Abstract

The marine medaka (Oryzias melastigma) has been increasingly used as a fish model for detecting environmental stresses and chemical contaminants in the marine environment. Recent mammalian studies have shown that environmental stresses can alter the expression profiles of microRNAs (miRNAs), leading to transgenerational effects. Here, we use high-throughput Illumina RNA sequencing (RNA-Seq) for miRNA transcriptome analysis of brain, liver, and gonads from sexually mature male and female marine medaka. A total of 128,883,806 filtered sequence reads were generated from six small RNA libraries, identifying a total of 2,125,663 non-redundant sequences. These sequences were aligned and annotated to known animal miRNAs (miRBase) using the BLAST method. A total of 223 distinct miRNA types were identified, with the greatest number expressed in brain tissue. Our data suggested that 55 miRNA types from 34 families are common to all tested tissues, while some of the miRNAs are tissue-enriched or sex-enriched. Quantitative real-time PCR analysis further demonstrated that let-7a, miR-122, and miR-9-3p were downregulated in hypoxic female medaka, while miR-2184 was specifically upregulated in the testis of hypoxic male fish. This is the first study to identify miRNAs in O. melastigma using small RNA deep sequencing technology. Because miRNA expression is highly conserved between marine medaka and other vertebrates, marine medaka may serve as a good model for studies on the functional roles of miRNAs in hypoxia stress response and signaling in marine fish.

Highlights

  • MicroRNAs are small non-coding RNA molecules (,22 nucleotides in length) encoded in the genome

  • The primary aim of the present study is to identify the known miRNAs in the organs along the brain-pituitary-gonad axis and the center of detoxification, liver in marine medaka

  • BLAST-based method was utilized to identify 223 distinct miRNA candidates in the brain, ovary, testis and liver of marine medaka based on homology to reported orthologous miRNAs

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Summary

Introduction

MicroRNAs (miRNAs) are small non-coding RNA molecules (,22 nucleotides in length) encoded in the genome. They have emerged as one of the most important and abundant group of gene expression regulator in a wide range of species spanning from mammals to plants and viruses [1]. MiRNAs are first transcribed into primary miRNAs (pri-miRNAs) and processed in the nucleus into precursor miRNAs (pre-miRNAs) with hairpin stemloop structures. Pre-miRNAs are exported to the cytoplasm, where they are processed into mature miRNAs [2]. Mature miRNAs preferentially target 39-untranslated regions (39UTRs) of mRNAs with which they share partial complementary sequence, leading to post-transcriptional gene silencing through translational repression. They can lead to degradation of the target mRNA when complete sequence complementarity exists

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