Genomic organization and embryonic expression of miR-430 in medaka ( Oryzias latipes): Insights into the post-transcriptional gene regulation in early development

Abstract

MicroRNAs (miRNAs, miRs) are short noncoding RNA molecules that negatively control the target mRNAs by binding to the 3′ untranslated region (UTR). Previous studies have demonstrated that miR-430 is encoded by a clustered multigene family and is abundantly expressed in early development. In zebrafish, miR-430 is needed to suppress primordial germ cell (PGC)-specific genes, such as nanos1, in somatic cells. However, the molecular characteristics of the miR-430 family in other teleost species have not been reported, and it is unclear whether such a function of miR-430 in PGC specification is a conserved feature of animals or not. In medaka ( Oryzias latipes), a distantly related teleost, it has been suggested that PGC might be established in a different mode of specification from that of zebrafish. We characterized 16 miR-430 precursors in the medaka genomic sequence. These miR-430 genes form clusters on chromosome 4, which might share its evolutionary origin with that of the very large miR-430 clusters in zebrafish chromosome 4. However, none of the medaka miR-430 genes are identical to the zebrafish miR-430 paralogs. Medaka miR-430 expression starts during epiboly and decreases after axis formation. Functional analysis using reporter gene constructs showed that miR-430 repressed protein expression by binding to the 3′UTR of zebrafish TDRD7. Consistently, the 3′UTR of medaka TDRD7 contains at least two significant candidates for the putative miR-430 binding site. The ubiquitous and early expression of medaka miR-430 and its ability to downregulate GFP:TDRD7 reporter mRNA imply that miR-430 has a conserved role in early embryogenesis. Smaller copy numbers of miR-430 genes and relatively brief expression in medaka might represent the characteristics of this miRNA family in the common ancestor of teleosts. Changes in the relationships between miR-430 and the target mRNA might be related to differences in the localization patterns of PGC-related genes in medaka and zebrafish.