4.8 Article

Photo-Facilitated Detection and Sequencing of 5-Formylcytidine RNA

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Single-Base Resolution Mapping Reveals Distinct 5-Formylcytidine in Saccharomyces cerevisiae mRNAs

Yafen Wang et al.

Summary: This study presents a method for detecting f(5)C modifications in RNA and a transcriptome-wide f(5)C mapping technique called f(5)C-seq. Over 1000 f(5)C sites were identified in Saccharomyces cerevisiae using f(5)C-seq, and it was found that f(5)C has a preference for wobble sites in mRNA, suggesting its potential role in translation regulation.

ACS CHEMICAL BIOLOGY (2022)

Article Biochemistry & Molecular Biology

Chemical Method to Sequence 5-Formylcytosine on RNA

Ang Li et al.

Summary: Epitranscriptomic RNA modifications play a regulatory role in biological processes. This study presents a chemical method, Mal-Seq, for sequencing 5-formylcytosine (f(5)C) modifications on RNA. The method involves the selective and efficient labeling of f(5)C residues, which are read as C-to-T mutations. The study shows that high-level f(5)C modification is present in mammals but lacking in lower eukaryotes. These findings shed light on mitochondrial tRNA modifications throughout eukaryotic evolution and provide a general platform for characterizing the f(5)C epitranscriptome.

ACS CHEMICAL BIOLOGY (2022)

Article Chemistry, Multidisciplinary

A chemical labeling of N6-formyl adenosine (f6A) RNA

Li-Jun Xie et al.

Summary: N-6-methyl adenosine (m(6)A) is an important epigenetic mark in mRNA that affects a wide range of biological functions in various species. However, current approaches for m(6)A labeling have limitations in terms of efficiency. This study presents a novel covalent labeling approach that allows for efficient affinity purification, detection, and genome-wide profiling.

CHINESE CHEMICAL LETTERS (2022)

Article Biochemistry & Molecular Biology

Protonation-Dependent Sequencing of 5-Formylcytidine in RNA

Courtney N. Link et al.

Summary: Chemical modification of cytidine in noncoding RNAs is important for translation regulation and disease. However, the distribution and dynamics of these modifications are still unknown due to a lack of sensitive sequencing technologies. In this study, a protonation-dependent sequencing reaction is developed to detect 5fC and 5caC in RNA, enhancing the reactivity and sensitive detection of these modified cytidine residues. This method provides a molecular foundation for studying the role of oxidized RNA cytidine residues in diseases.

BIOCHEMISTRY (2022)

Article Multidisciplinary Sciences

Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases

A. Emilia Arguello et al.

Summary: Kleiner and his colleagues profile RNA 5-methylcytidine dioxygenase enzymes using an activity-based metabolic probing strategy, identifying ALKBH1 as the major writer of 5-formylcytidine. Their study characterizes modification sites across mRNA and tRNA, revealing the regulatory role of epitranscriptomic RNA modifications. They propose a chemoproteomic strategy to study RNA 5-methylcytidine dioxygenases in their native context and map oxidative m5C modifications. The research uncovers novel epitranscriptomic pathways for regulating RNA function.

NATURE COMMUNICATIONS (2022)

Article Chemistry, Multidisciplinary

A Light-Controllable Chemical Modulation of m6A RNA Methylation

Ling Lan et al.

Summary: The study presented the design, synthesis, computational, and experimental evaluation of the first photo-activatable small-molecule methyltransferase agonist, which demonstrated spatial and temporal control of biological effects through the use of a photo-removable protecting group. The results indicated rapid release of the active compound from the caged molecule upon short UV light exposure in cells, leading to significant hypermethylation of m(6)A modification in transcriptome RNAs and validating the concept of photo-activatable small organic molecules in RNA epigenetic research.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

Article Chemistry, Multidisciplinary

Comparative Nucleosomal Reactivity of 5-Formyl-Uridine and 5-Formyl-Cytidine

Leander Simon Runtsch et al.

Summary: fdU and fdC are formyl-containing nucleosides created by oxidative stress in differentiated cells, with fdU showing a higher reactivity towards lysine side chains compared with fdC. While fdC is not only formed as an oxidative lesion but also commonly seen in stem cells in an epigenetically important oxidation reaction.

CHEMISTRY-A EUROPEAN JOURNAL (2021)

Article Chemistry, Multidisciplinary

Wittig reagents for chemoselective sulfenic acid ligation enables global site stoichiometry analysis and redox-controlled mitochondrial targeting

Yunlong Shi et al.

Summary: This study introduces a chemoselective ligation reaction utilizing Wittig reagents and the unique chemical properties of sulfenic acid, enabling the formation of covalent bonds under biocompatible conditions for protein modification and mitochondrial redox studies.

NATURE CHEMISTRY (2021)

Article Chemistry, Multidisciplinary

A photo-responsive chemical modulation of m6A RNA demethylase FTO

Ling Lan et al.

Summary: The article describes a new design, synthesis, and evaluation method for a photo-responsive and selective inhibitor of FTO, providing important insights for the development of novel cancer therapies.

CHEMICAL COMMUNICATIONS (2021)

Article Chemistry, Multidisciplinary

Chemical Deprenylation of N6-Isopentenyladenosine (i6A) RNA

Hou-Ping Cheng et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2020)

Article Multidisciplinary Sciences

Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping

Aldema Sas-Chen et al.

NATURE (2020)

Article Chemistry, Multidisciplinary

Identification of Flavin Mononucleotide as a Cell-Active Artificial N6-Methyladenosine RNA Demethylase

Li-Jun Xie et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2019)

Article Biotechnology & Applied Microbiology

Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution

Yibin Liu et al.

NATURE BIOTECHNOLOGY (2019)

Article Chemistry, Applied

A Chemical Photo-Oxidation of 5-Methyl Cytidines

Xiao-Yang Jin et al.

ADVANCED SYNTHESIS & CATALYSIS (2019)

Article Chemistry, Applied

Visible-Light Facilitated Fluorescence Switch-On Labelling of 5-Formylpyrimidine RNA

Rui-Li Wang et al.

ADVANCED SYNTHESIS & CATALYSIS (2019)

Review Cell Biology

The dynamic RNA modification 5-methylcytosine and its emerging role as an epitranscriptomic mark

Lukas Trixl et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2019)

Article Chemistry, Multidisciplinary

A Chemical Signature for Cytidine Acetylation in RNA

Justin M. Thomas et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

Article Biochemistry & Molecular Biology

TET1-Mediated Oxidation of 5-Formylcytosine (5fC) to 5-Carboxycytosine (5caC) in RNA

Maria Basanta-Sanchez et al.

CHEMBIOCHEM (2017)

Article Biochemistry & Molecular Biology

ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA modifications

Layla Kawarada et al.

NUCLEIC ACIDS RESEARCH (2017)

Editorial Material Biochemistry & Molecular Biology

The chemistries and consequences of DNA and RNA methylation and demethylation

Franziska R. Traube et al.

RNA BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Understanding RNA modifications: the promises and technological bottlenecks of the 'epitranscriptome'

Matthias Schaefer et al.

OPEN BIOLOGY (2017)

Article Chemistry, Multidisciplinary

Visible-light-mediated oxidative demethylation of N6-methyl adenines

Li-Jun Xie et al.

CHEMICAL COMMUNICATIONS (2017)

Article Chemistry, Organic

Synthesis of new 4-amino-substituted 7-iminopyrido[2,3-d]pyrimidines

Anna N. Zinchenko et al.

CHEMISTRY OF HETEROCYCLIC COMPOUNDS (2017)

Review Biochemistry & Molecular Biology

Dynamic RNA Modifications in Gene Expression Regulation

Ian A. Roundtree et al.

Article Chemistry, Multidisciplinary

Fluorogenic Labeling of 5-Formylpyrimidine Nucleotides in DNA and RNA

Biswajit Samanta et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2016)

Article Chemistry, Multidisciplinary

The Mechanism of Phosphonium Ylide Alcoholysis and Hydrolysis: Concerted Addition of the O-H Bond Across the P=C Bond

Peter A. Byrne et al.

CHEMISTRY-A EUROPEAN JOURNAL (2016)

Article Biochemistry & Molecular Biology

A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations

Dali Han et al.

MOLECULAR CELL (2016)

Article Multidisciplinary Sciences

The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA

Dan Dominissini et al.

NATURE (2016)

Article Multidisciplinary Sciences

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

Benjamin Delatte et al.

SCIENCE (2016)

Article Chemistry, Organic

Photocatalytic E Z Isomerization of Alkenes

J. B. Metternich et al.

SYNLETT (2016)

Article Multidisciplinary Sciences

Deficient methylation and formylation of mt- tRNAMet wobble cytosine in a patient carrying mutations in NSUN3

Lindsey Van Haute et al.

NATURE COMMUNICATIONS (2016)

Article Biochemistry & Molecular Biology

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

Xiao Wang et al.

Article Biochemistry & Molecular Biology

Formation and Abundance of 5-Hydroxymethylcytosine in RNA

Sabrina M. Huber et al.

CHEMBIOCHEM (2015)

Article Biochemical Research Methods

Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale

Bo Xia et al.

NATURE METHODS (2015)

Article Chemistry, Multidisciplinary

Tet-Mediated Formation of 5-Hydroxymethylcytosine in RNA

Lijuan Fu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2014)

Article Biochemistry & Molecular Biology

A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation

Jianzhao Liu et al.

NATURE CHEMICAL BIOLOGY (2014)

Article Chemistry, Multidisciplinary

Deamination, Oxidation, and C-C Bond Cleavage Reactivity of 5-Hydroxymethylcytosine, 5-Formylcytosine, and 5-Carboxycytosine

Stefan Schiesser et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)

Review Multidisciplinary Sciences

TET enzymes, TDG and the dynamics of DNA demethylation

Rahul M. Kohli et al.

NATURE (2013)

Article Multidisciplinary Sciences

Expanded use of sense codons is regulated by modified cytidines in tRNA

William A. Cantara et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

Shinsuke Ito et al.

SCIENCE (2011)

Article Chemistry, Multidisciplinary

Reactivity and selectivity in the Wittig reaction: A computational study

R Robiette et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)

Article Chemistry, Organic

Water is an efficient medium for Wittig reactions employing stabilized ylides and aldehydes

J Dambacher et al.

TETRAHEDRON LETTERS (2005)

Review Multidisciplinary Sciences

Light microscopy techniques for live cell Imaging

DJ Stephens et al.

SCIENCE (2003)