Characterization of novel precursor miRNAs using next generation sequencing and prediction of miRNA targets in Atlantic halibut

PLoS One. 2013 Apr 23;8(4):e61378. doi: 10.1371/journal.pone.0061378. Print 2013.

Abstract

Background: microRNAs (miRNAs) are implicated in regulation of many cellular processes. miRNAs are processed to their mature functional form in a step-wise manner by multiple proteins and cofactors in the nucleus and cytoplasm. Many miRNAs are conserved across vertebrates. Mature miRNAs have recently been characterized in Atlantic halibut (Hippoglossus hippoglossus L.). The aim of this study was to identify and characterize precursor miRNA (pre-miRNAs) and miRNA targets in this non-model flatfish. Discovery of miRNA precursor forms and targets in non-model organisms is difficult because of limited source information available. Therefore, we have developed a methodology to overcome this limitation.

Methods: Genomic DNA and small transcriptome of Atlantic halibut were sequenced using Roche 454 pyrosequencing and SOLiD next generation sequencing (NGS), respectively. Identified pre- miRNAs were further validated with reverse-transcription PCR. miRNA targets were identified using miRanda and RNAhybrid target prediction tools using sequences from public databases. Some of miRNA targets were also identified using RACE-PCR. miRNA binding sites were validated with luciferase assay using the RTS34st cell line.

Results: We obtained more than 1.3 M and 92 M sequence reads from 454 genomic DNA sequencing and SOLiD small RNA sequencing, respectively. We identified 34 known and 9 novel pre-miRNAs. We predicted a number of miRNA target genes involved in various biological pathways. miR-24 binding to kisspeptin 1 receptor-2 (kiss1-r2) was confirmed using luciferase assay.

Conclusion: This study demonstrates that identification of conserved and novel pre-miRNAs in a non-model vertebrate lacking substantial genomic resources can be performed by combining different next generation sequencing technologies. Our results indicate a wide conservation of miRNA precursors and involvement of miRNA in multiple regulatory pathways, and provide resources for further research on miRNA in non-model animals.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Binding Sites
  • Cell Line
  • Conserved Sequence
  • Fish Proteins / genetics*
  • Fish Proteins / metabolism
  • Flounder / classification
  • Flounder / genetics*
  • Gene Expression Profiling
  • Gene Expression Regulation
  • Genes, Reporter
  • Genome*
  • High-Throughput Nucleotide Sequencing
  • Luciferases
  • MicroRNAs / classification
  • MicroRNAs / genetics*
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Phylogeny
  • Protein Binding
  • RNA Precursors / chemistry
  • RNA Precursors / genetics*
  • Receptors, G-Protein-Coupled / genetics*
  • Receptors, G-Protein-Coupled / metabolism
  • Transcriptome

Substances

  • Fish Proteins
  • MicroRNAs
  • RNA Precursors
  • Receptors, G-Protein-Coupled
  • Luciferases

Grants and funding

This work was supported by the Research Council of Norway (www.forskningsradet.no), grants 182653/V10 and 165272/S40. TTB thanks Research Council of Norway and University of Nordland (www.uin.no) for funding his PhD scholarship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.