LincRNA gene-neighborhood conservation in neurodevelopmental and non-neurodevelopmental tissue.

<p>(A) Schematic of the protocol used for determining lincRNA gene-neighborhood conservation across species. In the example given, only chimp is scored as conserved. Chromosomal synteny is not a condition for gene-neighborhood conservation. (B) Gene-neighborhood conservation of 142 lincRNAs expressed during human neurogenesis across 29 mammalian species (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131818#pone.0131818.s003" target="_blank">S2 Table</a>). Gene-neighborhood conservation is shown to be above null phylogenetic expectations in high-GI species (red) and below expectations for low-GI species (blue). The two exceptions are the marmoset, a low-GI primate, and the manatee, a large-brained lissencephalic Afrotherian; both of these show lincRNA gene-neighborhood conservation considerably above null expectations The chicken is not shown. (C) Gene-neighborhood conservation for neurodevelopmental lincRNAs (green) and lincRNAs showing maximum levels of expression in non-brain human tissue (lilac) for three high-GI (red) and three low-GI (blue) species. Conservation in the naked mole rat, rabbit, and elephant are significantly different for neurodevelopmental compared to non-brain (Other) lincRNAs, while similar levels of conservation are observed for both classes of lincRNAs in macaque, mouse, and horse. Predicted conservation values for each species (dashed lines) were calculated from null evolutionary models based on divergence times with human. Asterisks denote significantly different values from predicted (P < 0.05). (D) Plot of neurodevelopmental <i>versus</i> non-neurodevelopmental (absolute) conservation deviation scores based on a phylogenetic expectation model (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131818#sec002" target="_blank">Materials and Methods</a>) for 29 mammalian species. From the regression slope delineating no deviation from expected scores, it is clear that neurodevelopmental lincRNAs deviate more frequently and more sizeably from conservation expectations than non-neurodevelopmental lincRNAs. Crosses and Xs indicate negative deviations for neurodevelopmental and non-neurodevelopmental lincRNAs, respectively. (B) is adapted from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131818#pone.0131818.ref020" target="_blank">20</a>].