Analisi dei trascritti alternativi nella Vite
A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype
by Vitulo N, Forcato C, Corteggiani Carpinelli E, Telatin A, Campagna D, D’Angelo M, Zimbello R, Corso M, Vannozzi A, Bonghi C, Lucchin M and Valle G
Di cosa parla l’articolo
La pubblicazione riporta il sequenziamento degli RNA di 124 campioni di Vite ottenuti da vari genotipi diversi di Vite, da vari tessuti e da varie condizioni di crescita. Questi dati ci hanno consentito di migliorare la predizione genica disponibile per questo organismo e di aggiungere informazioni riguardo agli RNA regolatori. Inoltre siamo riusciti a determinare la presenza di trascritti alternativi ed a quantificare la loro espressione nei vari tessuti e genotipi. L’analisi ha messo in luce che dei possibili trascritti alternativi espressi nei vari campioni la quasi totalità è sempre rappresentata da una o due varianti e che quale sia la variante più espressa è determinato dal tessuto che stiamo esaminando e dal genotipo di appartenenza, mentre le diverse condizioni di crescita non sembrano avere un effetto sull’abbondanza delle varianti alternative.
Abstract
Background
Alternative splicing (AS) significantly enhances transcriptome complexity. It is differentially regulated in a wide variety of cell types and plays a role in several cellular processes. Here we describe a detailed survey of alternative splicing in grape based on 124 SOLiD RNAseq analyses from different tissues, stress conditions and genotypes.
Results
We used the RNAseq data to update the existing grape gene prediction with 2,258 new coding genes and 3,336 putative long non-coding RNAs. Several gene structures have been improved and alternative splicing was described for about 30% of the genes. A link between AS and miRNAs was shown in 139 genes where we found that AS affects the miRNA target site. A quantitative analysis of the isoforms indicated that most of the spliced genes have one major isoform and tend to simultaneously co-express a low number of isoforms, typically two, with intron retention being the most frequent alternative splicing event.
Conclusions
As described in Arabidopsis, also grape displays a marked AS tissue-specificity, while stress conditions produce splicing changes to a minor extent. Surprisingly, some distinctive splicing features were also observed between genotypes. This was further supported by the observation that the panel of Serine/Arginine-rich splicing factors show a few, but very marked differences between genotypes. The finding that a part the splicing machinery can change in closely related organisms can lead to some interesting hypotheses for evolutionary adaptation, that could be particularly relevant in the response to sudden and strong selective pressures.