Abstract
BackgroundAnimal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous smRNAs and potential gene targets in dinoflagellates, we conducted smRNA and mRNA expression profiling over 9 experimental treatments of cultures from Symbiodinium microadriaticum, a photosynthetic symbiont of scleractinian corals.ResultsWe identified a set of 21 novel smRNAs that share stringent key features with functional microRNAs from other model organisms. smRNAs were predicted independently over all 9 treatments and their putative gene targets were identified. We found 1,720 animal-like target sites in the 3'UTRs of 12,858 mRNAs and 19 plant-like target sites in 51,917 genes. We assembled a transcriptome of 58,649 genes and determined differentially expressed genes (DEGs) between treatments. Heat stress was found to produce a much larger number of DEGs than other treatments that yielded only few DEGs. Analysis of DEGs also revealed that minicircle-encoded photosynthesis proteins seem to be common targets of transcriptional regulation. Furthermore, we identified the core RNAi protein machinery in Symbiodinium.ConclusionsIntegration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. protein modification, signaling, gene expression, and response to DNA damage. Given that Symbiodinium seems to have a paucity of transcription factors and differentially expressed genes, identification and characterization of its smRNA repertoire establishes the possibility of a range of gene regulatory mechanisms in dinoflagellates acting post-transcriptionally.
Highlights
Animal and plant genomes produce numerous small RNAs that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance
Results small RNAs (smRNAs) diversity in Symbiodinium microadriaticum A total of 137 million small RNA reads were sequenced over 9 experimental treatments (Table 1, Figure 1)
In this study we generated and analyzed a comprehensive smRNA and mRNA expression data set over 9 experimental treatments in order to gain insights into smRNA and mRNA diversity and expression in Symbiodinium
Summary
Animal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. Recently it has been shown that animal and plant genomes produce numerous small, noncoding RNAs that act as a guide for the Argonaute effector protein regulating gene expression and affecting processes of metabolism, development, epigenetic inheritance, and others [1,2,3,4]. MiRNAs are ~22 nt small noncoding RNAs implicated in the regulation of gene expression in development and cell differentiation, the immune system, and homeostasis [7,8]. MiRNAs are assumed to occur at a frequency of approximately 1% - 2% of the total number of genes in the genome of an organism [15]. The authors stated that while the RNAi core molecular pathway and genes are conserved among eukaryotes (e.g. Dicer and Argonaute proteins), the products they produce are not, and RNAi might be an example of molecular exaptation [19]
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