Introduction

Various types of mutation and editing (M/E) events in microRNAs (miRNAs) can change the stabilities of pre-miRNAs and/or complementarities between miRNAs and their targets. Small RNA (sRNA) high-throughput sequencing (HTS) profiles can contain many mutated and edited miRNAs. Systematic detection of miRNA mutation and editing sites from the huge volume of sRNA HTS profiles is computationally difficult, as high sensitivity and low false positive rate (FPR) are both required. We propose a novel method (named MiRME) for an accurate and fast detection of miRNA M/E sites using a progressive sequence alignment approach which refines sensitivity and improves FPR step-by-step. From 70 sRNA HTS profiles with over 1.3 billion reads, MiRME has detected thousands of statistically significant M/E sites, including 3'-editing sites, 57 A-to-I editing sites (of which 32 are novel), as well as some putative non-canonical editing sites. We demonstrated that a few non-canonical editing sites were not resulted from mutations in genome by integrating the analysis of genome HTS profiles of two human cell lines, suggesting the existence of new editing types to further diversify the functions of miRNAs. Compared with six existing studies or methods, MiRME has shown much superior performance for the identification and visualization of the M/E sites of miRNAs from the ever-increasing sRNA HTS profiles.

Publications

  1. Accurate detection for a wide range of mutation and editing sites of microRNAs from small RNA high-throughput sequencing profiles.
    Cite this
    Zheng Y, Ji B, Song R, Wang S, Li T, Zhang X, Chen K, Li T, Li J, 2016-08-01 - Nucleic acids research

Credits

  1. Yun Zheng
    Developer

    Faculty of Life Science and Technology, Kunming University of Science and Technology Kunming, China

  2. Bo Ji
    Developer

    Faculty of Life Science and Technology, Kunming University of Science and Technology Kunming, China

  3. Renhua Song
    Developer

    Advanced Analytics Institute & Centre for Health Technologies, Faculty of Engineering & IT University of Technology Sydney, Australia

  4. Shengpeng Wang
    Developer

    Faculty of Life Science and Technology, Kunming University of Science and Technology Kunming, China

  5. Ting Li
    Developer

    Faculty of Life Science and Technology, Kunming University of Science and Technology Kunming, China

  6. Xiaotuo Zhang
    Developer

    Faculty of Information Engineering and Automation, Kunming University of Science and Technology Kunming, China

  7. Kun Chen
    Developer

    Faculty of Life Science and Technology, Kunming University of Science and Technology Kunming, China

  8. Tianqing Li
    Developer

    Yunnan Key Lab of Primate Biomedicine Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, China

  9. Jinyan Li
    Investigator

    Advanced Analytics Institute & Centre for Health Technologies, Faculty of Engineering & IT University of Technology Sydney, Australia

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Summary
AccessionBT006430
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionAustralia
Submitted ByJinyan Li