Thiebaut et al. BMC Genomics 2012, 13:290 http://www.biomedcentral.com/1471-2164/13/290 R E S E A R C H A R T I C L E Open Access Computational identification and analysis of novel sugarcane microRNAs Flávia Thiebaut1†, Clícia Grativol1†, Mariana Carnavale-Bottino1, Cristian Antonio Rojas2†, Milos Tanurdzic4, Laurent Farinelli5, Robert A Martienssen3, Adriana Silva Hemerly1 and Paulo Cavalcanti Gomes Ferreira1* Abstract Background: MicroRNA-regulation of gene expression plays a key role in the development and response to biotic and abiotic stresses. Deep sequencing analyses accelerate the process of small RNA discovery in many plants and expand our understanding of miRNA-regulated processes. We therefore undertook small RNA sequencing of sugarcane miRNAs in order to understand their complexity and to explore their role in sugarcane biology. Results: A bioinformatics search was carried out to discover novel miRNAs that can be regulated in sugarcane plants submitted to drought and salt stresses, and under pathogen infection. By means of the presence of miRNA precursors in the related sorghum genome, we identified 623 candidates of new mature miRNAs in sugarcane. Of these, 44 were classified as high confidence miRNAs. The biological function of the new miRNAs candidates was assessed by analyzing their putative targets. The set of bona fide sugarcane miRNA includes those likely targeting serine/threonine kinases, Myb and zinc finger proteins. Additionally, a MADS-box transcription factor and an RPP2B protein, which act in development and disease resistant processes, could be regulated by cleavage (21-nt-species) and DNA methylation (24-nt-species), respectively. Conclusions: A large scale investigation of sRNA in sugarcane using a computational approach has identified a substantial number of new miRNAs and provides detailed genotype-tissue-culture miRNA expression profiles. Comparative analysis between monocots was valuable to clarify aspects about conservation of miRNA and their targets in a plant whose genome has not yet been sequenced. Our findings contribute to knowledge of miRNA roles in regulatory pathways in the complex, polyploidy sugarcane genome. Keywords: Small RNA, Biotic stress, Abiotic stress, Deep sequencing Background Small RNA (sRNA) has direct and versatile involvement as regulator of gene expression in many eukaryotes [1]. This sRNA consists of small endogeneous RNAs, 20–25 nucleotides (nt) in length, grouped into two major classes: microRNA (miRNA) and small interfering RNA (siRNA) [2]. The biosynthesis of plant miRNA starts with the tran- scription of MIR genes by RNA polymerase II (Pol II) into primary miRNA (pri-miRNA), generating a long-single strand RNA that has partial self-complementary, forming a characteristic hairpin structure. In Arabidopsis, this * Correspondence: paulof@bioqmed.ufrj.br †Equal contributors 1Laboratorio de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rua Rodolpho Paulo Rocco s/n°, CCS, Bl.B-33A, Cidade Universitária 21941-590, Rio de Janeiro, RJ, Brazil Full list of author information is available at the end of the article stem-loop precursor is processed by Dicer-like protein (DCL1), HYPONASTIC LEAVES 1 (HYL1) and SER- RATA resulting in a duplex miRNA-miRNA*. The duplex is methylated by HUA ENHANCER 1 (HEN1) [3] and transported from the nucleus to the cytoplasm by HASTY [4]. Finally, one strand of the duplex, the mature miRNA, is inserted into a ribonucleoprotein complex, called RISC, containing the ARGONAUTE1 (AGO1) protein [5] that binds to its target messenger RNA by sequence comple- mentarity. miRNA regulates the expression of mRNA tar- get by mRNA target cleavage, and through translational or transcriptional repression [6,7]. However, in plants, the most frequent mechanism of miRNA regulation is direct cleavage of mRNA-target by near-perfect complementarity [8]. Several studies have reported that miRNA-guided gene regulation is essential for developmental processes © 2012 Thiebaut et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.