The noncoding transcriptome of marine microorganisms

Considered as the dark matter of genomes, the non-protein coding DNA portion of eukaryotic genomes has, in the last decade, been shown to be much bigger than what was thought. Furthermore, with the advent of deep sequencing it became clear that genomes are pervasively transcribed and that the noncoding fraction generates huge amounts of transcripts that cannot be accounted for as simple “junk” or transcriptional noise. This challenges the central dogma of molecular biology where, for over 50 years, proteins have been considered to be the sole drivers of biological processes. Recent evidence strongly supports that noncoding (nc)RNAs are indeed functional and responsible for a multitude of regulatory processes such as gene regulation, nucleus organization and post-transcriptional regulation. In Phaeodactylum tricornutum over ∼1,500 long intergenic (li)ncRNAs and ∼3,300 natural antisense lncRNAs (NATs) have been identified. These are polyadenylated bona fide discrete transcripts that are expressed under specific physiological states. A ‘guilt by association’ hypothesis driven approach has allowed us to identify several candidate lncRNAs with possible putative functions in nutrient stress responses, namely in cell cycle arrest and lipid accumulation. These findings open novel routes to explore the function and regulatory roles of lncRNAs in diatoms while addressing the evolutionary significance of the non-protein coding transcriptome in these ecological successful marine microorganisms.