Format

Send to

Choose Destination
BMC Biol. 2019 Feb 18;17(1):14. doi: 10.1186/s12915-019-0635-7.

Identification of functional long non-coding RNAs in C. elegans.

Author information

1
Wellcome CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
2
Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
3
Earlham Institute, Norwich Research Park, Norwich, UK.
4
MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
5
Wellcome CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK. eam29@cam.ac.uk.
6
Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK. eam29@cam.ac.uk.
7
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK. eam29@cam.ac.uk.
8
Earlham Institute, Norwich Research Park, Norwich, UK. Wilfried.Haerty@earlham.ac.uk.

Abstract

BACKGROUND:

Functional characterisation of the compact genome of the model organism Caenorhabditis elegans remains incomplete despite its sequencing 20 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 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.

CONCLUSIONS:

Our 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.

KEYWORDS:

C. elegans; CRISPR; Long non-coding RNA; Non-coding; lincRNA; lncRNA

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center