Long non-coding RNAs during embryogenesis of the sea urchin

Intriguing studies suggest that long non-coding RNAs (lncRNAs) tend to act in cis with neighboring protein-coding genes. Based on this notion, we assessed whether lncRNAs originate from adjacent genomic regions of selected protein-coding genes, such as early-H2A histone and strim1, that play important functions during development of the sea urchin Paracentrotus lividus. Downregulation of H2A expression relies on the sns5 chromatin insulator placed at the 3'-end of H2A. Northern blot hybridization show that a lncRNA (of ~600 nt), not overlapping with the H2A mRNA, is transcribed from sns5, following H2A expression. The strim1 locus encodes the first echinoderm TRIM-containing factor which functional role has been characterized. By RT-PCR and gene-transfer analysis we found that a lncRNA originates from the strim1 gene promoter, and that its transcription positively correlates with that of strim1. Our preliminary findings are consistent with the notion that lncRNAs might be important regulators for developmental processes.