Patterns of variant polyadenylation signal usage in human genes

The formation of mature mRNAs in vertebrates involves the cleavage and poly adenylation of the pre-mRNA, 10-30 nt downstream of an AAUAAA or AUUAAA sig nal sequence. The extensive cDNA data now available shows that these hexame rs are not strictly conserved. In order to identify variant polyadenylation signals on a large scale, we compared over 8700 human 3' untranslated sequ ences to 157,775 polyadenylated expressed sequence tags (ESTs], used as mar kers of actual mRNA 3' ends. About 5600 EST-supported putative mRNA 3' ends were collected and analyzed for significant hexameric sequences. Known pol yadenylation signals were found in only 73% of the 3' fragments. Ten single -base variants of the AAUAAA sequence were identified with a highly signifi cant occurrence rate, potentially representing 14.9% of the actual polyaden ylation signals. Of the mRNAs, 28.6% displayed two or more polyadenylation sites. In these mRNAs, the poly(A) sites proximal to the coding sequence te nd to use variant signals more often, while the 3'-most site tends to use a canonical signal. The average number of ESTs associated with each signal t ype suggests that variant signals (including the common AUUAAA] are process ed less efficiently than the canonical signal and could therefore be select ed for regulatory purposes. However, the position of the site in the untran slated region may also play a role in polyadenylation rate.