4.8 Article

Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

MODOMICS: a database of RNA modification pathways. 2021 update

Pietro Boccaletto et al.

Summary: MODOMICS database, established since 2006, has evolved from containing basic chemical structures of modified ribonucleosides to a comprehensive resource with new functionalities such as a catalog of RNA modifications linked to human diseases. The database, which is extensively linked to RCSB Protein Data Bank, provides users with an enhanced tool for research on RNA modification.

NUCLEIC ACIDS RESEARCH (2022)

Article Multidisciplinary Sciences

A multiplex platform for small RNA sequencing elucidates multifaceted tRNA stress response and translational regulation

Christopher P. Watkins et al.

Summary: This paper introduces a multiplex RNA-seq method that can investigate tRNA abundance, modification, charging, and fragmentation simultaneously. The findings reveal the impact of stress-induced regulation on translational elongation and the association between modification and tRNA fragment biogenesis.

NATURE COMMUNICATIONS (2022)

Article Biochemistry & Molecular Biology

Dynamic queuosine changes in tRNA couple nutrient levels to codon choice in Trypanosoma brucei

Sameer Dixit et al.

Summary: Research shows that the levels of tRNA Q in Trypanosoma brucei dynamically change in response to variations in amino acid concentrations, particularly tyrosine. These changes have negligible effects on global translation or growth rate, but can impact codon choice in tRNA(Tyr).

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq

Andrew Behrens et al.

Summary: The study overcame the challenges in measuring cellular tRNA abundance by using modification-induced misincorporation tRNA sequencing (mim-tRNAseq) method, accurately capturing tRNA abundance and modification status in cells. The research revealed significant heterogeneity of tRNA isodecoder pools among diverse human cell lines and surprising interdependence of modifications at distinct sites within the same tRNA transcript.

MOLECULAR CELL (2021)

Article Microbiology

Queuine Is a Nutritional Regulator of Entamoeba histolytica Response to Oxidative Stress and a Virulence Attenuator

Shruti Nagaraja et al.

Summary: Queuine has a dual role in promoting oxidative stress resistance and reducing virulence in the eukaryotic parasite Entamoeba histolytica. It is efficiently incorporated into the parasite's tRNAs and stimulates methylation, leading to protection against oxidative stress and downregulation of virulence-associated genes. Silencing of EhTGT prevents queuine incorporation, impairing parasite growth, oxidative stress resistance, and cytopathic activity.
Article Biology

Twelve years of SAMtools and BCFtools

Petr Danecek et al.

Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.

GIGASCIENCE (2021)

Article Multidisciplinary Sciences

Queuine, a bacterial-derived hypermodified nucleobase, shows protection in in vitro models of neurodegeneration

Patricia Richard et al.

Summary: Growing evidence suggests a connection between human gut bacteria and neurodegenerative disorders, with the microbiome playing a crucial role. The molecule queuine, derived from microbiome, is important for brain function and its depletion may lead to protein misfolding and neurodegeneration. A chemical synthesized queuine, STL-101, shows promising potential in protecting neurons in models of Parkinson's and Alzheimer's diseases by reducing protein aggregation and improving cell survival.

PLOS ONE (2021)

Article Biochemistry & Molecular Biology

A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine

Sweta Vangaveti et al.

JOURNAL OF MOLECULAR BIOLOGY (2020)

Article Multidisciplinary Sciences

Complete chemical structures of human mitochondrial tRNAs

Takeo Suzuki et al.

NATURE COMMUNICATIONS (2020)

Article Biochemistry & Molecular Biology

Queuine links translational control in eukaryotes to a micronutrient from bacteria

Martin Mueller et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemical Research Methods

Evolution of a reverse transcriptase to map N1-methyladenosine in human messenger RNA

Huiqing Zhou et al.

NATURE METHODS (2019)

Article Chemistry, Multidisciplinary

Selective and sensitive fluorescence turn-on detection of 4-thiouridine in nucleic acids via oxidative amination

Jingyi Wang et al.

CHEMICAL COMMUNICATIONS (2019)

Article Biochemistry & Molecular Biology

Elongator-a tRNA modifying complex that promotes efficient translational decoding

Marcus J. O. Johansson et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2018)

Article Biochemistry & Molecular Biology

Queuosine modification protects cognate tRNAs against ribonuclease cleavage

Xiaoyun Wang et al.

Article Biochemistry & Molecular Biology

Queuosine-modified tRNAs confer nutritional control of protein translation

Francesca Tuorto et al.

EMBO JOURNAL (2018)

Article Multidisciplinary Sciences

Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis

Michael H. Schwartz et al.

NATURE COMMUNICATIONS (2018)

Review Biochemistry & Molecular Biology

Deazaguanine derivatives, examples of crosstalk between RNA and DNA modification pathways

Geoffrey Hutinet et al.

RNA BIOLOGY (2017)

Review Genetics & Heredity

Detecting RNA modifications in the epitranscriptome: predict and validate

Mark Helm et al.

NATURE REVIEWS GENETICS (2017)

Article Biochemistry & Molecular Biology

Determination of tRNA aminoacylation levels by high-throughput sequencing

Molly E. Evans et al.

NUCLEIC ACIDS RESEARCH (2017)

Review Biochemistry & Molecular Biology

Cross-Talk between Dnmt2-Dependent tRNA Methylation and Queuosine Modification

Ann E. Ehrenhofer-Murray

BIOMOLECULES (2017)

Article Biochemistry & Molecular Biology

Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome

Xiaoyu Li et al.

NATURE CHEMICAL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

tRNA base methylation identification and quantification via high-throughput sequencing

Wesley C. Clark et al.

Review Chemistry, Organic

Sodium periodate mediated oxidative transformations in organic synthesis

Arumugam Sudalai et al.

ORGANIC & BIOMOLECULAR CHEMISTRY (2015)

Review Nutrition & Dietetics

The Queuine Micronutrient: Charting a Course from Microbe to Man

Claire Fergus et al.

NUTRIENTS (2015)

Article Biochemistry & Molecular Biology

TtcA a new tRNA-thioltransferase with an Fe-S cluster

Denis Bouvier et al.

NUCLEIC ACIDS RESEARCH (2014)

Review Chemistry, Multidisciplinary

Selective sensing of saccharides using simple boronic acids and their aggregates

Xin Wu et al.

CHEMICAL SOCIETY REVIEWS (2013)

Article Biochemistry & Molecular Biology

HAMR: high-throughput annotation of modified ribonucleotides

Paul Ryvkin et al.

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

Selective charging of tRNA isoacceptors induced by amino-acid starvation

KA Dittmar et al.

EMBO REPORTS (2005)

Article Biochemical Research Methods

Determination of queuosine derivatives by reverse-phase liquid chromatography for the hypomodification study of Q-bearing tRNAs from various mammal liver cells

A Costa et al.

JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES (2004)