Poly(A) site choice in an Arabidopsis CPSF30 mutant

Alternative polyadenylation is a common and important means for regulating gene expression in eukaryotes, and has been implicated in important growth processes in plants. However, little is known about the mechanisms that govern alternative polyadenylation in plants. One Arabidopsis polyadenylation factor subunit, the ortholog of the 30 kD subunit of the mammalian Cleavage and Polyadenylation Specificity Factor (CPSF30), has been implicated in the responses of plants to oxidative stress (Zhang et al., PLoS ONE 3, e2410, 2008). To understand the basis of this role, poly(A) site choice was studied in a mutant (oxt6) deficient in CPSF30 expression using a genome-scale approach. The results indicate that poly(A) site choice in a vast majority of Arabidopsis genes is altered in the oxt6 mutant. However, there is little indication of increased transcriptional readthrough or antisense transcription, suggesting that overall polyadenylation efficiency is not affected by the deficit in CPSF30. A number of poly(A) sites were identified that are seen in only the wild-type or oxt6 mutant. Interestingly, putative polyadenylation signals associated with sites that are seen only in the oxt6 mutant are decidedly different from the canonical plant polyadenylation signal, lacking the characteristic A-rich near-upstream element; this suggests that CPSF30 may function in the handling of the near-upstream element. Taken together, these studies provide insight into the means by which CPSF30 may contribute to alternative polyadenylation in plants.