miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining

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...

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Bibliographic Details
Published in:Scientific reports 2016-01, Vol.6 (1), p.18901-18901, Article 18901
Main Authors: Yu, Lan, Shao, Chaogang, Ye, Xinghuo, Meng, Yijun, Zhou, Yincong, Chen, Ming
Format: Article
Language:English
Subjects:
49
631/114/794
631/1647/48
Arabidopsis - genetics
Computational Biology - methods
Data Mining - methods
DEAD-box RNA Helicases
Gene expression
Genetic Loci
Genome-Wide Association Study - methods
Genomes
Genomics - methods
Humanities and Social Sciences
MicroRNAs - genetics
MicroRNAs - metabolism
miRNA
multidisciplinary
Next-generation sequencing
Organ Specificity - genetics
Ribonuclease III - genetics
RNA Interference
RNA Stability
Science
Software
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Summary: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 .
ISSN:2045-2322
2045-2322
DOI:10.1038/srep18901