2019
Akay, Alper; Jordan, David; Navarro, Isabela Cunha; Wrzesinski, Tomasz; Ponting, Chris P; Miska, Eric A; Haerty, Wilfried
Identification of functional long non-coding RNAs in C. elegans Journal Article
In: BMC Biol., vol. 17, no. 1, pp. 14, 2019, ISSN: 1741-7007.
Abstract | Links | BibTeX | Tags: Akay_Lab/lncRNA, C. elegans, CRISPR, lincRNA, lncRNA, Long non-coding RNA, Non-coding
@article{akay_identification_2019,
title = {Identification of functional long non-coding RNAs in C. elegans},
author = {Alper Akay and David Jordan and Isabela Cunha Navarro and Tomasz Wrzesinski and Chris P Ponting and Eric A Miska and Wilfried Haerty},
url = {http://dx.doi.org/10.1186/s12915-019-0635-7},
doi = {10.1186/s12915-019-0635-7},
issn = {1741-7007},
year = {2019},
date = {2019-02-01},
journal = {BMC Biol.},
volume = {17},
number = {1},
pages = {14},
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 = {Akay_Lab/lncRNA, C. elegans, CRISPR, lincRNA, lncRNA, Long non-coding RNA, Non-coding},
pubstate = {published},
tppubtype = {article}
}
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.
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.