Dynamic and widespread lncRNA expression in the sponge and the origin of animal complexity

Long non-coding RNAs (lncRNAs) are important developmental regulators in bilaterian animals. A correlation has been claimed between the lncRNA repertoire expansion and morphological complexity in vertebrate evolution. However, this claim has not been tested by examining morphologically simple animals.

Here, researchers from the University of Queensland undertake a systematic investigation of lncRNAs in the demosponge Amphimedon queenslandica, a morphologically-simple, early-branching metazoan. They combine RNA-Seq data across multiple developmental stages of Amphimedon with a filtering pipeline to conservatively predict 2,935 lncRNAs. These include intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, long intergenic ncRNAs and precursors for small RNAs. Sponge lncRNAs are remarkably similar to their bilaterian counterparts in being relatively short with few exons and having low primary sequence conservation relative to protein-coding genes. As in bilaterians, a majority of sponge lncRNAs exhibit typical hallmarks of regulatory molecules, including high temporal specificity and dynamic developmental expression. Specific lncRNA expression profiles correlate tightly with conserved protein-coding genes likely involved in a range of developmental and physiological processes, such as the Wnt signaling pathway. Although the majority of Amphimedon lncRNAs appear to be taxonomically-restricted with no identifiable orthologues, the researchers find a few cases of conservation between demosponges in lncRNAs that are antisense to coding sequences. Based on the high similarity in the structure, organisation and dynamic expression of sponge lncRNAs to their bilaterian counterparts, they propose that these non-coding RNAs are an ancient feature of the metazoan genome. These results are consistent with lncRNAs regulating the development of animals, regardless of their level of morphological complexity.

  • Gaiti F, Fernandez-Valverde SL, Nakanishi N, Calcino AD, Yanai I, Tanurdzic M, Degnan BM. (2015) Dynamic and widespread lncRNA expression in the sponge and the origin of animal complexity. Mol Biol Evol [Epub ahead of print]. [abstract]

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