Cnidarian microRNAs frequently regulate targets by cleavage

Abstract

In bilaterians, which comprise most of extant animals, microRNAs (miRNAs) regulate the majority of messenger RNAs (mRNAs) via base-pairing of a short sequence (the miRNA ''seed'') to the target, subsequently promoting translational inhibition and transcript instability. In plants, many miRNAs guide endonucleolytic cleavage of highly complementary targets. Because little is known about miRNA function in nonbilaterian animals, we investigated the repertoire and biological activity of miRNAs in the sea anemone Nematostella vectensis, a representative of Cnidaria, the sister phylum of Bilateria. Our work uncovers scores of novel miRNAs in Nematostella, increasing the total miRNA gene count to 87. Yet only a handful are conserved in corals and hydras, suggesting that microRNA gene turnover in Cnidaria greatly exceeds that of other metazoan groups. We further show that Nematostella miRNAs frequently direct the cleavage of their mRNA targets via nearly perfect complementarity. This mode of action resembles that of small interfering RNAs (siRNAs) and plant miRNAs. It appears to be common in Cnidaria, as several of the miRNA target sites are conserved among distantly related anemone species, and we also detected miRNA-directed cleavage in Hydra. Unlike in bilaterians, Nematostella miRNAs are commonly coexpressed with their target transcripts. In light of these findings, we propose that post-transcriptional regulation by miRNAs functions differently in Cnidaria and Bilateria. The similar, siRNA-like mode of action of miRNAs in Cnidaria and plants suggests that this may be an ancestral state.

Independent regulation of vertebral number and vertebral identity by microRNA-196 paralogs

“…Given the ancestral role of Hox activity in species that use a posterior growth zone (71), and the recurrent acquisition of miRNAs within the Hox clusters across metazoan taxa (15,17,72,73), variation in Hox-miRNA interactions may represent an important mechanism for the evolution of animal body plans.…”

Characterization of the piRNA pathway during development of the sea anemone Nematostella vectensis

“…17 While computational mapping of piRNAs to genomic loci hints to potential interactions, this approach enabled us to verify the interaction of piRNAs with their actual Figure 6. Developmental regulation of Nematostella piRNA expression.…”

“…Where available, miRNA, tRNA, lincRNA and snoRNA annotations were downloaded from the UCSC genome browser. miRNA annotations for N. vectensis were taken from, 17 and other annotations were downloaded from the JGI Genome Portal. 76 H. magnipapillata annotations were obtained from NCBI.…”

“…71 N. vectensis genome build Nemvec1 and H. magnipapillata build Hydra_RP_1.0 were used. 72,73 Small RNA data sets were downloaded from the NCBI Sequence Read Archive and derive from references, 16,17,19,20 summarized in Supplemental Table S2. 3 0 adaptors (also listed in Supplemental Table S2) were trimmed using trimmomatic 74 using the options trimomatic_adapt (Supplemental Table S3).…”

“…17 For each stage two libraries were generated: One untreated and one sodium periodate-treated library to remove small RNA classes lacking 2 0 -O-methylation. We considered reads as piRNAs if they mapped to no other annotated small RNAs or coding regions in the Nematostella genome (see Materials and Methods for details) and confirmed that these are indeed piRNAs by showing that they exhibit a so-called "pingpong signature" (Supplemental Fig.…”