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.

Comparative analysis of the liver tissue transcriptomes of Mongolian and Lanzhou fat-tailed sheep

“…In this study, about 50% of genes annotated in the sheep genome were covered by more than 80% of the sequenced reads, demonstrating that RNA-Seq was more sensitive in finding transcripts, even for genes with low expression patterns, which is in agreement with Wang et al (2009). Although several recent studies have identified DEGs in the liver tissue of pigs (Gunawan et al, 2013a,b;Sodhi et al, 2014), cows (Graugnard et al, 2013), rats (Tran and Huang, 2014;Wang et al, 2014) and fish (Yang et al, 2012;Lau et al, 2014;Magnanou et al, 2014) when using next-generation sequencing platforms, very few studies have clarified transcriptomic analyses regarding the liver tissue of sheep. In this study, seven genes were found to be differentially expressed (three were upregulated and four downregulated) in a DEG analysis comparing the liver tissues of the LCL and MCL libraries.…”

“…In addition, data from RNA-Seq can help identify new transcripts (Hansey et al, 2012), single nucleotide polymorphisms (Esteve-Codina et al, 2011), alternative splicing events (Xiong et al, 2012), and other information. Several recent studies have used this type of next-generation sequencing platform in the liver tissue of pigs (Gunawan et al, 2013a,b;Sodhi et al, 2014), cows (Graugnard et al, 2013), rats (Tran and Huang, 2014;Wang et al, 2014), and fish (Yang et al, 2012;Lau et al, 2014;Magnanou et al, 2014).…”

Hypoxia induces miR-210, leading to anti-apoptosis in ovarian follicular cells of marine medaka Oryzias melastigma

“…But studies of the functional role of miRNA in teleosts are still limited. By using a small RNA sequencing platform, we have reported the profile of miRNA in different tissues of marine medaka, O. melastigma (Lau et al, 2014). Our previous studies also demonstrated that the global environmental problem of hypoxia is that it acts as an endocrine disruptor, resulting in reproductive impairment of aquatic fish (Shang et al, 2006).…”

“…We have shown the induction of miR-210 in ovarian follicular cells under hypoxic stress. Furthermore, we used bioinformatics algorithms together with our recent de novo transcriptome reports of O. melastigma to strengthen the target gene prediction of miR-210 in the ovary of marine medaka (Lai et al, 2015;Lau et al, 2014). The top 10 ranked biological processes in gene ontology (GO) analysis suggested the roles of miR-210 in cell apoptosis, cell division, cell cycle, and cell differentiation of ovarian cells in response to hypoxia.…”

Expression of miRNAs in response to freezing and anoxia stresses in the freeze tolerant fly Eurosta solidaginis

“…A next-generation sequencing-based approach revealed miR-9 modulation in a marine model of hypometabolism, the aestivating sea cucumber A. japonicus [7]. Interestingly, the marine medaka Oryzias melastigma, a fish model used to characterize responses to environmental stresses, displayed reduced miR-9 levels under hypoxia [28]. Recent work also reported miR-9 induction in hypoxic rat pulmonary artery smooth muscle cells further highlighting the potential importance of this miRNA in the hypoxic response [42].…”