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[SANET-MG] alternate spling and GM crops



The article below shows that, like animals, plants engage in alternate splicing extensively. In eukaryotes most genes are "split" they are made up of exons, the DNA code for active protein domains separated by introns which are spliced out as pre-messenger RNA exits the nucleus. Many split genes can be spliced alternatively to create two or more proteins for each gene sequence. Can alternate splicing influence the transgenes of gm crops? There is , as yet , no answer to that question. The commercial gm crops presently contain bacterial transgenes which are "tuned" to fit the codon preference of the crop plant but the protein codes are not interrupted with introns. However, plant introns are usually added to the transgenes but just upstream of the translation start signal, such introns are split from the pre-messenger RNA to enhance movement of the message to the cytoplasm for translation. Thus alternate splicing can , in theory, effect transgenes in plants but that effect has not been reported in gm crops. The main reason seems to be that it has not yet been studied.
Published online before print April 21, 2006
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0602039103

Bing-Bing Wang  and Volker Brendel
Genomewide comparative analysis of alternative splicing in plants

Alternative splicing (AS) has been extensively studied in mammalian systems but much less in plants. Here we report AS events deduced from EST/cDNA analysis in two model plants: Arabidopsis and rice. In Arabidopsis, 4,707 (21.8%) of the genes with EST/cDNA evidence show 8,264 AS events. Approximately 56% of these events are intron retention (IntronR), and only 8% are exon skipping. In rice, 6,568 (21.2%) of the expressed genes display 14,542 AS events, of which 53.5% are IntronR and 13.8% are exon skipping. The consistent high frequency of IntronR suggests prevalence of splice site recognition by intron definition in plants. Different AS events within a given gene occur, for the most part, independently. In total, 36-43% of the AS events produce transcripts that would be targets of the non-sense-mediated decay pathway, if that pathway were to operate in plants as in humans. Forty percent of Arabidopsis AS genes are alternatively spliced also in rice, with some examples strongly suggesting a role of the AS event as an evolutionary conserved mechanism of posttranscriptional regulation. We created a comprehensive web-interfaced database to compile and visualize the evidence for alternative splicing in plants (Alternative Splicing in Plants, available at www.plantgdb.org/ASIP).

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