The evolution of lncRNA repertoires and expression patterns in tetrapods

Only a very small fraction of long noncoding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but the absence of lncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of lncRNA repertoires and expression patterns, in 11 tetrapod species. We identify approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have originated more than 300 million years ago. We find that lncRNAs, in particular ancient ones, are in general actively regulated and may function predominantly in embryonic development. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network suggests potential functions for lncRNAs in fundamental processes such as spermatogenesis and synaptic transmission, but also in more specific mechanisms such as placenta development through microRNA production. Evolutionary study of long noncoding RNA (lncRNA) repertoires and expression patterns in 11 tetrapod species identifies approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have ancient origins; many lncRNAs, particularly ancient ones, are actively regulated and may function mainly in embryonic development. Regulatory lncRNAs go back a long way Little is known about the evolutionary history of long noncoding RNAs (lncRNAs), but such insight could shed light on their functionality. To this end Henrik Kaessmann and colleagues present the first large-scale evolutionary study of lncRNA repertoires and expression patterns, in eleven tetrapod species. They identify more than 10,000 primate-specific lncRNAs and about 2,500 highly conserved lncRNAs, about 400 of which probably originated at least 300 million years ago, very early in tetrapod history. Many lncRNAs, especially the more ancient ones, are still in active use and may function largely in the regulation of embryonic development as well as other functions from spermatogenesis to synaptic transmission.