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Open AccessArticle

Sponge Long Non-Coding RNAs Are Expressed in Specific Cell Types and Conserved Networks

1
School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia
2
Department of Medicine, Weill Cornell Medicine, and New York Genome Center, New York, NY 10021, USA
3
Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
*
Author to whom correspondence should be addressed.
Non-Coding RNA 2018, 4(1), 6; https://doi.org/10.3390/ncrna4010006
Received: 1 December 2017 / Revised: 5 February 2018 / Accepted: 27 February 2018 / Published: 7 March 2018
(This article belongs to the Special Issue Non-Coding RNAs, from an Evolutionary Perspective)
Although developmental regulation by long non-coding RNAs (lncRNAs) appears to be a widespread feature amongst animals, the origin and level of evolutionary conservation of this mode of regulation remain unclear. We have previously demonstrated that the sponge Amphimedon queenslandica—a morphologically-simple animal—developmentally expresses an array of lncRNAs in manner akin to more complex bilaterians (insects + vertebrates). Here, we first show that Amphimedon lncRNAs are expressed in specific cell types in larvae, juveniles and adults. Thus, as in bilaterians, sponge developmental regulation involves the dynamic, cell type- and context-specific regulation of specific lncRNAs. Second, by comparing gene co-expression networks between Amphimedon queenslandica and Sycon ciliatum—a distantly-related calcisponge—we identify several putative co-expression modules that appear to be shared in sponges; these network-embedded sponge lncRNAs have no discernable sequence similarity. Together, these results suggest sponge lncRNAs are developmentally regulated and operate in conserved gene regulatory networks, as appears to be the case in more complex bilaterians. View Full-Text
Keywords: evolution; cell type; gene expression; complexity; animals; long non-coding RNAs; development evolution; cell type; gene expression; complexity; animals; long non-coding RNAs; development
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Gaiti, F.; Hatleberg, W.L.; Tanurdžić, M.; Degnan, B.M. Sponge Long Non-Coding RNAs Are Expressed in Specific Cell Types and Conserved Networks. Non-Coding RNA 2018, 4, 6.

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