Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes (Q35628447)

9 August 2017

Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes (English)

1 reference

9 August 2017

1

1 reference

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6 June 2020

Peter Dedon

7

1 reference

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6 June 2020

author name string

Wenjun Deng

2

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6 June 2020

Fugen Li

3

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6 June 2020

Michael S DeMott

4

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6 June 2020

I Ramesh Babu

5

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6 June 2020

Thomas J Begley

6

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6 June 2020

publication date

13 April 2015

1 reference

Chemical Research in Toxicology

9 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25772370%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

volume

28

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6 June 2020

issue

5

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6 June 2020

page(s)

978-988

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Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number

6 June 2020

cites work

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A system of RNA modifications and biased codon use controls cellular stress response at the level of translation

27 July 2018

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27 July 2018

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27 July 2018

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Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response

27 July 2018

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Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications

27 July 2018

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Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins

27 July 2018

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27 July 2018

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A domain of the actin binding protein Abp140 is the yeast methyltransferase responsible for 3-methylcytidine modification in the tRNA anti-codon loop

27 July 2018

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27 July 2018

Bring on the biomarkers

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Innate immune and chemically triggered oxidative stress modifies translational fidelity.

27 July 2018

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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

27 July 2018

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Adaptive threonine increase in transmembrane regions of mitochondrial proteins in higher primates

27 July 2018

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Systems based mapping demonstrates that recovery from alkylation damage requires DNA repair, RNA processing, and translation associated networks

27 July 2018

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Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

27 July 2018

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Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae

27 July 2018

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Trm9-catalyzed tRNA modifications link translation to the DNA damage response

27 July 2018

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Transcriptional networks in S. cerevisiae linked to an accumulation of base excision repair intermediates.

27 July 2018

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Evaluation of metabolite profiles as biomarkers for the pharmacological effects of thiazolidinediones in Type 2 diabetes mellitus patients and healthy volunteers

27 July 2018

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MODOMICS: a database of RNA modification pathways

27 July 2018

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Genomic and proteomic profiling for biomarkers and signature profiles of toxicity.

27 July 2018

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Yeast flavohemoglobin, a nitric oxide oxidoreductase, is located in both the cytosol and the mitochondrial matrix: effects of respiration, anoxia, and the mitochondrial genome on its intracellular level and distribution

27 July 2018

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Saccharomyces genome database: underlying principles and organisation

27 July 2018

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Reactive nitrogen species in the chemical biology of inflammation

27 July 2018

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Improvement of reading frame maintenance is a common function for several tRNA modifications

27 July 2018

1 reference

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Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes

27 July 2018

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Internal packing of helical membrane proteins

27 July 2018

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The RNA Modification Database: 1999 update

27 July 2018

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The Escherichia coli AlkB protein protects human cells against alkylation-induced toxicity

27 July 2018

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Alkylation of haemoglobin, plasma proteins and DNA in the mouse by diethylnitrosamine

27 July 2018

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Thiolation of transfer RNA in Escherichia coli varies with growth rate

27 July 2018

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Oxidative damage to DNA in mammalian chromatin

27 July 2018

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A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding

27 July 2018

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Primary structure of tRNA Thr 1a and b from brewer's yeast

27 July 2018

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The chemical effects of nucleic acid alkylation and their relation to mutagenesis and carcinogenesis

27 July 2018

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Evaluation of genetic risks of alkylating agents IV. Quantitative determination of alkylated amino acids in haemoglobin as a measure of the dose after treatment of mice with methyl methanesulfonate

27 July 2018

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Toxicogenomics: the challenges and opportunities to identify biomarkers, signatures and thresholds to support mode-of-action.

27 July 2018

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Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4438938

A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress

25 September 2018

1 reference

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tRNA stabilization by modified nucleotides

25 September 2018

1 reference

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Systems analysis of protein modification and cellular responses induced by electrophile stress

25 September 2018

1 reference

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Systems medicine: the future of medical genomics and healthcare

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4438938

MODOMICS: a database of RNA modification pathways. 2008 update

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4438938

Systems biology approaches for toxicology

25 September 2018

1 reference

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tRNA's wobble decoding of the genome: 40 years of modification

25 September 2018

1 reference

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Rapid tRNA decay can result from lack of nonessential modifications.

25 September 2018

1 reference

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Study of the mass spectrometric fragmentation of pseudouridine: comparison of fragmentation data obtained by matrix-assisted laser desorption/ionisation post-source decay, electrospray ion trap multistage mass spectrometry, and by a method [...]

25 September 2018

1 reference

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Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards.

25 September 2018

1 reference

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Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway

25 September 2018

1 reference

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Network responses to DNA damaging agents

25 September 2018

1 reference

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Motifs of serine and threonine can drive association of transmembrane helices

25 September 2018

1 reference

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A violation of the Swain-Scott principle, and not SN1 versus SN2 reaction mechanisms, explains why carcinogenic alkylating agents can form different proportions of adducts at oxygen versus nitrogen in DNA.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4438938

Cytotoxicity of monofunctional alkylating agents. Methyl methanesulfonate and methyl-N'-nitro-N-nitrosoguanidine have different mechanisms of toxicity for 10T1/2 cells.

25 September 2018

1 reference

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Selection conflicts, gene expression, and codon usage trends in yeast

25 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25772370

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Stressing out over tRNA cleavage

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25772370

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/ACS.CHEMRESTOX.5B00004

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25772370%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25772370%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

1 reference