Identification and developmental profiling of microRNAs in the acoel worm .

The acoel worm has recently emerged as a model organism for studying whole-body regeneration and embryonic development. Previous studies suggest that post-transcriptional mechanisms likely play important roles in whole-body regeneration. Here, we establish a resource for studying microRNA-mediated gene regulation, a major aspect of post-transcriptional control in animals. Using small RNA-sequencing samples spanning key developmental stages, we annotated microRNAs. Our analysis uncovered a total of 1,050 microRNA loci, including 479 high-confidence loci based on structural and read abundance criteria. Comparison of microRNA seed sequences with those in other bilaterian species revealed that encodes the majority of known conserved bilaterian microRNA families and that several microRNA families previously reported only in protostomes or deuterostomes likely have ancient bilaterian origins. We profiled the expression dynamics of the miRNAs across embryonic and post-embryonic development. We observed that the and microRNAs are unconventionally enriched at early embryonic stages. To generate hypotheses for miRNA function, we annotated the 3' UTRs of protein-coding genes and performed miRNA target site predictions. Focusing on genes that are known to function in the wound response, posterior patterning, and neural differentiation in , we found that these processes may be under substantial miRNA regulation. Notably, we found that miRNAs in MIR-7 and MIR-9 families which have target sites in the posterior genes , , and are indeed expressed in the anterior of the animal, consistent with a repressive effect on their corresponding target genes. Our annotation offers candidate miRNAs for further functional investigation, providing a resource for future studies of post-transcriptional control during development and regeneration.