Abstract
Embryonic development of Austrofundulus limnaeus can occur along two phenotypic trajectories that are physiologically and biochemically distinct. Phenotype appears to be influenced by maternal provisioning based on the observation that young females produce predominately non-diapausing embryos and older females produce mostly diapausing embryos. Embryonic incubation temperature can override this pattern and alter trajectory. We hypothesized that temperature-induced phenotypic plasticity may be regulated by post-transcriptional modification via noncoding RNAs. As a first step to exploring this possibility, RNA-seq was used to generate transcriptomic profiles of small noncoding RNAs in embryos developing along the two alternative trajectories. We find distinct profiles of mature sequences belonging to the miR-10 family expressed in increasing abundance during development and mature sequences of miR-430 that follow the opposite pattern. Furthermore, miR-430 sequences are enriched in escape trajectory embryos. MiR-430 family members are known to target maternally provisioned mRNAs in zebrafish and may operate similarly in A. limnaeus in the context of normal development, and also by targeting trajectory-specific mRNAs. This expression pattern and function for miR-430 presents a potentially novel model for maternal-embryonic conflict in gene regulation that provides the embryo the ability to override maternal programming in the face of altered environmental conditions.
Highlights
The genetic toolkit for vertebrate development provides the evolutionary foundation that supports diverse phenotypic outcomes[1,2]
The length distribution of unique small RNAs identified two highly abundant size classes with peaks at 22 and 17 nts (Fig. 1c). These transcriptomes were annotated to databases of known small RNAs and further categorized as ribosomal RNA, miRNA, transfer RNA, or small nuclear RNA among many others (Fig. 1d)
This study is the first to characterize the small non-coding RNAs (ncRNAs) transcriptome associated with development along the two developmental trajectories possible in embryos of annual killifishes
Summary
The genetic toolkit for vertebrate development provides the evolutionary foundation that supports diverse phenotypic outcomes[1,2]. Small ncRNAs can regulate chromatin structure as well as induce RNA degradation and translational repression by serving as RNA scaffolds that can target specific nucleotide sequences for alteration by a variety of partner protein complexes[6]. This unifying mechanism for the action of small ncRNAs, and an apparent high degree of evolutionary conservation of function, allows for the identification of potential gene targets of small ncRNAs during vertebrate development. The genomic proximity of miR-10 miRNAs to their target Hox genes further supports the critical importance of gene silencing and post-transcriptional regulation in highly evolutionary conserved processes
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