Open Access Highly Accessed Research article

High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera

Erica Mica12, Viviana Piccolo1, Massimo Delledonne3, Alberto Ferrarini3, Mario Pezzotti4, Cesare Casati1, Cristian Del Fabbro5, Giorgio Valle6, Alberto Policriti7, Michele Morgante57, Graziano Pesole89, M Enrico Pè2 and David S Horner1*

Author Affiliations

1 Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milano, Italy

2 Scuola Superiore Sant'Anna, Pisa, Italy

3 Dipartimento di Biotecnologie, Università degli Studi di Verona, Verona, Italy

4 Dipartimento di Scienze Tecnologie e Mercati della Vite e Vino, Università degli Studi di Verona, Verona, Italy

5 Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Udine, Udine, Italy

6 CRIBI Biotechnology Centre, Dipartimento di Biologia, Università degli Studi di Padova, Padova, Italy

7 Istituto di Genomica Applicata, Udine, Italy

8 Istituto Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Bari, Italy

9 Dipartimento di Biochimica e Biologia Molecolare "E. Quagliariello", Università di Bari, Bari, Italy

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BMC Genomics 2009, 10:558  doi:10.1186/1471-2164-10-558

Published: 25 November 2009



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. The recent annotation of the genome of the grapevine (Vitis vinifera L.) 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 small RNA fractions can be used both to identify which microRNA precursors are expressed in different tissues and to estimate genomic coordinates and patterns of splicing and alternative splicing for many primary miRNA transcripts.


Our results show that many microRNAs are differentially expressed in different tissues and during fruit maturation in the grapevine. Furthermore, the demonstration that whole transcriptome sequencing can be used to identify candidate splicing events and approximate primary microRNA transcript coordinates represents a significant step towards the large-scale elucidation of mechanisms regulating the expression of microRNAs at the transcriptional and post-transcriptional levels.