Sequence analysis of mRNA polyadenylation signals of rice genes

The formation of eukaryotic mRNAs involves the cleavage and polyadenylation of pre-mRNAs. To investigate the sequence requirement of putative polyadenylation signals (PASs), poly(A) sites and downstream elements (DUEs) in 3′-end-processing in rice, we compared expressed sequences tags (ESTs) with poly(A) extremity to full-length cDNA sequences and constructed a database of 12969 pre-mRNA sequences in −40–+40 nt surrounding the poly(A) sites, which were from 9953 genes. The alternative poly(A) sites were revealed in approximately 25% of mRNAs. Nearly 80% of pre-mRNAs showed stringent requirement of the YA (CA or UA) at poly (A) sites for polyadenylation. About 7.9% had the AAUAAA signals on −40–−1 nt upstream of the poly(A) sites. Over 60% of mRNAs probably used the one-or two-base variants of AAUAAA hexamers as their PASs in 3′ fragments. The single-base variants of AAUGAA revealed the high frequency in 11.5% of 3′ fragments. The DUEs were detected in 90% of pre-mRNAs, especially more than half of the pre-mRNAs with multi-base variants of AAUAAA had the DUEs surrounding the poly(A) site. The location of DUE is also important for defining the cleavage site. Although most of the rice pre-mRNAs did not contain AAUAAA signal, the existence of downstream elements ensured the efficiency of cleavage-polyadenylation