 Abstract Alternative Polydenylation, APA, is a process whereby different lengths of polyadenylation are used for the same gene, resulting in differential protein production. This process has been shown to be regulated by both CIS and transacting factors, but its extent of divergence during evolution and the relative contribution of each have not yet been explored. In this study, researchers compared the APA patterns of two mouse strains, C57BL, 6J and SPIETDIJ, and found that 3,747 out of 24,721 polydenylation sites showed significant divergence between the two strains. By analyzing the allele-specific data from F1 hybrid mice, they were able to show that most of these differences were due to CIS regulatory effects. Further analysis of the sequences near the CIS Divergent Polydenylation sites revealed that the presence of a poly-U tracked in the upstream region can lead to negative modulation of the polydenylation site usage. This article was authored by Mai Xingxiao, Bin Zhong, Yi Xingli, and others. We are article.tv, links in the description below.