Journal
BMC BIOLOGY
Volume 17, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s12915-019-0635-7
Keywords
C. elegans; lncRNA; lincRNA; CRISPR; Non-coding; Long non-coding RNA
Categories
Funding
- Cancer Research UK [C13474/A18583, C6946/A14492]
- Wellcome Trust [104640/Z/14/Z, 092096/Z/10/Z]
- European Research Council [260688]
- Herchel Smith postdoctoral fellowship
- Science without Borders Full PhD scholarship (CNPq) [205589/2014-6]
- BBSRC Core Strategic Programme Grant [BBS/E/T/000PR9818, BBS/E/T/000PR9783]
- UK Medical Research Council [MR/P026028/1]
- UK Medical Research Council
- NBI Computing Infrastructure for Science Group
- European Research Council (ERC) [260688] Funding Source: European Research Council (ERC)
- BBSRC [BBS/E/T/000PR9819, BBS/E/T/000PR9783, BBS/E/T/000PR9817, BBS/E/T/000PR9818] Funding Source: UKRI
- MRC [MR/P026028/1, MC_UU_00007/15, MC_UU_12008/1] Funding Source: UKRI
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BackgroundFunctional characterisation of the compact genome of the model organism Caenorhabditis elegans remains incomplete despite its sequencing 20years 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.ResultsBy analysing hundreds of published transcriptome datasets, we annotated 3392 potential lncRNAs including 143 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.ConclusionsOur results highlight that a large section of the non-coding regions of the C. elegans genome remains 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 a biological function at either the genomic or the transcript level.
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