2020
Navarro, Isabela Cunha; Tuorto, Francesca; Jordan, David; Legrand, Carine; Price, Jonathan; Braukmann, Fabian; Hendrick, Alan G.; Akay, Alper; Kotter, Annika; Helm, Mark; Lyko, Frank; Miska, Eric A.
Translational adaptation to heat stress is mediated by RNA 5‐methylcytosine in Caenorhabditis elegans Journal Article
In: The EMBO Journal, vol. 40, no. 6, pp. EMBJ2020105496, 2020, ISSN: 1460-2075.
Abstract | Links | BibTeX | Tags: 5‐methylcytosine, Caenorhabditis elegans, NSUN, RNA modifications, translation efficiency
@article{navarro_translational_2020,
title = {Translational adaptation to heat stress is mediated by RNA 5‐methylcytosine in Caenorhabditis elegans},
author = {Isabela Cunha Navarro and Francesca Tuorto and David Jordan and Carine Legrand and Jonathan Price and Fabian Braukmann and Alan G. Hendrick and Alper Akay and Annika Kotter and Mark Helm and Frank Lyko and Eric A. Miska},
url = {https://doi.org/10.15252/embj.2020105496},
doi = {10.15252/embj.2020105496},
issn = {1460-2075},
year = {2020},
date = {2020-12-01},
urldate = {2026-02-03},
journal = {The EMBO Journal},
volume = {40},
number = {6},
pages = {EMBJ2020105496},
abstract = {Methylation of carbon‐5 of cytosines (m5C) is a post‐transcriptional nucleotide modification of RNA found in all kingdoms of life. While individual m5C‐methyltransferases have been studied, the impact of the global cytosine‐5 methylome on development, homeostasis and stress remains unknown. Here, using Caenorhabditis elegans, we generated the first organism devoid of m5C in RNA, demonstrating that this modification is non‐essential. Using this genetic tool, we determine the localisation and enzymatic specificity of m5C sites in the RNome in vivo. We find that NSUN‐4 acts as a dual rRNA and tRNA methyltransferase in C. elegans mitochondria. In agreement with leucine and proline being the most frequently methylated tRNA isoacceptors, loss of m5C impacts the decoding of some triplets of these two amino acids, leading to reduced translation efficiency. Upon heat stress, m5C loss leads to ribosome stalling at UUG triplets, the only codon translated by an m5C34‐modified tRNA. This leads to reduced translation efficiency of UUG‐rich transcripts and impaired fertility, suggesting a role of m5C tRNA wobble methylation in the adaptation to higher temperatures.},
keywords = {5‐methylcytosine, Caenorhabditis elegans, NSUN, RNA modifications, translation efficiency},
pubstate = {published},
tppubtype = {article}
}
Methylation of carbon‐5 of cytosines (m5C) is a post‐transcriptional nucleotide modification of RNA found in all kingdoms of life. While individual m5C‐methyltransferases have been studied, the impact of the global cytosine‐5 methylome on development, homeostasis and stress remains unknown. Here, using Caenorhabditis elegans, we generated the first organism devoid of m5C in RNA, demonstrating that this modification is non‐essential. Using this genetic tool, we determine the localisation and enzymatic specificity of m5C sites in the RNome in vivo. We find that NSUN‐4 acts as a dual rRNA and tRNA methyltransferase in C. elegans mitochondria. In agreement with leucine and proline being the most frequently methylated tRNA isoacceptors, loss of m5C impacts the decoding of some triplets of these two amino acids, leading to reduced translation efficiency. Upon heat stress, m5C loss leads to ribosome stalling at UUG triplets, the only codon translated by an m5C34‐modified tRNA. This leads to reduced translation efficiency of UUG‐rich transcripts and impaired fertility, suggesting a role of m5C tRNA wobble methylation in the adaptation to higher temperatures.
2017
Delft, Pieter; Akay, Alper; Huber, Sabrina M; Bueschl, Christoph; Rudolph, Konrad L M; Domenico, Tomás Di; Schuhmacher, Rainer; Miska, Eric A; Balasubramanian, Shankar
The Profile and Dynamics of RNA Modifications in Animals Journal Article
In: Chembiochem, vol. 18, no. 11, pp. 979–984, 2017, ISSN: 1439-4227.
Abstract | Links | BibTeX | Tags: Caenorhabditis elegans, isotopic labeling, mass spectrometry, RNA modifications, stress response, tRNA
@article{van_delft_profile_2017,
title = {The Profile and Dynamics of RNA Modifications in Animals},
author = {Pieter Delft and Alper Akay and Sabrina M Huber and Christoph Bueschl and Konrad L M Rudolph and Tomás Di Domenico and Rainer Schuhmacher and Eric A Miska and Shankar Balasubramanian},
url = {http://dx.doi.org/10.1002/cbic.201700093},
doi = {10.1002/cbic.201700093},
issn = {1439-4227},
year = {2017},
date = {2017-06-01},
journal = {Chembiochem},
volume = {18},
number = {11},
pages = {979–984},
abstract = {More than a hundred distinct modified nucleosides have been identified in
RNA, but little is known about their distribution across different
organisms, their dynamic nature and their response to cellular and
environmental stress. Mass-spectrometry-based methods have been at the
forefront of identifying and quantifying modified nucleosides. However,
they often require synthetic reference standards, which do not exist in
the case of many modified nucleosides, and this therefore impedes their
analysis. Here we use a metabolic labelling approach to achieve rapid
generation of bio-isotopologues of the complete Caenorhabditis elegans
transcriptome and its modifications and use them as reference standards to
characterise the RNA modification profile in this multicellular organism
through an untargeted liquid-chromatography tandem high-resolution mass
spectrometry (LC-HRMS) approach. We furthermore show that several of these
RNA modifications have a dynamic response to environmental stress and
that, in particular, changes in the tRNA wobble base modification
5-methoxycarbonylmethyl-2-thiouridine (mcm5 s2 U) lead to codon-biased
gene-expression changes in starved animals.},
keywords = {Caenorhabditis elegans, isotopic labeling, mass spectrometry, RNA modifications, stress response, tRNA},
pubstate = {published},
tppubtype = {article}
}
More than a hundred distinct modified nucleosides have been identified in
RNA, but little is known about their distribution across different
organisms, their dynamic nature and their response to cellular and
environmental stress. Mass-spectrometry-based methods have been at the
forefront of identifying and quantifying modified nucleosides. However,
they often require synthetic reference standards, which do not exist in
the case of many modified nucleosides, and this therefore impedes their
analysis. Here we use a metabolic labelling approach to achieve rapid
generation of bio-isotopologues of the complete Caenorhabditis elegans
transcriptome and its modifications and use them as reference standards to
characterise the RNA modification profile in this multicellular organism
through an untargeted liquid-chromatography tandem high-resolution mass
spectrometry (LC-HRMS) approach. We furthermore show that several of these
RNA modifications have a dynamic response to environmental stress and
that, in particular, changes in the tRNA wobble base modification
5-methoxycarbonylmethyl-2-thiouridine (mcm5 s2 U) lead to codon-biased
gene-expression changes in starved animals.
RNA, but little is known about their distribution across different
organisms, their dynamic nature and their response to cellular and
environmental stress. Mass-spectrometry-based methods have been at the
forefront of identifying and quantifying modified nucleosides. However,
they often require synthetic reference standards, which do not exist in
the case of many modified nucleosides, and this therefore impedes their
analysis. Here we use a metabolic labelling approach to achieve rapid
generation of bio-isotopologues of the complete Caenorhabditis elegans
transcriptome and its modifications and use them as reference standards to
characterise the RNA modification profile in this multicellular organism
through an untargeted liquid-chromatography tandem high-resolution mass
spectrometry (LC-HRMS) approach. We furthermore show that several of these
RNA modifications have a dynamic response to environmental stress and
that, in particular, changes in the tRNA wobble base modification
5-methoxycarbonylmethyl-2-thiouridine (mcm5 s2 U) lead to codon-biased
gene-expression changes in starved animals.
2013
Akay, Alper; Craig, Ashley; Lehrbach, Nicolas; Larance, Mark; Pourkarimi, Ehsan; Wright, Jane E; Lamond, Angus; Miska, Eric; Gartner, Anton
RNA-binding protein GLD-1/quaking genetically interacts with the mir-35 and the let-7 miRNA pathways in Caenorhabditis elegans Journal Article
In: Open Biol., vol. 3, no. 11, pp. 130151, 2013, ISSN: 2046-2441.
Abstract | Links | BibTeX | Tags: Caenorhabditis elegans, gld-1, let-7, miRNA, SILAC
@article{akay_rna-binding_2013,
title = {RNA-binding protein GLD-1/quaking genetically interacts with the mir-35 and the let-7 miRNA pathways in Caenorhabditis elegans},
author = {Alper Akay and Ashley Craig and Nicolas Lehrbach and Mark Larance and Ehsan Pourkarimi and Jane E Wright and Angus Lamond and Eric Miska and Anton Gartner},
url = {http://dx.doi.org/10.1098/rsob.130151},
doi = {10.1098/rsob.130151},
issn = {2046-2441},
year = {2013},
date = {2013-11-01},
journal = {Open Biol.},
volume = {3},
number = {11},
pages = {130151},
abstract = {Messenger RNA translation is regulated by RNA-binding proteins and small
non-coding RNAs called microRNAs. Even though we know the majority of
RNA-binding proteins and microRNAs that regulate messenger RNA expression,
evidence of interactions between the two remain elusive. The role of the
RNA-binding protein GLD-1 as a translational repressor is well studied
during Caenorhabditis elegans germline development and maintenance.
Possible functions of GLD-1 during somatic development and the mechanism
of how GLD-1 acts as a translational repressor are not known. Its human
homologue, quaking (QKI), is essential for embryonic development. Here, we
report that the RNA-binding protein GLD-1 in C. elegans affects multiple
microRNA pathways and interacts with proteins required for microRNA
function. Using genome-wide RNAi screening, we found that nhl-2 and vig-1,
two known modulators of miRNA function, genetically interact with GLD-1.
gld-1 mutations enhance multiple phenotypes conferred by mir-35 and let-7
family mutants during somatic development. We used stable isotope
labelling with amino acids in cell culture to globally analyse the changes
in the proteome conferred by let-7 and gld-1 during animal development. We
identified the histone mRNA-binding protein CDL-1 to be, in part,
responsible for the phenotypes observed in let-7 and gld-1 mutants. The
link between GLD-1 and miRNA-mediated gene regulation is further supported
by its biochemical interaction with ALG-1, CGH-1 and PAB-1, proteins
implicated in miRNA regulation. Overall, we have uncovered genetic and
biochemical interactions between GLD-1 and miRNA pathways.},
keywords = {Caenorhabditis elegans, gld-1, let-7, miRNA, SILAC},
pubstate = {published},
tppubtype = {article}
}
Messenger RNA translation is regulated by RNA-binding proteins and small
non-coding RNAs called microRNAs. Even though we know the majority of
RNA-binding proteins and microRNAs that regulate messenger RNA expression,
evidence of interactions between the two remain elusive. The role of the
RNA-binding protein GLD-1 as a translational repressor is well studied
during Caenorhabditis elegans germline development and maintenance.
Possible functions of GLD-1 during somatic development and the mechanism
of how GLD-1 acts as a translational repressor are not known. Its human
homologue, quaking (QKI), is essential for embryonic development. Here, we
report that the RNA-binding protein GLD-1 in C. elegans affects multiple
microRNA pathways and interacts with proteins required for microRNA
function. Using genome-wide RNAi screening, we found that nhl-2 and vig-1,
two known modulators of miRNA function, genetically interact with GLD-1.
gld-1 mutations enhance multiple phenotypes conferred by mir-35 and let-7
family mutants during somatic development. We used stable isotope
labelling with amino acids in cell culture to globally analyse the changes
in the proteome conferred by let-7 and gld-1 during animal development. We
identified the histone mRNA-binding protein CDL-1 to be, in part,
responsible for the phenotypes observed in let-7 and gld-1 mutants. The
link between GLD-1 and miRNA-mediated gene regulation is further supported
by its biochemical interaction with ALG-1, CGH-1 and PAB-1, proteins
implicated in miRNA regulation. Overall, we have uncovered genetic and
biochemical interactions between GLD-1 and miRNA pathways.
non-coding RNAs called microRNAs. Even though we know the majority of
RNA-binding proteins and microRNAs that regulate messenger RNA expression,
evidence of interactions between the two remain elusive. The role of the
RNA-binding protein GLD-1 as a translational repressor is well studied
during Caenorhabditis elegans germline development and maintenance.
Possible functions of GLD-1 during somatic development and the mechanism
of how GLD-1 acts as a translational repressor are not known. Its human
homologue, quaking (QKI), is essential for embryonic development. Here, we
report that the RNA-binding protein GLD-1 in C. elegans affects multiple
microRNA pathways and interacts with proteins required for microRNA
function. Using genome-wide RNAi screening, we found that nhl-2 and vig-1,
two known modulators of miRNA function, genetically interact with GLD-1.
gld-1 mutations enhance multiple phenotypes conferred by mir-35 and let-7
family mutants during somatic development. We used stable isotope
labelling with amino acids in cell culture to globally analyse the changes
in the proteome conferred by let-7 and gld-1 during animal development. We
identified the histone mRNA-binding protein CDL-1 to be, in part,
responsible for the phenotypes observed in let-7 and gld-1 mutants. The
link between GLD-1 and miRNA-mediated gene regulation is further supported
by its biochemical interaction with ALG-1, CGH-1 and PAB-1, proteins
implicated in miRNA regulation. Overall, we have uncovered genetic and
biochemical interactions between GLD-1 and miRNA pathways.