The Identification and Characteristics of Immune-Related MicroRNAs in Haemocytes of Oyster Crassostrea gigas

Abstract

BackgroundMicroRNAs (miRNAs) represent a class of small ncRNAs that repress gene expression on the post-transcriptional level by the degradation or translation inhibition of target mRNA.MethodologyThree small RNA libraries from oyster haemocytes were sequenced on the Illumina platform to investigate the latent immunomodulation of miRNAs after bacteria challenge and heat stress. Totally, 10,498,663, 8,588,606 and 9,679,663 high-quality reads were obtained in the control, bacteria and bacteria+heat library, respectively, from which 199 oyster miRNAs including 71 known and 128 novel ones were identified. Among these miRNAs, 6 known and 23 novel ones were predicted to possess more than one precursor-coding region, and cgi-miR-10a, cgi-miR-184b, cgi-miR-100, cgi-miR-1984 and cgi-miR-67a were observed to be the most abundant miRNAs in the control library. The expression levels of 22 miRNAs in the bacteria library were significantly higher than those in the control library, while there were another 33 miRNAs whose expression levels were significantly lower than that in the control library. Meanwhile, the expression levels of 65 miRNAs in the bacteria+heat library changed significantly compared to those in the bacteria library. The target genes of these differentially expressed miRNAs were annotated, and they fell in immune and stress-related GO terms including antioxidant, cell killing, death, immune system process, and response to stimulus. Furthermore, there were 42 differentially expressed miRNAs detected in both control/bacteria and bacteria/bacteria+heat comparisons, among which 9 miRNAs displayed the identical pattern in the two comparisons, and the expression alterations of 8 miRNAs were confirmed using quantitative RT-PCR.ConclusionsThese results indicated collectively that immune challenge could induce the expression of immune-related miRNAs, which might modulate the immune response such as redox reaction, phagocytosis and apoptosis, and the expression of some immune-related miRNAs could be also regulated by heat stress to improve the environmental adaption of oyster.

The identification and characteristics of salinity-related microRNAs in gills of Portunus trituberculatus

“…MicroRNAs (miRNAs) are 20-22 nt non-coding RNAs that play an important role in the regulation of many biological processes, such as signal transduction, organ development, cellular proliferation, apoptosis, oncogenesis, and immunity (Ma et al 2012;Zhou et al 2014;Nilsen 2007;Yang et al 2013;Pushpavalli et al 2014). In animals, miRNAs regulate their target genes through mRNA destabilization and translational inhibition (Bushati and Cohen 2007).…”

An invertebrate-specific miRNA targeted the ancient cholinergic neuroendocrine system of oyster

“…In previous studies, some immune-responsive miRNAs were identified in oysters [27] and were reassessed here for their involvement in expressional modulation of CgCTL1. As a result, the miRNA cgi-miR-2d increased significantly during V. splendidus challenge, and was predicted to target CgCTL1 via the 3′-UTR region [27].…”

Peer Review #2 of "The miRNA biogenesis in marine bivalves (v0.2)"

“…Small RNAs are important regulators of the gene expression, as recognized in various model and nonmodel organisms (Kim Myung-Chul et al 2014;Martini et al 2014;Hussain and Asgari 2014;Sahoo et al 2014;Britton et al 2014;Poole et al 2014;Solofoharivelo et al 2014), including some bivalves (Jiao et al 2014;Zhou et al 2014). In addition to the identification of miRNAs, a general comprehension of the miRNA biogenesis in itself is also significant (Grimson et al 2008;Wu et al 2011;Moran et al 2013).…”

“…The basic set of genes involved in the miRNA biogenesis, and related protein interactions, are well known in mammals (Lau and MacRae 2009), and also in other metazoans like Cnidaria (Moran et al 2013), Platyhelminthes (Resch and Palakodeti 2012) and insects (Lucas and Raikhel 2013;Hussain and Asgari 2014). Regarding mollusks, lists of miRNAs have been reported for a few species (Jiao et al 2014;Chen et al 2014;Martín-Gómez et al 2014;Zhou et al 2014), miRNA families have been investigated in the limpet genome (Kenny et al 2015) and one study has considered bivalve DICER sequences for phylogenetic analysis (Gao et al 2014). A general overview on the bivalve miRNA biogenesis complements is still lacking, so we took advantage of several genomic and transcriptomic datasets available for Lophotrochozoa (GIGA Community of Scientists et al 2014) to identify and characterize the core elements involved in the miRNA formation pathway in Mytilus and Crassostrea spp.…”