title: Computational exploration of microRNAs from expressed sequence tags of Humulus lupulus, target predictions and expression analysis.
abstract: Among computationally predicted and experimentally validated plant miRNAs, several are conserved across species boundaries in the plant kingdom. In this study, a combined experimental-in silico computational based approach was adopted for the identification and characterization of miRNAs in Humulus lupulus (hop), which is widely cultivated for use by the brewing industry and apart from, used as a medicinal herb. A total of 22 miRNAs belonging to 17 miRNA families were identified in hop following comparative computational approach and EST-based homology search according to a series of filtering criteria. Selected miRNAs were validated by end-point PCR and quantitative reverse transcription-polymerase chain reaction (qRT-PCR), confirmed the existence of conserved miRNAs in hop. Based on the characteristic that miRNAs exhibit perfect or nearly perfect complementarity with their targeted mRNA sequences, a total of 47 potential miRNA targets were identified in hop. Strikingly, the majority of predicted targets were belong to transcriptional factors which could regulate hop growth and development, including leaf, root and even cone development. Moreover, the identified miRNAs may also be involved in other cellular and metabolic processes, such as stress response, signal transduction, and other physiological processes. The cis-regulatory elements relevant to biotic and abiotic stress, plant hormone response, flavonoid biosynthesis were identified in the promoter regions of those miRNA genes. Overall, findings from this study will accelerate the way for further researches of miRNAs, their functions in hop and shows a path for the prediction and analysis of miRNAs to those species whose genomes are not available.
authors.affiliation: Biology Centre ASCR, v.v.i, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice 37005, Czech Republic.
authors.forename: Ajay Kumar
authors.initials: AK
authors.lastname: Mishra
authors.affiliation: Biology Centre ASCR, v.v.i, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice 37005, Czech Republic.
authors.forename: Ganesh Selvaraj
authors.initials: GS
authors.lastname: Duraisamy
authors.affiliation: Biology Centre ASCR, v.v.i, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice 37005, Czech Republic.
authors.forename: Anna
authors.initials: A
authors.lastname: Týcová
authors.affiliation: Biology Centre ASCR, v.v.i, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice 37005, Czech Republic. Electronic address: jmat@umbr.cas.cz.
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Matoušek
mesh_terms: D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics; D027582:Humulus / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012984:Software
chemical_list: D035683:MicroRNAs
keywords: Comparative genomics; Expressed sequence tags; Humulus lupulus; Posttranscriptional gene regulation; microRNA