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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 558.
Published online Nov 25, 2009. doi:  10.1186/1471-2164-10-558
PMCID: PMC2822795
High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera
Erica Mica,#1,2 Viviana Piccolo,#1 Massimo Delledonne,3 Alberto Ferrarini,3 Mario Pezzotti,4 Cesare Casati,1 Cristian Del Fabbro,5 Giorgio Valle,6 Alberto Policriti,7 Michele Morgante,5,7 Graziano Pesole,8,9 M Enrico Pè,2 and David S Hornercorresponding author1
1Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milano, Italy
2Scuola Superiore Sant'Anna, Pisa, Italy
3Dipartimento di Biotecnologie, Università degli Studi di Verona, Verona, Italy
4Dipartimento di Scienze Tecnologie e Mercati della Vite e Vino, Università degli Studi di Verona, Verona, Italy
5Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Udine, Udine, Italy
6CRIBI Biotechnology Centre, Dipartimento di Biologia, Università degli Studi di Padova, Padova, Italy
7Istituto di Genomica Applicata, Udine, Italy
8Istituto Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Bari, Italy
9Dipartimento di Biochimica e Biologia Molecolare "E. Quagliariello", Università di Bari, Bari, Italy
corresponding authorCorresponding author.
#Contributed equally.
Erica Mica: erica.mica/at/sssup.it; Viviana Piccolo: viviana.piccolo/at/unimi.it; Massimo Delledonne: massimo.delledonne/at/univr.it; Alberto Ferrarini: alberto.ferrarini/at/gmail.com; Mario Pezzotti: mario.pezzotti/at/univr.it; Cesare Casati: cesare.casati/at/studenti.unimi.it; Cristian Del Fabbro: delfabbro/at/appliedgenomics.org; Giorgio Valle: Giorgio.valle/at/unipd.it; Alberto Policriti: policriti/at/dimi.uniud.it; Michele Morgante: michele.morgante/at/uniud.it; Graziano Pesole: graziano.pesole/at/biologia.uniba.it; M Enrico Pè: m.pe/at/sssup.it; David S Horner: david.horner/at/unimi.it
Received May 6, 2009; Accepted November 25, 2009.
Abstract
Background
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.
Results
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.
Conclusion
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.
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