Identification of polyadenylation signals and alternative polyadenylation in Vitis vinifera based on ESTs data

Polyadenylation, one of the post-transcriptional processing events, requires some sequence signals on the 3′ end of pre-mRNA to determine the polyadenylation site (PS). Some pre-mRNAs contain multiple polyadenylation sites, producing mature transcripts with 3′ end of variable length. To elucidate polyadenylation signals and alternative polyadenylation in Vitis vinifera, we extracted 62,811 3′ expressed sequence tags (ESTs) of V. vinifera in each UniGene entry and aligned the clustered ESTs of each transcription unit. After filtering artificial poly(A) sites, a total of 27.9% of the sequences examined were found to contain alternative polyadenylation sites. To clarify the pattern of polyadenylation signals, three datasets of sequences containing polyadenylation site were built. Analysis of sequence features in the datasets indicated that the content of uracil begins to increase up to 40% 100 nucleotides (nt) before the PS. Nearly half of the sequences examined showed stringent requirement of CA or UA at cleavage and poly(A) addition sites. The sequence at −15 nt to −25 nt upstream of the PS has been characterized as an A-rich motif, corresponding to the strict polyadenylation signal, AAUAAA, in animals. In grape, most A-rich motifs are variants of AAUAAA. PS commonly occurs following and preceding U-rich element, without a dominant specific hexanucleotide motif. The whole pattern of polyadenylation signals in V. vinifera is more similar to yeasts than animals.