The cohesin complex is at the heart of many chromosomal activities, including sister chromatid cohesion and transcriptional regulation^,,. Cohesin loading onto chromosomes depends on the Scc2–Scc4 cohesin loader complex^,,, but the chromatin features that form cohesin loading sites remain poorly understood. Here we show that the RSC chromatin remodeling complex recruits budding yeast Scc2–Scc4 to broad nucleosome-free regions, which the cohesin loader helps to maintain. Consequently, inactivation of either the cohesin loader or the RSC complex has similar effects on nucleosome positioning, gene expression and sister chromatid cohesion. These results show an intimate link between local chromatin structure and higher-order chromosome architecture. Our findings pertain to the similarities between two severe human disorders, Cornelia de Lange syndrome, which is caused by alterations in the human cohesin loader, and Coffin-Siris syndrome, which results from alterations in human RSC complex components^,,. Both syndromes can arise from gene misregulation due to related changes in the nucleosome landscape.