student t-test (two-sided) for the ratio of prey in the pull-down versus empty control. A negative log2 fold change indicates less interaction of the prey under HU stress. SAGA component proteins are indicated in blue. c, Western blot of C-terminally GFP-tagged Spt7 under control and HU stress (single replicate; MW, molecular weight). d, Volcano plot showing differential abundance of acetylated peptides between yeast grown under HU stress and control conditions. A positive fold change corresponds to higher acetylation under HU stress. P values were determined with an ANOVA test (one-way) and corrected for multiple testing (Benjamini–Hochberg). The protein corresponding to each peptide is indicated. Known acetylation targets are indicated in red, proteins belonging to a protein complex suggested to undergo changes in assembly state are indicated with a star.
