Evolutionary Signatures of Conserved and Species-Specific Long Noncoding RNAs in Induced Pluripotent Stem Cells

We carry out an in-depth analysis of the evolutionary signatures of lncRNA transcripts and lncRNA promoters. We restricted our analysis to pluripotent cells, a cellular state relatively easier to match across species and a system in which lncRNAs have been studied extensively and are known to play important roles. We performed a comprehensive search for both lncRNA orthologs and syntologs across lab mouse, castaneous mouse, rat, chimpanzee and human. We developed a method to sensitively align noncoding genes and discovered transcriptional evolutionary signatures that classify lncRNAs into functional categories, including a set of 28 lncRNAs highly conserved in both exonic sequence and structure across all species used in our study. Our method and database of lncRNA alignments are publicly available for use by the experimental community. Finally, we compared promoter and genic properties of species-specific lncRNAs to those of conserved lncRNAs to formulate a hypothesis of the evolutionary mechanisms through which transcription is selected for and a gene is born. We present a novel and compelling idea of mechanisms of lncRNA birth whereby transposable insertions give rise to tissue-specific transcription which is selected for higher and more ubiquitous transcription as the transcript gains function.