MOTIVATION: In addition to alternative splicing, alternative polyadenylation has 
also been identified as a critical and prevalent regulatory mechanism in human 
gene expression. However, the mechanism of alternative polyadenylation selection 
and the involved factors is still largely unknown.
RESULTS: We use the ENCODE data to scan DNA functional elements, including 
chromatin accessibility and histone modification, around transcript cleavage 
sites. Our results demonstrate that polyadenylation sites tend to be less 
sensitive to DNase I. However, these polyadenylation sites have preference in 
nucleosome-depleted regions, indicating the involvement of chromatin 
higher-order structure rather than nucleosomes in the resultant lower chromatin 
accessibility. More interestingly, for genes using two polyadenylation sites, 
the distal sites show even lower chromatin accessibility compared with the 
proximal sites or the unique sites of genes using only one polyadenylation site. 
We also observe that the histone modification mark, histone H3 lysine 36 
tri-methylation (H3K36Me3), exhibits different patterns around the cleavage 
sites of genes using multiple polyadenylation sites from those of genes using a 
single polyadenylation site. Surprisingly, the H3K36Me3 levels are comparable 
among the alternative polyadenylation sites themselves. In summary, 
polyadenylation and alternative polyadenylation are closely related to 
functional elements on the DNA level.
CONTACT: liang.chen@usc.edu.