Nucleosomes in active chromatin are dynamic, but whether they have distinct 
structural conformations is unknown. To identify nucleosomes with alternative 
structures genome-wide, we used H4S47C-anchored cleavage mapping, which revealed 
that 5% of budding yeast (Saccharomyces cerevisiae) nucleosome positions have 
asymmetric histone-DNA interactions. These asymmetric interactions are enriched 
at nucleosome positions that flank promoters. Micrococcal nuclease (MNase) 
sequence-based profiles of asymmetric nucleosome positions revealed a 
corresponding asymmetry in MNase protection near the dyad axis, suggesting that 
the loss of DNA contacts around H4S47 is accompanied by protection of the DNA 
from MNase. Chromatin immunoprecipitation mapping of selected nucleosome 
remodelers indicated that asymmetric nucleosomes are bound by the RSC chromatin 
remodeling complex, which is required for maintaining nucleosomes at asymmetric 
positions. These results imply that the asymmetric nucleosome-RSC complex is a 
metastable intermediate representing partial unwrapping and protection of 
nucleosomal DNA on one side of the dyad axis during chromatin remodeling.