Grape miRNAs expression profiling in different organs.. Vitis vinifera

MicroRNAs are short (~21 base) single stranded RNAs that, in plants, are generally coded by specific genes and cleaved specifically from hairpin precursors. MicroRNAs are critical for the regulation of multiple developmental, stress related and other physiological processes in plants. Their action is generally mediated through complementary interactions with mRNA molecules - leading to their degradation or sequestration from the translational apparatus. The recent annotation of the genome of the grapevine Vitis vinifera allowed the identification of many putative conserved microRNA precursors, grouped into multiple gene families. Here we use oligonucleotide arrays to provide the first indication that many of these microRNAs show differential expression patterns between tissues and during the maturation of fruit in the grapevine. Furthermore we demonstrate that whole transcriptome sequencing and deep-sequencing of smallRNA fractions can be used both to identify which microRNA precursors are expressed in different tissues and to estimate genomic cordinates of primary microRNA transcripts, a critical first step towards the elucidation of specific mechanisms regulating the expression of microRNAs at the transcriptional level. Overall design: Six grapevine (V. vinifera L. cv Corvina) tissues were analyzed: ripening berries (three stages analyzed), roots, leaves and young inflorescences. Each hybridization and LMW-RNA extraction was performed twice. One color labeling was performed.