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.
2017
Akay, Alper; Domenico, Tomas Di; Suen, Kin M; Nabih, Amena; Parada, Guillermo E; Larance, Mark; Medhi, Ragini; Berkyurek, Ahmet C; Zhang, Xinlian; Wedeles, Christopher J; Rudolph, Konrad L M; Engelhardt, Jan; Hemberg, Martin; Ma, Ping; Lamond, Angus I; Claycomb, Julie M; Miska, Eric A
The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription Journal Article
In: Dev. Cell, vol. 42, no. 3, pp. 241–255.e6, 2017, ISSN: 1534-5807.
Abstract | Links | BibTeX | Tags: C. elegans, epigenetic inheritance, nuclear RNAi, piRNA, Piwi, RNA processing, RNAi, splicing, transcription, transposable elements
@article{akay_helicase_2017,
title = {The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription},
author = {Alper Akay and Tomas Di Domenico and Kin M Suen and Amena Nabih and Guillermo E Parada and Mark Larance and Ragini Medhi and Ahmet C Berkyurek and Xinlian Zhang and Christopher J Wedeles and Konrad L M Rudolph and Jan Engelhardt and Martin Hemberg and Ping Ma and Angus I Lamond and Julie M Claycomb and Eric A Miska},
url = {http://dx.doi.org/10.1016/j.devcel.2017.07.002},
doi = {10.1016/j.devcel.2017.07.002},
issn = {1534-5807},
year = {2017},
date = {2017-08-01},
journal = {Dev. Cell},
volume = {42},
number = {3},
pages = {241–255.e6},
abstract = {Small RNAs play a crucial role in genome defense against transposable
elements and guide Argonaute proteins to nascent RNA transcripts to induce
co-transcriptional gene silencing. However, the molecular basis of this
process remains unknown. Here, we identify the conserved RNA helicase
Aquarius/EMB-4 as a direct and essential link between small RNA pathways
and the transcriptional machinery in Caenorhabditis elegans. Aquarius
physically interacts with the germline Argonaute HRDE-1. Aquarius is
required to initiate small-RNA-induced heritable gene silencing. HRDE-1
and Aquarius silence overlapping sets of genes and transposable elements.
Surprisingly, removal of introns from a target gene abolishes the
requirement for Aquarius, but not HRDE-1, for small RNA-dependent gene
silencing. We conclude that Aquarius allows small RNA pathways to compete
for access to nascent transcripts undergoing co-transcriptional splicing
in order to detect and silence transposable elements. Thus, Aquarius and
HRDE-1 act as gatekeepers coordinating gene expression and genome defense.},
keywords = {C. elegans, epigenetic inheritance, nuclear RNAi, piRNA, Piwi, RNA processing, RNAi, splicing, transcription, transposable elements},
pubstate = {published},
tppubtype = {article}
}
Small RNAs play a crucial role in genome defense against transposable
elements and guide Argonaute proteins to nascent RNA transcripts to induce
co-transcriptional gene silencing. However, the molecular basis of this
process remains unknown. Here, we identify the conserved RNA helicase
Aquarius/EMB-4 as a direct and essential link between small RNA pathways
and the transcriptional machinery in Caenorhabditis elegans. Aquarius
physically interacts with the germline Argonaute HRDE-1. Aquarius is
required to initiate small-RNA-induced heritable gene silencing. HRDE-1
and Aquarius silence overlapping sets of genes and transposable elements.
Surprisingly, removal of introns from a target gene abolishes the
requirement for Aquarius, but not HRDE-1, for small RNA-dependent gene
silencing. We conclude that Aquarius allows small RNA pathways to compete
for access to nascent transcripts undergoing co-transcriptional splicing
in order to detect and silence transposable elements. Thus, Aquarius and
HRDE-1 act as gatekeepers coordinating gene expression and genome defense.
elements and guide Argonaute proteins to nascent RNA transcripts to induce
co-transcriptional gene silencing. However, the molecular basis of this
process remains unknown. Here, we identify the conserved RNA helicase
Aquarius/EMB-4 as a direct and essential link between small RNA pathways
and the transcriptional machinery in Caenorhabditis elegans. Aquarius
physically interacts with the germline Argonaute HRDE-1. Aquarius is
required to initiate small-RNA-induced heritable gene silencing. HRDE-1
and Aquarius silence overlapping sets of genes and transposable elements.
Surprisingly, removal of introns from a target gene abolishes the
requirement for Aquarius, but not HRDE-1, for small RNA-dependent gene
silencing. We conclude that Aquarius allows small RNA pathways to compete
for access to nascent transcripts undergoing co-transcriptional splicing
in order to detect and silence transposable elements. Thus, Aquarius and
HRDE-1 act as gatekeepers coordinating gene expression and genome defense.