title: miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining.
abstract: MicroRNAs (miRNAs) are important regulators of gene expression. The recent advances in high-throughput sequencing (HTS) technique have greatly facilitated large-scale detection of the miRNAs. However, thoroughly discovery of novel miRNAs from the available HTS data sets remains a major challenge. In this study, we observed that Dicer-mediated cleavage sites for the processing of the miRNA precursors could be mapped by using degradome sequencing data in both animals and plants. In this regard, a novel tool, miRNA Digger, was developed for systematical discovery of miRNA candidates through genome-wide screening of cleavage signals based on degradome sequencing data. To test its sensitivity and reliability, miRNA Digger was applied to discover miRNAs from four organs of Arabidopsis. The results revealed that a majority of already known mature miRNAs along with their miRNA*s expressed in these four organs were successfully recovered. Notably, a total of 30 novel miRNA-miRNA* pairs that have not been registered in miRBase were discovered by miRNA Digger. After target prediction and degradome sequencing data-based validation, eleven miRNA-target interactions involving six of the novel miRNAs were identified. Taken together, miRNA Digger could be applied for sensitive detection of novel miRNAs and it could be freely downloaded from http://www.bioinfolab.cn/miRNA_Digger/index.html.
authors.affiliation: College of Life Sciences, Huzhou University, Huzhou 313000, P.R. China.
authors.forename: Lan
authors.initials: L
authors.lastname: Yu
authors.affiliation: College of Life Sciences, Huzhou University, Huzhou 313000, P.R. China.
authors.forename: Chaogang
authors.initials: C
authors.lastname: Shao
authors.affiliation: College of Life Sciences, Huzhou University, Huzhou 313000, P.R. China.
authors.forename: Xinghuo
authors.initials: X
authors.lastname: Ye
authors.affiliation: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, P.R. China.
authors.forename: Yijun
authors.initials: Y
authors.lastname: Meng
authors.affiliation: Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
authors.forename: Yincong
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D053487:DEAD-box RNA Helicases; D057225:Data Mining / Q000379:methods*; D056426:Genetic Loci; D055106:Genome-Wide Association Study / Q000379:methods*; D023281:Genomics / Q000379:methods*; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D009928:Organ Specificity / Q000235:genetics; D034622:RNA Interference; D020871:RNA Stability; D043244:Ribonuclease III / Q000235:genetics; D012984:Software
chemical_list: D035683:MicroRNAs; C408087:DICER1 protein, human; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases