MOTIVATION: The intrinsic DNA sequence is an important determinant of nucleosome 
positioning. Some DNA sequence patterns can facilitate nucleosome formation, 
while others can inhibit nucleosome formation. Nucleosome positioning influences 
the overall rate of sequence evolution. However, its impacts on specific 
patterns of sequence evolution are still poorly understood.
RESULTS: Here, we examined whether nucleosomal DNA and nucleosome-depleted DNA 
show distinct polymorphism patterns to maintain adequate nucleosome architecture 
on a genome scale in yeast. We found that sequence polymorphisms in nucleosomal 
DNA tend to facilitate nucleosome formation, whereas polymorphisms in 
nucleosome-depleted DNA tend to inhibit nucleosome formation, which is 
especially evident at nucleosome-disfavored sequences in nucleosome-free regions 
at both ends of genes. Sequence polymorphisms facilitating nucleosome 
positioning correspond to stable nucleosome positioning. These results reveal 
that sequence polymorphisms are under selective constraints to maintain 
nucleosome positioning.
CONTACT: zhimdai@gmail.com; issdxh@mail.sysu.edu.cn