| Functional noncoding RNAs participate in a variety of biological processes: for example, modulating translation, catalyzing biochemical reactions, sensing environments etc. Independent of conventional approaches such as transcriptomics and computational comparative analysis, we took advantage of the unusual genomic organization of the ciliated unicellular protozoan Oxytricha trifallax to screen for eukaryotic independent functional noncoding RNA genes. The Oxytricha macronuclear genome consists of thousands of gene-sized "nanochromosomes", each of which usually contains only a single gene. Using a draft Oxytricha trifallax genome assembly and a custom-written noncoding nanochromosome classifier, we identified a subset of nanochromosomes that lack any detectable protein coding gene, thereby strongly enriching for nanochromosomes that carry noncoding RNA genes. Surprisingly, we found only a small proportion of noncoding nanochromosomes, suggesting that Oxytricha has few independent functional noncoding RNA genes besides homologs of already known noncoding RNAs. Other than new members of known noncoding RNA classes including C/D and H/ACA snoRNAs, our screen identified a single novel family of small RNA genes, named the Arisong RNAs, which share some of the features of small nuclear RNAs. The small number of novel independent functional noncoding RNA genes identified in this screen contrasts to numerous recent reports of a large number of noncoding RNAs in a variety of eukaryotes. We think the difficulty of distinguishing functional noncoding RNA genes from other sources of putative noncoding RNAs has been underestimated. |
