TY - JOUR T1 - Identification of functional long non-coding RNAs in <em>C. elegans</em> JF - bioRxiv DO - 10.1101/383919 SP - 383919 AU - Alper Akay AU - David Jordan AU - Isabela C. Navarro AU - Tomasz Wrzesinski AU - Chris P. Ponting AU - Eric A. Miska AU - Wilfried Haerty Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/08/02/383919.abstract N2 - Background Functional characterisation of the compact genome of the model organism Caenorhabditis elegans remains incomplete despite its sequencing twenty years ago. The last decade of research has seen a tremendous increase in the number of non-coding RNAs identified in various organisms. While we have mechanistic understandings of small non-coding RNA pathways, long non-coding RNAs represent a diverse class of active transcripts whose function remains less well characterised.Results By analysing hundreds of published transcriptome datasets, we annotated 3,397 potential lncRNAs including 146 multi-exonic loci that showed increased nucleotide conservation and GC content relative to other non-coding regions. Using CRISPR / Cas9 genome editing we generated deletion mutants for ten long non-coding RNA loci. Using automated microscopy for in-depth phenotyping, we show that six of the long non-coding RNA loci are required for normal development and fertility. Using RNA interference mediated gene knock-down, we provide evidence that for two of the long non-coding RNA loci, the observed phenotypes are dependent on the corresponding RNA transcripts.Conclusions Our results highlight that a large section of the non-coding regions of the C. elegans genome remain unexplored. Based on our in vivo analysis of a selection of high-confidence lncRNA loci, we expect that a significant proportion of these high-confidence regions is likely to have biological function at either the genomic or the transcript level. ER -