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.