BACKGROUND: MicroRNAs are short (approximately 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.
BACKGROUND: MicroRNAs are short (approximately 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.
Authors: Omer Barad; Eti Meiri; Amir Avniel; Ranit Aharonov; Adi Barzilai; Isaac Bentwich; Uri Einav; Shlomit Gilad; Patrick Hurban; Yael Karov; Edward K Lobenhofer; Eilon Sharon; Yoel M Shiboleth; Marat Shtutman; Zvi Bentwich; Paz Einat Journal: Genome Res Date: 2004-12 Impact factor: 9.043
Authors: Nick Lauter; Archana Kampani; Shawn Carlson; Mark Goebel; Stephen P Moose Journal: Proc Natl Acad Sci U S A Date: 2005-06-15 Impact factor: 11.205
Authors: Erica Mica; Viviana Piccolo; Massimo Delledonne; Alberto Ferrarini; Mario Pezzotti; Cesare Casati; Cristian Del Fabbro; Giorgio Valle; Alberto Policriti; Michele Morgante; Graziano Pesole; M Enrico Pè; David S Horner Journal: BMC Genomics Date: 2010-02-12 Impact factor: 3.969