Computational Prediction, Expeirmental Validation And Function Prediction Of Ciona Savignyi MicroRNAs

Prediction of miRNAs for3Urochordates (C. savignyi, C. intestinalis andOikopleura dioica) were carried out with bioinformatic approaches. We predicted527conservative miRNA genes from the3species, including52miRNA genesspecific to the Urochordata family Ciona and37miRNA gene clusters. Wereported the first collection of6experimentally validated miRNAs in C. savignyi.We clustered the180predicted C savignyi miRNAs into140families by PBCbootstrap analysis among6Deuterostomias, and found that80.00%of them arespecific to family Ciona, only16.43%and3.57%are conserved with otherChordates and Deuterostomias, respectively. The profound change in miRNArepertoire might have played an important role in the dramatic change of life styleand morphology during Ascidians phylogenesis.Function of6experimentally validated C. savignyi miRNAs are analyzed bycomputational prediction of their potential target genes. Gene ontology analysissuggests that multiple biological progresses are regulated by these miRNAs, amongwhich embryonic development may be regulated by csa_m-27c and csa_9com, andheart development may be the targeted progress of csa₂-com and csa₇.Temporal and spacial expression profile of the novel miRNA csa_m-27c showsthat its expression was low in the gonad, but increased significantly duringembryonic development before dropped abruptly while the C. savignyi developedinto tadpole larva, indicting an important role of csa_m-27c in the embryonicdevelopment, which is accordant to the bioinformatic function analysis.Ciona savignyi shares many sequencially similar miRNAs with non-Urochordataanimals, but only a third of them are homologous. Numerous analogous miRNAssuggests sequencially selective pressure from miRNA targets. By comparison between predicted targets of conservative C. savignyi miRNAsand reported experimental evidences, we found that conservative miRNAs maysometime maintain their regulation of a specific biological progress even if they lostthe control of a target gene. csa_m-27c is an analogy of miR-27c family. Itfunctions similar to miR-27but have a different origin, like a miRNA equivalent ofan isozyme. This suggests that conservation of miRNA mediated transcriptionalregulation system may exceed sequence level and live up to progress level.