Slx5/Slx8-dependent ubiquitin hotspots on chromatin contribute to stress tolerance [Gene expression]

Chromatin is a highly regulated environment, and protein association with chromatin is often controlled by post-translational modifications and the corresponding enzymatic machinery. Specifically, SUMO-targeted ubiquitin ligases (STUbLs) have emerged as key players in nuclear quality control, genome maintenance and transcription. However, how STUbLs select specific substrates amongst myriads of SUMOylated proteins on chromatin remains unclear. Here, we reveal a remarkable co-localization of the budding yeast STUbL Slx5/Slx8 and ubiquitin at seven genomic loci that we term ‘ubiquitin hotspots’. Ubiquitylation at these sites depends on Slx5/Slx8 and protein turnover on the Cdc48 segregase. We identify the transcription factor-like Ymr111c/Euc1 to associate with these sites and be a critical determinant of ubiquitylation. Euc1 specifically targets Slx5/Slx8 to ubiquitin hotspots via bipartite binding of Slx5 that involves the Slx5 SUMO-interacting motifs and an additional, novel substrate recognition domain. Interestingly, the Euc1-ubiquitin hotspot pathway acts redundantly with chromatin modifiers of the H2A.Z and Rpd3L pathways in specific stress responses. Thus, our data suggest that STUbL-dependent ubiquitin hotspots shape chromatin during stress adaptation. Gene expression profiling was performed in biological triplicates to compare transcriptomes of ymr111c/euc1∆ or ymr111c/euc1-K231R mutant strains with a wild-type strain as reference. RMA-normalized expression intensities were obtained for each sample and pair-wise comparisons between sample groups were performed to obtain log2-fold-change values.