Identification and Characterization of microRNAs and Their Predicted Functions in Biomineralization in the Pearl Oyster (Pinctada fucata).

Songqian Huang,Shigeharu Kinoshita,Kazutoshi Yoshitake,Kaoru Maeyama,Yuki Ichikawa,Kiyohito Nagai,Yoji Igarashi,Shugo Watabe,Shuichi Asakawa,Fumito Omori

doi:10.3390/biology8020047

Songqian Huang, Shigeharu Kinoshita + Show 8 more

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https://doi.org/10.3390/biology8020047

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Abstract

The biological process of pearl formation is an ongoing research topic, and a number of genes associated with this process have been identified. However, the involvement of microRNAs (miRNAs) in biomineralization in the pearl oyster, Pinctada fucata, is not well understood. In order to investigate the divergence and function of miRNAs in P. fucata, we performed a transcriptome analysis of small RNA libraries prepared from adductor muscle, gill, ovary, and mantle tissues. We identified 186 known and 42 novel miRNAs in these tissues. Clustering analysis showed that the expression patterns of miRNAs were similar among the somatic tissues, but they differed significantly between the somatic and ovary tissues. To validate the existence of the identified miRNAs, nine known and three novel miRNAs were verified by stem-loop qRT-PCR using U6 snRNA as an internal reference. The expression abundance and target prediction between miRNAs and biomineralization-related genes indicated that miR-1990c-3p, miR-876, miR-9a-3p, and novel-3 may be key factors in the regulatory network that act by controlling the formation of matrix proteins or the differentiation of mineralogenic cells during shell formation in mantle tissue. Our findings serve to further clarify the processes underlying biomineralization in P. fucata.

Highlights

The pearl oyster (Pinctada fucata) is a well-studied organism, owing to the economic potential of pearl production as well as the fascinating biology of mollusks
Up to 30% of human protein coding genes may be regulated by miRNAs [18]. miRNAs play a vital role in the regulation of gene expression at the post-transcriptional level, especially for signaling pathways involved in cellular development, proliferation, apoptosis, oncogenesis, and differentiation [19,20]. miRNAs negatively regulate gene expression through sequence-specific interactions with the 30 untranslated regions (UTRs) of target genes, and thereby cause translational repression or mRNA destabilization [21,22]
Eight small RNA libraries from the adductor muscle (Ad), gill (Gi), ovary (Ov), and mantle (Ma) tissues of two individual P. fucata were sequenced by Ion Proton sequencing to survey the miRNA diversity in P. fucata

Summary

Introduction

The pearl oyster (Pinctada fucata) is a well-studied organism, owing to the economic potential of pearl production as well as the fascinating biology of mollusks. A number of genes involved in biomineralization have been identified, and their functions in pearl and shell formation have been clarified [3,4,5,6,7]. MicroRNAs (miRNAs) are a class of small endogenous noncoding RNAs, 20–25 nucleotides (nt) in length. They are embedded within the stem regions of hairpin transcripts that exist in a wide range of invertebrates and vertebrates [17]. A single miRNA can regulate hundreds of target genes. MiRNAs play a vital role in the regulation of gene expression at the post-transcriptional level, especially for signaling pathways involved in cellular development, proliferation, apoptosis, oncogenesis, and differentiation [19,20]. Prior research has shown that some miRNAs, such as miR-223, miR-125b and, miR-302a, participate in the control of biomineralization during bone formation in animals [23,24,25]

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