RT Journal Article SR Electronic T1 Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci JF bioRxiv FD Cold Spring Harbor Laboratory SP 051052 DO 10.1101/051052 A1 Paulo P. Amaral A1 Tommaso Leonardi A1 Namshik Han A1 Emmanuelle Viré A1 Dennis Gascoigne A1 Raúl Arias-Carrasco A1 Magdalena Büscher A1 Anda Zhang A1 Stefano Pluchino A1 Vinicius Maracaja-Coutinho A1 Helder I. Nakaya A1 Martin Hemberg A1 Ramin Shiekhattar A1 Anton J. Enright A1 Tony Kouzarides YR 2016 UL http://biorxiv.org/content/early/2016/04/29/051052.abstract AB The mammalian genome is transcribed into large numbers of long noncoding RNAs (lncRNAs), but the definition of functional lncRNA groups has proven difficult, partly due to their low sequence conservation and lack of identified shared properties. Here we consider positional conservation across mammalian genomes as an indicator of functional commonality. We identify 665 conserved lncRNA promoters in mouse and human genomes that are preserved in genomic position relative to orthologous coding genes. The identified ‘positionally conserved’ lncRNA genes are primarily associated with developmental transcription factor loci with which they are co-expressed in a tissue-specific manner. Strikingly, over half of all positionally conserved RNAs in this set are linked distinct to chromatin organization structures, overlapping the binding sites for the CTCF chromatin organizer and located at chromatin loop anchor points and borders of topologically associating domains (TADs). These topological anchor point (tap)RNAs possess conserved sequence domains that are enriched in potential recognition motifs for Zinc Finger proteins. Characterization of these non-coding RNAs and their associated coding genes shows that they are functionally connected: they regulate each other’s expression and influence the metastatic phenotype of cancer cells in vitro in a similar fashion. Thus, interrogation of positionally conserved lncRNAs identifies a new subset of tapRNAs with shared functional properties. These results provide a large dataset of lncRNAs that conform to the “extended gene” model, in which conserved developmental genes are genomically and functionally linked to regulatory lncRNA loci across mammalian evolution.