Next, we explored the impact of Cas5 on global responses to cell wall stress. We mapped genome-wide RNA PolII occupancy during caspofungin treatment in wild-type and cas5Δ/cas5Δ strains. In a wild-type strain, 546 genes had distinct RNA PolII-binding profiles in response to caspofungin treatment, with increased binding for 294 genes and reduced binding for 252 genes (Supplementary Data 2). As expected, many genes with increased RNA PolII binding upon caspofungin exposure were important for tolerating cell wall stress (Fig. 1d and Supplementary Data 2), whereas genes with reduced RNA PolII binding were involved in diverse biological processes, including cell cycle progression (Fig. 1e and Supplementary Data 2). Strikingly, comparison of genes that were differentially bound in response to caspofungin between the wild-type strain and the cas5∆/cas5∆ mutant, revealed that >60% of caspofungin-responsive genes were dependent on Cas5. Specifically, 163 of the 294 genes with increased PolII occupancy in response to caspofungin exposure and 178 of the 252 genes with reduced occupancy were dependent on Cas5 (Fig. 1f and Supplementary Data 2–4). These findings suggest that Cas5 has a profound impact on global transcriptional responses to cell wall stress.