Advances in the profiling of DNA modifications: cytosine methylation and beyond

Genome-wide DNA methylation analysis of formalin-fixed paraffin embedded colorectal cancer tissue

(2014) Troy D. Dumenil et al.   GENES CHROMOSOMES & CANCER

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

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

Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation

(2013) Tyson A Clark et al.   BMC BIOLOGY

Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing

(2013) Junwen Wang et al.   BMC GENOMICS

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

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Optical detection of epigenetic marks: sensitive quantification and direct imaging of individual hydroxymethylcytosine bases

(2013) Yael Michaeli et al.   CHEMICAL COMMUNICATIONS

Selective Chemical Labelling of 5-Formylcytosine in DNA by Fluorescent Dyes

(2013) Jianlin Hu et al.   CHEMISTRY-A EUROPEAN JOURNAL

5-Hydroxymethylcytosine: generation, fate, and genomic distribution

(2013) Li Shen et al.   CURRENT OPINION IN CELL BIOLOGY

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

(2013) H. Guo et al.   GENOME RESEARCH

High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice

(2013) H. Kobayashi et al.   GENOME RESEARCH

Chemical Modification-Assisted Bisulfite Sequencing (CAB-Seq) for 5-Carboxylcytosine Detection in DNA

(2013) Xingyu Lu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX

(2013) Myunggon Ko et al.   NATURE

DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

(2013) Mingchao Xie et al.   NATURE GENETICS

Large conserved domains of low DNA methylation maintained by Dnmt3a

(2013) Mira Jeong et al.   NATURE GENETICS

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

(2013) Gary C Hon et al.   NATURE GENETICS

Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine

(2013) Michael J Booth et al.   Nature Protocols

Tagmentation-based whole-genome bisulfite sequencing

(2013) Qi Wang et al.   Nature Protocols

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques

(2013) John P. Thomson et al.   NUCLEIC ACIDS RESEARCH

In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes

(2013) Maxim Ivanov et al.   NUCLEIC ACIDS RESEARCH

Laser capture microdissection–reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse

(2013) Maximiliaan Schillebeeckx 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

Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells

(2013) P. J. Murphy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Single-Cell DNA-Methylation Analysis Reveals Epigenetic Chimerism in Preimplantation Embryos

(2013) C. Lorthongpanich et al.   SCIENCE

A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples

(2013) Verity F Oliver et al.   Epigenetics & Chromatin

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

(2013) Zhiyi Sun et al.   Cell Reports

Mouse Oocyte Methylomes at Base Resolution Reveal Genome-Wide Accumulation of Non-CpG Methylation and Role of DNA Methyltransferases

(2013) Kenjiro Shirane et al.   PLoS Genetics

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

Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing

(2012) Andrew Adey et al.   GENOME RESEARCH

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA

(2012) Aaron L. Statham et al.   GENOME RESEARCH

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

(2012) Arie B. Brinkman et al.   GENOME RESEARCH

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

(2012) T. K. Kelly et al.   GENOME RESEARCH

MeDIP coupled with a promoter tiling array as a platform to investigate global DNA methylation patterns in AML cells

(2012) Arzu Yalcin et al.   LEUKEMIA RESEARCH

Tet1 controls meiosis by regulating meiotic gene expression

(2012) Shinpei Yamaguchi et al.   NATURE

Mapping recently identified nucleotide variants in the genome and transcriptome

(2012) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

Library-free methylation sequencing with bisulfite padlock probes

(2012) Dinh Diep et al.   NATURE METHODS

DNA methylome analysis using short bisulfite sequencing data

(2012) Felix Krueger et al.   NATURE METHODS

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

(2012) Adam B Robertson et al.   Nature Protocols

Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine

(2012) Miao Yu et al.   Nature Protocols

The GLIB technique for genome-wide mapping of 5-hydroxymethylcytosine

(2012) William A Pastor et al.   Nature Protocols

Methylome analysis using MeDIP-seq with low DNA concentrations

(2012) Oluwatosin Taiwo et al.   Nature Protocols

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

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

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

(2012) Fumihito Miura et al.   NUCLEIC ACIDS RESEARCH

A Comparison of the Whole Genome Approach of MeDIP-Seq to the Targeted Approach of the Infinium HumanMethylation450 BeadChip® for Methylome Profiling

(2012) Christine Clark et al.   PLoS One

Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel

(2012) B. R. Cipriany et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells

(2012) S. Ruiz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) M. J. Booth et al.   SCIENCE

MBD-seq as a cost-effective approach for methylome-wide association studies: demonstration in 1500 case–control samples

(2012) Karolina A Aberg et al.   Epigenomics

In Vivo Control of CpG and Non-CpG DNA Methylation by DNA Methyltransferases

(2012) Julia Arand et al.   PLoS Genetics

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

(2012) Patrick Boyle et al.   GENOME BIOLOGY

High resolution profiling of human exon methylation by liquid hybridization capture-based bisulfite sequencing

(2011) Junwen Wang et al.   BMC GENOMICS

Generation and replication-dependent dilution of 5fC and 5caC during mouse preimplantation development

(2011) Azusa Inoue et al.   CELL RESEARCH

Limiting dilution bisulfite (pyro)sequencing reveals parent-specific methylation patterns in single early mouse embryos and bovine oocytes

(2011) Nady El Hajj et al.   Epigenetics

Application of microdroplet PCR for large-scale targeted bisulfite sequencing

(2011) H. K. Komori et al.   GENOME RESEARCH

Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes

(2011) C. E. Nestor et al.   GENOME RESEARCH

High density DNA methylation array with single CpG site resolution

(2011) Marina Bibikova et al.   GENOMICS

Tissue-specific Distribution and Dynamic Changes of 5-Hydroxymethylcytosine in Mammalian Genomes

(2011) Shannon Morey Kinney et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

5-Hydroxymethylcytosine: a new kid on the epigenetic block?

(2011) F. Matarese et al.   Molecular Systems Biology

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams et al.   NATURE

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister 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

Single-tube linear DNA amplification (LinDA) for robust ChIP-seq

(2011) Pattabhiraman Shankaranarayanan et al.   NATURE METHODS

5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging

(2011) Keith E Szulwach et al.   NATURE NEUROSCIENCE

A high-throughput DNA methylation analysis of a single cell

(2011) Martin Kantlehner et al.   NUCLEIC ACIDS RESEARCH

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing

(2011) Eun-Joon Lee et al.   NUCLEIC ACIDS RESEARCH

High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology

(2011) Xun Lan et al.   PLoS One

Nucleotide Discrimination with DNA Immobilized in the MspA Nanopore

(2011) Elizabeth A. Manrao et al.   PLoS One

OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes

(2011) J. S. You et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) S. Ito et al.   SCIENCE

Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types

(2011) Michael J. Ziller et al.   PLoS Genetics

5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells

(2011) Hume Stroud et al.   GENOME BIOLOGY

Single Molecule Epigenetic Analysis in a Nanofluidic Channel

(2010) Benjamin R. Cipriany et al.   ANALYTICAL CHEMISTRY

Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples

(2010) K. E. Varley et al.   GENOME RESEARCH

Discrimination of Methylcytosine from Hydroxymethylcytosine in DNA Molecules

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

AutoMeDIP-seq: A high-throughput, whole genome, DNA methylation assay

(2010) Lee M. Butcher et al.   METHODS

Whole-genome DNA methylation profiling using MethylCap-seq

(2010) Arie B. Brinkman et al.   METHODS

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification

(2010) Shinsuke Ito et al.   NATURE

Conserved role of intragenic DNA methylation in regulating alternative promoters

(2010) Alika K. Maunakea et al.   NATURE

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

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

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

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA

(2010) Aleksandra Szwagierczak et al.   NUCLEIC ACIDS RESEARCH

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

(2010) Yun Huang et al.   PLoS One

High-throughput method for analyzing methylation of CpGs in targeted genomic regions

(2010) Shivani Nautiyal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming

(2009) Jie Deng et al.   NATURE BIOTECHNOLOGY

Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore

(2009) D. Stoddart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive high-throughput arrays for relative methylation (CHARM)

(2008) R. A. Irizarry et al.   GENOME RESEARCH

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

Single-molecule DNA detection with an engineered MspA protein nanopore

(2008) T. Z. Butler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE