TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

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

(2013) Tyson A Clark et al.   BMC BIOLOGY

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

Replacement of Oct4 by Tet1 during iPSC Induction Reveals an Important Role of DNA Methylation and Hydroxymethylation in Reprogramming

(2013) Yawei Gao et al.   Cell Stem Cell

Stage-Specific Roles for Tet1 and Tet2 in DNA Demethylation in Primordial Germ Cells

(2013) John J. Vincent et al.   Cell Stem Cell

TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS

(2013) Rachel Deplus et al.   EMBO JOURNAL

Structural Basis of the Versatile DNA Recognition Ability of the Methyl-CpG Binding Domain of Methyl-CpG Binding Domain Protein 4

(2013) Junji Otani et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

O-GlcNAcylation and 5-Methylcytosine Oxidation: An Unexpected Association between OGT and TETs

(2013) Anand Balasubramani et al.   MOLECULAR CELL

Tet Proteins Connect the O-Linked N-acetylglucosamine Transferase Ogt to Chromatin in Embryonic Stem Cells

(2013) Pietro Vella et al.   MOLECULAR CELL

NANOG-dependent function of TET1 and TET2 in establishment of pluripotency

(2013) Yael Costa et al.   NATURE

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

(2013) Myunggon Ko et al.   NATURE

Dynamics of 5-Hydroxymethylcytosine and Chromatin Marks in Mammalian Neurogenesis

(2013) Maria A. Hahn et al.   Cell Reports

Mechanism and Stem-Cell Activity of 5-Carboxycytosine Decarboxylation Determined by Isotope Tracing

(2012) Stefan Schiesser et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

CpG site-specific alteration of hydroxymethylcytosine to methylcytosine beyond DNA replication

(2012) Atsutaka Kubosaki et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Loss of 5-Hydroxymethylcytosine Is an Epigenetic Hallmark of Melanoma

(2012) Christine Guo Lian et al.   CELL

MeCP2 Binds to 5hmC Enriched within Active Genes and Accessible Chromatin in the Nervous System

(2012) Marian Mellén et al.   CELL

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

Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development

(2012) Yufei Xu et al.   CELL

Transcriptional activation of transposable elements in mouse zygotes is independent of Tet3-mediated 5-methylcytosine oxidation

(2012) Azusa Inoue et al.   CELL RESEARCH

Tet family proteins and 5-hydroxymethylcytosine in development and disease

(2012) L. Tan et al.   DEVELOPMENT

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

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

The Mammaliande NovoDNA Methyltransferases DNMT3A and DNMT3B Are Also DNA 5-Hydroxymethylcytosine Dehydroxymethylases

(2012) Chun-Chang Chen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

TET2 is essential for survival and hematopoietic stem cell homeostasis

(2012) K Shide et al.   LEUKEMIA

Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2

(2012) Claudia A. Doege et al.   NATURE

TET2 promotes histone O-GlcNAcylation during gene transcription

(2012) Qiang Chen et al.   NATURE

Tet1 controls meiosis by regulating meiotic gene expression

(2012) Shinpei Yamaguchi et al.   NATURE

The ontogeny of cKIT+ human primordial germ cells proves to be a resource for human germ line reprogramming, imprint erasure and in vitro differentiation

(2012) Sofia Gkountela et al.   NATURE CELL BIOLOGY

AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation

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

Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA

(2012) Liang Zhang et al.   Nature Chemical Biology

DNA methylome analysis using short bisulfite sequencing data

(2012) Felix Krueger et al.   NATURE METHODS

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

(2012) William A Pastor et al.   Nature Protocols

The anti-CMS technique for genome-wide mapping of 5-hydroxymethylcytosine

(2012) Yun Huang et al.   Nature Protocols

5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription

(2012) Matthew W Kellinger et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation

(2012) Hideharu Hashimoto et al.   NUCLEIC ACIDS RESEARCH

Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers

(2012) Aurélien A. Sérandour et al.   NUCLEIC ACIDS RESEARCH

AID Enzymatic Activity Is Inversely Proportional to the Size of Cytosine C5 Orbital Cloud

(2012) Gopinath Rangam et al.   PLoS One

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

(2012) M. J. Booth et al.   SCIENCE

Germline DNA Demethylation Dynamics and Imprint Erasure Through 5-Hydroxymethylcytosine

(2012) J. A. Hackett et al.   SCIENCE

Parallel mechanisms of epigenetic reprogramming in the germline

(2012) Jamie A. Hackett et al.   TRENDS IN GENETICS

Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome

(2012) John P Thomson et al.   GENOME BIOLOGY

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

Cross Talk Between O-GlcNAcylation and Phosphorylation: Roles in Signaling, Transcription, and Chronic Disease

(2011) Gerald W. Hart et al.   Annual Review of Biochemistry

Deletion of Tet2 in mice leads to dysregulated hematopoietic stem cells and subsequent development of myeloid malignancies

(2011) Z. Li et al.   BLOOD

TET2 Inactivation Results in Pleiotropic Hematopoietic Abnormalities in Mouse and Is a Recurrent Event during Human Lymphomagenesis

(2011) Cyril Quivoron et al.   CANCER CELL

Tet2 Loss Leads to Increased Hematopoietic Stem Cell Self-Renewal and Myeloid Transformation

(2011) Kelly Moran-Crusio et al.   CANCER CELL

Thymine DNA Glycosylase Is Essential for Active DNA Demethylation by Linked Deamination-Base Excision Repair

(2011) Salvatore Cortellino et al.   CELL

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

(2011) Junjie U. Guo et al.   CELL

Mbd3/NURD Complex Regulates Expression of 5-Hydroxymethylcytosine Marked Genes in Embryonic Stem Cells

(2011) Ozlem Yildirim 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

Tet1 and 5-hydroxymethylation

(2011) Hao Wu et al.   CELL CYCLE

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

(2011) Azusa Inoue et al.   CELL RESEARCH

TET Family Proteins and Their Role in Stem Cell Differentiation and Transformation

(2011) Luisa Cimmino et al.   Cell Stem Cell

Tet1 Is Dispensable for Maintaining Pluripotency and Its Loss Is Compatible with Embryonic and Postnatal Development

(2011) Meelad M. Dawlaty et al.   Cell Stem Cell

Tet1 and Tet2 Regulate 5-Hydroxymethylcytosine Production and Cell Lineage Specification in Mouse Embryonic Stem Cells

(2011) Kian Peng Koh et al.   Cell Stem Cell

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

(2011) Armin Thalhammer et al.   CHEMICAL COMMUNICATIONS

DNA methylation: TET proteins—guardians of CpG islands?

(2011) Kristine Williams et al.   EMBO REPORTS

Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation

(2011) H. Wu et al.   GENES & DEVELOPMENT

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells

(2011) H. Wu et al.   GENES & DEVELOPMENT

Thymine DNA Glycosylase Can Rapidly Excise 5-Formylcytosine and 5-Carboxylcytosine

(2011) Atanu Maiti et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Unraveling the Molecular Pathophysiology of Myelodysplastic Syndromes

(2011) Rafael Bejar et al.   JOURNAL OF CLINICAL ONCOLOGY

The Dinucleotide CG as a Genomic Signalling Module

(2011) Adrian Bird   JOURNAL OF MOLECULAR BIOLOGY

Genome-wide Regulation of 5hmC, 5mC, and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells

(2011) Yufei Xu et al.   MOLECULAR CELL

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

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

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

(2011) Daniel Cortázar et al.   NATURE

The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes

(2011) Tian-Peng Gu et al.   NATURE

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams 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

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells

(2011) Hao Wu et al.   NATURE

Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine

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

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

(2011) Keith E Szulwach et al.   NATURE NEUROSCIENCE

A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA

(2011) Adam B. Robertson et al.   NUCLEIC ACIDS RESEARCH

Genomic mapping of 5-hydroxymethylcytosine in the human brain

(2011) Seung-Gi Jin et al.   NUCLEIC ACIDS RESEARCH

Different Binding Properties and Function of CXXC Zinc Finger Domains in Dnmt1 and Tet1

(2011) Carina Frauer et al.   PLoS One

Ten-Eleven-Translocation 2 (TET2) negatively regulates homeostasis and differentiation of hematopoietic stem cells in mice

(2011) M. Ko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine

(2011) Khursheed Iqbal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Replication-Dependent Loss of 5-Hydroxymethylcytosine in Mouse Preimplantation Embryos

(2011) A. Inoue et al.   SCIENCE

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

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

(2011) S. Ito et al.   SCIENCE

5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming

(2011) Mark Wossidlo et al.   Nature Communications

Role of TET2 Mutations in Myeloproliferative Neoplasms

(2011) Elodie Pronier et al.   Current Hematologic Malignancy Reports

Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells

(2011) Keith E. Szulwach 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

Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA

(2010) Colm Nestor et al.   BIOTECHNIQUES

DNA Demethylase Activity Maintains Intestinal Cells in an Undifferentiated State Following Loss of APC

(2010) Kunal Rai et al.   CELL

TET1 is a DNA-binding protein that modulates DNA methylation and gene transcription via hydroxylation of 5-methylcytosine

(2010) Haikuo Zhang et al.   CELL RESEARCH

Dynamic link of DNA demethylation, DNA strand breaks and repair in mouse zygotes

(2010) Mark Wossidlo et al.   EMBO JOURNAL

Induced pluripotent stem cells: what lies beyond the paradigm shift

(2010) Jesse L Cox et al.   EXPERIMENTAL BIOLOGY AND MEDICINE

Mutual Relationship between Stacking and Hydrogen Bonding in DNA. Theoretical Study of Guanine−Cytosine, Guanine−5-methylcytosine, and Their Dimers

(2010) Carles Acosta-Silva et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DNA Methylation Increases Nucleosome Compaction and Rigidity

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

Neuronal MeCP2 Is Expressed at Near Histone-Octamer Levels and Globally Alters the Chromatin State

(2010) Peter J. Skene et al.   MOLECULAR CELL

CpG Islands Recruit a Histone H3 Lysine 36 Demethylase

(2010) Neil P. Blackledge et al.   MOLECULAR CELL

Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2

(2010) Myunggon Ko et al.   NATURE

Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency

(2010) Christian Popp et al.   NATURE

Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate

(2010) Ye Zheng et al.   NATURE

A role for the elongator complex in zygotic paternal genome demethylation

(2010) Yuki Okada et al.   NATURE

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

(2010) Shinsuke Ito et al.   NATURE

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

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

Targets and dynamics of promoter DNA methylation during early mouse development

(2010) Julie Borgel et al.   NATURE GENETICS

Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA

(2010) Aleksandra Szwagierczak et al.   NUCLEIC ACIDS RESEARCH

Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase

(2010) L. M. Iyer et al.   NUCLEIC ACIDS RESEARCH

Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine

(2010) Seung-Gi Jin 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

Genome-Wide Reprogramming in the Mouse Germ Line Entails the Base Excision Repair Pathway

(2010) P. Hajkova et al.   SCIENCE

Dnmt3a-Dependent Nonpromoter DNA Methylation Facilitates Transcription of Neurogenic Genes

(2010) H. Wu et al.   SCIENCE

Physiological and biochemical aspects of hydroxylations and demethylations catalyzed by human 2-oxoglutarate oxygenases

(2010) Christoph Loenarz et al.   TRENDS IN BIOCHEMICAL SCIENCES

Mouse models of MeCP2 disorders share gene expression changes in the cerebellum and hypothalamus

(2009) Shay Ben-Shachar et al.   HUMAN MOLECULAR GENETICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Reprogramming towards pluripotency requires AID-dependent DNA demethylation

(2009) Nidhi Bhutani et al.   NATURE

Cytosine-5-methyltransferases add aldehydes to DNA

(2009) Zita Liutkevičiūtė et al.   Nature Chemical Biology

Developmental programming of CpG island methylation profiles in the human genome

(2009) Ravid Straussman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2009) M. Tahiliani et al.   SCIENCE

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

Base J: Discovery, Biosynthesis, and Possible Functions

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

DNA Demethylation in Zebrafish Involves the Coupling of a Deaminase, a Glycosylase, and Gadd45

(2008) Kunal Rai et al.   CELL

Promoter CpG Methylation Contributes to ES Cell Gene Regulation in Parallel with Oct4/Nanog, PcG Complex, and Histone H3 K4/K27 Trimethylation

(2008) Shaun D. Fouse et al.   Cell Stem Cell

Cyclical DNA methylation of a transcriptionally active promoter

(2008) Raphaël Métivier et al.   NATURE

Transient cyclical methylation of promoter DNA

(2008) Sara Kangaspeska et al.   NATURE

Dissecting direct reprogramming through integrative genomic analysis

(2008) Tarjei S. Mikkelsen et al.   NATURE

Expanding chemical biology of 2-oxoglutarate oxygenases

(2008) Christoph Loenarz et al.   Nature Chemical Biology

Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes

(2007) Lakshminarayan M. Iyer et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY