Mapping and elucidating the function of modified bases in DNA

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

5-Formylcytosine does not change the global structure of DNA

(2017) Jack S Hardwick et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2017) Layla Kawarada et al.   NUCLEIC ACIDS RESEARCH

5-Formylcytosine does not change the global structure of DNA

(2017) Jack S Hardwick et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Accurate, Direct, and High-Throughput Analyses of a Broad Spectrum of Endogenously Generated DNA Base Modifications with Isotope-Dilution Two-Dimensional Ultraperformance Liquid Chromatography with Tandem Mass Spectrometry: Possible Clinical Implication

(2016) Daniel Gackowski et al.   ANALYTICAL CHEMISTRY

5-Formylcytosine Could Be a Semipermanent Base in Specific Genome Sites

(2016) Meng Su et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

An oligodeoxyribonucleotide containing 5-formyl-2′-deoxycytidine (fC) at the CpG site forms a covalent complex with DNA cytosine-5 methyltransferases (DNMTs)

(2016) Kousuke Sato et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

ALKBH1-Mediated tRNA Demethylation Regulates Translation

(2016) Fange Liu et al.   CELL

TALEored Epigenetics: A DNA-Binding Scaffold for Programmable Epigenome Editing and Analysis

(2016) Grzegorz Kubik et al.   CHEMBIOCHEM

The sequence of sequencers: The history of sequencing DNA

(2016) James M. Heather et al.   GENOMICS

Base-Resolution Analysis of 5-Hydroxymethylcytosine by One-Pot Bisulfite-Free Chemical Conversion with Peroxotungstate

(2016) Gosuke Hayashi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

DNA methylation on N6-adenine in mammalian embryonic stem cells

(2016) Tao P. Wu et al.   NATURE

Active DNA demethylation at enhancers during the vertebrate phylotypic period

(2016) Ozren Bogdanović et al.   NATURE GENETICS

MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma

(2016) Dongxue Wang et al.   NUCLEIC ACIDS RESEARCH

Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments

(2016) Gordon R. McInroy et al.   PLoS One

The DNA methyltransferase DNMT3C protects male germ cells from transposon activity

(2016) Joan Barau et al.   SCIENCE

Abundant DNA 6mA methylation during early embryogenesis of zebrafish and pig

(2016) Jianzhao Liu et al.   Nature Communications

Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability

(2016) Thuy T. M. Ngo et al.   Nature Communications

Histone H3 Variant Regulates RNA Polymerase II Transcription Termination and Dual Strand Transcription of siRNA Loci in Trypanosoma brucei

(2016) David Reynolds et al.   PLoS Genetics

5-hydroxymethylcytosine marks regions with reduced mutation frequency in human DNA

(2016) Marketa Tomkova et al.   eLife

A CRISPR-based approach for targeted DNA demethylation

(2016) Xingxing Xu et al.   Cell Discovery

Library construction for next-generation sequencing: Overviews and challenges

(2016) Steven R. Head et al.   BIOTECHNIQUES

Age-Dependent Levels of 5-Methyl-, 5-Hydroxymethyl-, and 5-Formylcytosine in Human and Mouse Brain Tissues

(2015) Mirko Wagner et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

DNA Methylation on N6-Adenine in C. elegans

(2015) Eric Lieberman Greer et al.   CELL

N6-Methyladenine DNA Modification in Drosophila

(2015) Guoqiang Zhang et al.   CELL

N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas

(2015) Ye Fu et al.   CELL

Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics

(2015) Xingyu Lu et al.   CELL RESEARCH

A Sensitive Approach to Map Genome-wide 5-Hydroxymethylcytosine and 5-Formylcytosine at Single-Base Resolution

(2015) Zhiyi Sun et al.   MOLECULAR CELL

Cell-of-origin chromatin organization shapes the mutational landscape of cancer

(2015) Paz Polak et al.   NATURE

5-Formylcytosine can be a stable DNA modification in mammals

(2015) Martin Bachman et al.   Nature Chemical Biology

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

(2015) Bo Xia et al.   NATURE METHODS

DNA methylation pathways and their crosstalk with histone methylation

(2015) Jiamu Du et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications

(2015) Magdalena J Koziol et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing

(2015) Paul-Andre Genest et al.   NUCLEIC ACIDS RESEARCH

Biochemical characterization of aNaegleriaTET-like oxygenase and its application in single molecule sequencing of 5-methylcytosine

(2015) June E. Pais et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications

(2015) Magdalena J Koziol et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Precision cancer mouse models through genome editing with CRISPR-Cas9

(2015) Haiwei Mou et al.   Genome Medicine

Abstract CT103: Clinical safety and activity in a phase I trial of AG-221, a first in class, potent inhibitor of the IDH2-mutant protein, in patients with IDH2 mutant positive advanced hematologic malignancies

(2015) Eytan Stein et al.   CANCER RESEARCH

Hydroxymethylation of DNA influences nucleosomal conformation and stability in vitro

(2014) Agnes Mendonca et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The role of 5-hydroxymethylcytosine in human cancer

(2014) Gerd P. Pfeifer et al.   CELL AND TISSUE RESEARCH

Chemical Methods for Decoding Cytosine Modifications in DNA

(2014) Michael J. Booth et al.   CHEMICAL REVIEWS

Loss of Tet Enzymes Compromises Proper Differentiation of Embryonic Stem Cells

(2014) Meelad M. Dawlaty et al.   DEVELOPMENTAL CELL

5-Hydroxymethylcytosine: A stable or transient DNA modification?

(2014) Maria A. Hahn et al.   GENOMICS

Identification of the Glucosyltransferase That Converts Hydroxymethyluracil to Base J in the Trypanosomatid Genome

(2014) Whitney Bullard et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Design of Sequence-Specific DNA Binding Molecules for DNA Methyltransferase Inhibition

(2014) JeenJoo S. Kang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Quantitative Mass Spectrometry-Based Analysis of β-D-Glucosyl-5-Hydroxymethyluracil in Genomic DNA of Trypanosoma brucei

(2014) Shuo Liu et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing

(2014) Hao Wu et al.   NATURE BIOTECHNOLOGY

Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA

(2014) Toni Pfaffeneder et al.   Nature Chemical Biology

5-Hydroxymethylcytosine is a predominantly stable DNA modification

(2014) Martin Bachman et al.   Nature Chemistry

Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution

(2014) Michael J. Booth et al.   Nature Chemistry

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

5-Formylcytosine alters the structure of the DNA double helix

(2014) Eun-Ang Raiber et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Multitarget Stool DNA Testing for Colorectal-Cancer Screening

(2014) Thomas F. Imperiale et al.   NEW ENGLAND JOURNAL OF MEDICINE

Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA

(2014) John R. Horton et al.   NUCLEIC ACIDS RESEARCH

Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases inCoprinopsis cinerea

(2014) Lukas Chavez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthetic CpG islands reveal DNA sequence determinants of chromatin structure

(2014) Elisabeth Wachter et al.   eLife

High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions

(2014) Arnaud R Krebs et al.   eLife

Genome-wide Analysis Reveals TET- and TDG-Dependent 5-Methylcytosine Oxidation Dynamics

(2013) Li Shen et al.   CELL

Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming

(2013) Chun-Xiao Song et al.   CELL

Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives

(2013) Cornelia G. Spruijt et al.   CELL

A robust, sensitive assay for genomic uracil determination by LC/MS/MS reveals lower levels than previously reported

(2013) Anastasia Galashevskaya et al.   DNA REPAIR

TET enzymes, TDG and the dynamics of DNA demethylation

(2013) Rahul M. Kohli et al.   NATURE

Effects of DNA methylation on nucleosome stability

(2013) Clayton K. Collings et al.   NUCLEIC ACIDS RESEARCH

Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA

(2013) A. H. Laszlo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Active demethylation in mouse zygotes involves cytosine deamination and base excision repair

(2013) Fátima Santos et al.   Epigenetics & Chromatin

DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes

(2013) Lin Liu et al.   Nature Communications

High-Resolution Enzymatic Mapping of Genomic 5-Hydroxymethylcytosine in Mouse Embryonic Stem Cells

(2013) Zhiyi Sun et al.   Cell Reports

Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic

(2013) Zhixing Feng et al.   PLoS Computational Biology

A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation

(2013) Mario Iurlaro et al.   GENOME BIOLOGY

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

(2012) Miao Yu et al.   CELL

Glucosylated Hydroxymethyluracil, DNA Base J, Prevents Transcriptional Readthrough in Leishmania

(2012) Henri G.A.M. van Luenen et al.   CELL

Transcription: Base J Blocks the Way

(2012) Dane Z. Hazelbaker et al.   CURRENT BIOLOGY

Low values of 5-hydroxymethylcytosine (5hmC), the “sixth base,” are associated with anaplasia in human brain tumors

(2012) Theo F.J. Kraus et al.   INTERNATIONAL JOURNAL OF CANCER

Chromatin organization is a major influence on regional mutation rates in human cancer cells

(2012) Benjamin Schuster-Böckler et al.   NATURE

AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation

(2012) Christopher S Nabel et al.   Nature Chemical Biology

Pull-down of 5-hydroxymethylcytosine DNA using JBP1-coated magnetic beads

(2012) Adam B Robertson et al.   Nature Protocols

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging

(2012) Fumihito Miura et al.   NUCLEIC ACIDS RESEARCH

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

(2012) M. J. Booth et al.   SCIENCE

Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase

(2012) Eun-Ang Raiber et al.   GENOME BIOLOGY

The Discovery of 5-Formylcytosine in Embryonic Stem Cell DNA

(2011) Toni Pfaffeneder et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain

(2011) Junjie U. Guo et al.   CELL

Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids

(2011) Lakshminarayan M. Iyer et al.   CELL CYCLE

Sequencing nucleic acids: from chemistry to medicine

(2011) Shankar Balasubramanian   CHEMICAL COMMUNICATIONS

Hydroxylation of methylated CpG dinucleotides reverses stabilisation of DNA duplexes by cytosine 5-methylation

(2011) Armin Thalhammer et al.   CHEMICAL COMMUNICATIONS

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

TET2 promoter methylation in low-grade diffuse gliomas lacking IDH1/2 mutations

(2011) Y.-H. Kim et al.   JOURNAL OF CLINICAL PATHOLOGY

Effects of DNA Methylation on the Structure of Nucleosomes

(2011) Ju Yeon Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability

(2011) Daniel Cortázar et al.   NATURE

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

(2011) William A. Pastor et al.   NATURE

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

(2011) Gabriella Ficz et al.   NATURE

Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine

(2011) Chun-Xiao Song et al.   NATURE METHODS

Quantification of the Sixth DNA Base Hydroxymethylcytosine in the Brain

(2010) Martin Münzel et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

DNA Methylation Increases Nucleosome Compaction and Rigidity

(2010) John S. Choy et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Discrimination of Methylcytosine from Hydroxymethylcytosine in DNA Molecules

(2010) Meni Wanunu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Epigenetic modifications and human disease

(2010) Anna Portela et al.   NATURE BIOTECHNOLOGY

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine

(2010) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

Two thymidine hydroxylases differentially regulate the formation of glucosylated DNA at regions flanking polymerase II polycistronic transcription units throughout the genome of Trypanosoma brucei

(2010) Laura J. Cliffe et al.   NUCLEIC ACIDS RESEARCH

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

(2010) Yun Huang et al.   PLoS One

Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates

(2010) Daniel Globisch et al.   PLoS One

The discovery of zinc fingers and their development for practical applications in gene regulation and genome manipulation

(2010) Aaron Klug   QUARTERLY REVIEWS OF BIOPHYSICS

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

Base J: Discovery, Biosynthesis, and Possible Functions

(2008) Piet Borst et al.   Annual Review of Microbiology

Modes of action of the DNA methyltransferase inhibitors azacytidine and decitabine

(2008) Carlo Stresemann et al.   INTERNATIONAL JOURNAL OF CANCER

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Quantification of DNA damage products resulting from deamination, oxidation and reaction with products of lipid peroxidation by liquid chromatography isotope dilution tandem mass spectrometry

(2008) Koli Taghizadeh et al.   Nature Protocols

The tektin family of microtubule-stabilizing proteins

(2008) Linda A Amos   GENOME BIOLOGY