title: Identification and expression profiling of microRNAs in the brain, liver and gonads of marine medaka (Oryzias melastigma) and in response to hypoxia.
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.
authors.affiliation: School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Hong Kong SAR, China; The State Key Laboratory in Marine Pollution, Hong Kong, Hong Kong SAR, China.
authors.forename: Karen
authors.initials: K
authors.lastname: Lau
authors.affiliation: School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Hong Kong SAR, China; The State Key Laboratory in Marine Pollution, Hong Kong, Hong Kong SAR, China.
authors.forename: Keng Po
authors.initials: KP
authors.lastname: Lai
authors.affiliation: Genome Research Centre, The Hong Kong Jockey Club Building for Interdisciplinary Research, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
authors.forename: Jessie Yun Juan
authors.initials: JY
authors.lastname: Bao
authors.affiliation: Genome Research Centre, The Hong Kong Jockey Club Building for Interdisciplinary Research, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
authors.forename: Na
authors.initials: N
authors.lastname: Zhang
authors.affiliation: School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Hong Kong SAR, China; The State Key Laboratory in Marine Pollution, Hong Kong, Hong Kong SAR, China.
authors.forename: Anna
authors.initials: A
authors.lastname: Tse
authors.affiliation: Genome Research Centre, The Hong Kong Jockey Club Building for Interdisciplinary Research, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
authors.forename: Amy
authors.initials: A
authors.lastname: Tong
authors.affiliation: School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China.
authors.forename: Jing Woei
authors.initials: JW
authors.lastname: Li
authors.affiliation: Genome Research Centre, The Hong Kong Jockey Club Building for Interdisciplinary Research, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
authors.forename: Si
authors.initials: S
authors.lastname: Lok
authors.affiliation: The State Key Laboratory in Marine Pollution, Hong Kong, Hong Kong SAR, China.
authors.forename: Richard Yuen Chong
authors.initials: RY
authors.lastname: Kong
authors.affiliation: School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Hong Kong SAR, China.
authors.forename: Wing Yee
authors.initials: WY
authors.lastname: Lui
authors.affiliation: School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Hong Kong SAR, China.
authors.forename: Alice
authors.initials: A
authors.lastname: Wong
authors.affiliation: School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Hong Kong SAR, China; The State Key Laboratory in Marine Pollution, Hong Kong, Hong Kong SAR, China.
authors.forename: Rudolf Shiu Sun
authors.initials: RS
authors.lastname: Wu
mesh_terms: D000818:Animals; D001921:Brain / Q000378:metabolism*; D005260:Female; D020869:Gene Expression Profiling; D015723:Gene Library; D006066:Gonads / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing; D000860:Hypoxia / Q000378:metabolism; D008099:Liver / Q000378:metabolism*; D008297:Male; D035683:MicroRNAs / Q000235:genetics*; D009990:Oryzias / Q000235:genetics* / Q000378:metabolism
chemical_list: D035683:MicroRNAs