Nonlinear sequence similarity analysis and validation of evolutionary convergent long noncoding RNAs involved in embryonic development.

Abstract

Long noncoding RNAs (lncRNAs) have been identified in almost all vertebrates, but the functional characterization of these RNA molecules is being challenging, mainly due to the lack of linear sequence homology between species. In this work, we aimed to find functional evolutionary convergent lncRNAs involved in development by screening of k-mer content (non linear similarity) and secondary structure-based approaches combined with in silico, in vitro and in vivo validation analysis. From the currently identified Madagascar gecko genes, we found a lncRNA with a similar k-mer content and structurally concordant with the human lncRNA EVX1AS. Analysis of function related characteristics together with locus-specific targeting of human and gecko EVX1AS (i.e. CRISPR Display) in human neuroepithelial cells and chicken mesencephalon confirmed that gecko Evx1as-like lncRNA mimics human EVX1AS function and induces EVX1 expression independently of the target species. Our data show functional conservation of non-homologous lncRNAs and presents a useful approach for the definition and manipulation of lncRNA function within different model organisms.