Evolutionary conservation of secondary structures in the lncRNAs of plants

LncRNAs are essential regulators of eukaryotic gene expression. They exert their gene regulatory functions by interacting with DNA, RNA, and protein. These functions are considered at least in part associated with their capacity to fold into complex three-dimensional structures. The conservation of lncRNA structure in mammalian genomes has been assessed in several studies, however, very little is known about the conservation of lncRNA structures in plants. Here, we analyze the structural conservation of lncRNAs in Brassicaceae, using a whole genome alignment of 16 Brassicaceae species. We found that 44.2% (1925 of 4354) of the intergenic lncRNAs (lincRNAs) and 75.1% (1549 of 2060) of the natural antisense transcripts (NATs) of Arabidopsis thaliana have conserved structural motifs in at least 2 of the 16 species. Also, 3612 lncRNAs have conserved structural motifs in multiple species; 2264 of which are tissue-specific, and 841 can be associated with a function by a co-expression network in A. thaliana. Indeed, we find evidence for the conservation of structural motifs in several lncRNAs with known functions, including, lncCOBRA1, FLORE, IPS1, ELENA1 and COOLAIR. The latter was shown previously to have a conserved structure. Overall, we have identified numerous lncRNAs with conserved structures in Brassicaceae that warrant further experimental exploration in vivo to understand whether these lncRNAs and their conserved structures are of biological significance.