Modifiers and Readers of DNA Modifications and Their Impact on Genome Structure, Expression, and Stability in Disease

Poly(ADP-ribosyl)ation of Methyl CpG Binding Domain Protein 2 Regulates Chromatin Structure

(2016) Annette Becker et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

De novo DNA methylation drives 5hmC accumulation in mouse zygotes

(2016) Rachel Amouroux et al.   NATURE CELL BIOLOGY

A computational investigation on the substrate preference of ten-eleven-translocation 2 (TET2)

(2016) Junyan Lu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

GADD45a physically and functionally interacts with TET1

(2015) Sabine Kienhöfer et al.   DIFFERENTIATION

DAZL regulates Tet1 translation in murine embryonic stem cells

(2015) M. Welling et al.   EMBO REPORTS

Phosphorylation of TET Proteins Is Regulated viaO-GlcNAcylation by theO-LinkedN-Acetylglucosamine Transferase (OGT)

(2015) Christina Bauer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CRL4VprBP E3 Ligase Promotes Monoubiquitylation and Chromatin Binding of TET Dioxygenases

(2015) Tadashi Nakagawa et al.   MOLECULAR CELL

Structural insight into substrate preference for TET-mediated oxidation

(2015) Lulu Hu et al.   NATURE

Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications

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

Gadd45a promotes DNA demethylation through TDG

(2015) Zheng Li et al.   NUCLEIC ACIDS RESEARCH

Structure ofNaegleriaTet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA

(2015) Hideharu Hashimoto et al.   NUCLEIC ACIDS RESEARCH

Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications

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

Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers

(2015) Michael Christoph Haffner et al.   Oncotarget

MBD3/NuRD Facilitates Induction of Pluripotency in a Context-Dependent Manner

(2014) Rodrigo L. dos Santos et al.   Cell Stem Cell

Differential Regulation of the Ten-Eleven Translocation (TET) Family of Dioxygenases byO-Linked β-N-Acetylglucosamine Transferase (OGT)

(2014) Qiao Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Mutations in the DNA methyltransferase gene DNMT3A cause an overgrowth syndrome with intellectual disability

(2014) Katrina Tatton-Brown et al.   NATURE GENETICS

TET-mediated oxidation of methylcytosine causes TDG or NEIL glycosylase dependent gene reactivation

(2014) Udo Müller et al.   NUCLEIC ACIDS RESEARCH

TET1 is a maintenance DNA demethylase that prevents methylation spreading in differentiated cells

(2014) C. Jin et al.   NUCLEIC ACIDS RESEARCH

Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells

(2014) Y. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MBD5 and MBD6 interact with the human PR-DUB complex through their methyl-CpG-binding domain

(2014) H. Irem Baymaz et al.   PROTEOMICS

Crystal Structure of TET2-DNA Complex: Insight into TET-Mediated 5mC Oxidation

(2013) Lulu Hu et al.   CELL

Methylation-Dependent and -Independent Genomic Targeting Principles of the MBD Protein Family

(2013) Tuncay Baubec 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

Tet1 Regulates Adult Hippocampal Neurogenesis and Cognition

(2013) Run-Rui Zhang 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

TET3-OGT interaction increases the stability and the presence of OGT in chromatin

(2013) Ryo Ito et al.   GENES TO CELLS

SUMOylation of MeCP2 is essential for transcriptional repression and hippocampal synapse development

(2013) Ju Cheng et al.   JOURNAL OF NEUROCHEMISTRY

Down-regulation of MeCP2 in Hirschsprung's disease

(2013) Zhigang Zhou et al.   JOURNAL OF PEDIATRIC SURGERY

Epigenetic changes in the progression of Alzheimer's disease

(2013) M.A. Bradley-Whitman et al.   MECHANISMS OF AGEING AND DEVELOPMENT

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

(2013) Pietro Vella et al.   MOLECULAR CELL

Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA

(2013) Hideharu Hashimoto et al.   NATURE

Deterministic direct reprogramming of somatic cells to pluripotency

(2013) Yoach Rais et al.   NATURE

Activity-dependent phosphorylation of MeCP2 threonine 308 regulates interaction with NCoR

(2013) Daniel H. Ebert et al.   NATURE

Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells

(2013) Kathryn Blaschke et al.   NATURE

Role of Tet1 in erasure of genomic imprinting

(2013) Shinpei Yamaguchi et al.   NATURE

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

Heritable gene targeting in the mouse and rat using a CRISPR-Cas system

(2013) Dali Li et al.   NATURE BIOTECHNOLOGY

Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain

(2013) Junjie U Guo et al.   NATURE NEUROSCIENCE

Rett syndrome mutations abolish the interaction of MeCP2 with the NCoR/SMRT co-repressor

(2013) Matthew J Lyst et al.   NATURE NEUROSCIENCE

Tet1 Is Critical for Neuronal Activity-Regulated Gene Expression and Memory Extinction

(2013) Andrii Rudenko et al.   NEURON

Dissection of cell cycle–dependent dynamics of Dnmt1 by FRAP and diffusion-coupled modeling

(2013) Katrin Schneider et al.   NUCLEIC ACIDS RESEARCH

PGC7 suppresses TET3 for protecting DNA methylation

(2013) C. Bian et al.   NUCLEIC ACIDS RESEARCH

Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and binding to exon sequences

(2013) Katharina Günther et al.   NUCLEIC ACIDS RESEARCH

Direct Homo- and Hetero-Interactions of MeCP2 and MBD2

(2013) Annette Becker et al.   PLoS One

Intrinsic and Extrinsic Connections of Tet3 Dioxygenase with CXXC Zinc Finger Modules

(2013) Nan Liu et al.   PLoS One

TET1 plays an essential oncogenic role in MLL-rearranged leukemia

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

CRL4 Complex Regulates Mammalian Oocyte Survival and Reprogramming by Activation of TET Proteins

(2013) C. Yu et al.   SCIENCE

NuRD Blocks Reprogramming of Mouse Somatic Cells into Pluripotent Stem Cells

(2013) Min Luo et al.   STEM CELLS

MBD3 Localizes at Promoters, Gene Bodies and Enhancers of Active Genes

(2013) Takashi Shimbo et al.   PLoS Genetics

The Involvement of 5-Hydroxymethylcytosine in Active DNA Demethylation in Mice1

(2012) Peng Zhang et al.   BIOLOGY OF REPRODUCTION

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

(2012) Marian Mellén 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

NuRD Suppresses Pluripotency Gene Expression to Promote Transcriptional Heterogeneity and Lineage Commitment

(2012) Nicola Reynolds et al.   Cell Stem Cell

SIRT1-mediated deacetylation of MeCP2 contributes to BDNF expression

(2012) Loredana Zocchi et al.   Epigenetics

NIRF/UHRF2 occupies a central position in the cell cycle network and allows coupling with the epigenetic landscape

(2012) Tsutomu Mori et al.   FEBS LETTERS

Mutations in DNMT1 cause autosomal dominant cerebellar ataxia, deafness and narcolepsy

(2012) Juliane Winkelmann et al.   HUMAN MOLECULAR GENETICS

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

Structural Insight into Coordinated Recognition of Trimethylated Histone H3 Lysine 9 (H3K9me3) by the Plant Homeodomain (PHD) and Tandem Tudor Domain (TTD) of UHRF1 (Ubiquitin-like, Containing PHD and RING Finger Domains, 1) Protein

(2012) Jingdong Cheng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Phosphorylation of Distinct Sites in MeCP2 Modifies Cofactor Associations and the Dynamics of Transcriptional Regulation

(2012) M. L. Gonzales et al.   MOLECULAR AND CELLULAR BIOLOGY

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

PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos

(2012) Toshinobu Nakamura et al.   NATURE

Tet1 controls meiosis by regulating meiotic gene expression

(2012) Shinpei Yamaguchi et al.   NATURE

Enhancer decommissioning by LSD1 during embryonic stem cell differentiation

(2012) Warren A. Whyte et al.   NATURE

Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation

(2012) Scott B Rothbart et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Germline ablation of SMUG1 DNA glycosylase causes loss of 5-hydroxymethyluracil- and UNG-backup uracil-excision activities and increases cancer predisposition of Ung−/−Msh2−/− mice

(2012) Kristin Kemmerich et al.   NUCLEIC ACIDS RESEARCH

Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation

(2012) Hideharu Hashimoto et al.   NUCLEIC ACIDS RESEARCH

Targeted manipulation of heterochromatin rescues MeCP2 Rett mutants and re-establishes higher order chromatin organization

(2012) Corella S. Casas-Delucchi et al.   NUCLEIC ACIDS RESEARCH

Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation

(2012) Hideharu Hashimoto et al.   NUCLEIC ACIDS RESEARCH

Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1

(2012) K. Arita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure-Based Mechanistic Insights into DNMT1-Mediated Maintenance DNA Methylation

(2012) J. Song et al.   SCIENCE

Germline DNA Demethylation Dynamics and Imprint Erasure Through 5-Hydroxymethylcytosine

(2012) J. A. Hackett et al.   SCIENCE

The Discovery of 5-Formylcytosine in Embryonic Stem Cell DNA

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

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

(2011) Z. Li et al.   BLOOD

Oncometabolite 2-Hydroxyglutarate Is a Competitive Inhibitor of α-Ketoglutarate-Dependent Dioxygenases

(2011) Wei Xu et al.   CANCER 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

Structural basis for site-specific reading of unmodified R2 of histone H3 tail by UHRF1 PHD finger

(2011) Chengkun Wang et al.   CELL RESEARCH

Crystal structure of PHD domain of UHRF1 and insights into recognition of unmodified histone H3 arginine residue 2

(2011) Lulu Hu et al.   CELL RESEARCH

S phase-dependent interaction with DNMT1 dictates the role of UHRF1 but not UHRF2 in DNA methylation maintenance

(2011) Jiqin Zhang et al.   CELL RESEARCH

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

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

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

MeCP2 Rett mutations affect large scale chromatin organization

(2011) Noopur Agarwal et al.   HUMAN MOLECULAR GENETICS

Recognition of Multivalent Histone States Associated with Heterochromatin by UHRF1 Protein

(2011) Nataliya Nady et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Cooperative DNA and histone binding by Uhrf2 links the two major repressive epigenetic pathways

(2011) Garwin Pichler et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Recurrent DNMT3A mutations in patients with myelodysplastic syndromes

(2011) M J Walter et al.   LEUKEMIA

PHD Finger Recognition of Unmodified Histone H3R2 Links UHRF1 to Regulation of Euchromatic Gene Expression

(2011) Eerappa Rajakumara et al.   MOLECULAR CELL

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

(2011) Yufei Xu et al.   MOLECULAR CELL

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

Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss

(2011) Christopher J Klein et al.   NATURE GENETICS

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

(2011) Keith E Szulwach et al.   NATURE NEUROSCIENCE

Genome-Wide Activity-Dependent MeCP2 Phosphorylation Regulates Nervous System Development and Function

(2011) Sonia Cohen et al.   NEURON

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

Recognition of 5-Hydroxymethylcytosine by the Uhrf1 SRA Domain

(2011) Carina Frauer et al.   PLoS One

p66 -MBD2 coiled-coil interaction and recruitment of Mi-2 are critical for globin gene silencing by the MBD2-NuRD complex

(2011) M. N. Gnanapragasam 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

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

Regulation of DNA methyltransferase 1 by interactions and modifications

(2011) Weihua Qin et al.   Nucleus

Unique Physical Properties and Interactions of the Domains of Methylated DNA Binding Protein 2

(2010) Rajarshi P. Ghosh et al.   BIOCHEMISTRY

UHRF1-mediated tumor suppressor gene inactivation in nonsmall cell lung cancer

(2010) Alexandros Daskalos et al.   CANCER

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

UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications

(2010) Hideharu Hashimoto et al.   Epigenetics

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

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

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

(2010) Myunggon Ko et al.   NATURE

L1 retrotransposition in neurons is modulated by MeCP2

(2010) Alysson R. Muotri 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

DNMT3AMutations in Acute Myeloid Leukemia

(2010) Timothy J. Ley et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Human Proteins MBD5 and MBD6 Associate with Heterochromatin but They Do Not Bind Methylated DNA

(2010) Sophie Laget et al.   PLoS One

Structure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation

(2010) J. Song et al.   SCIENCE

Autism and other neuropsychiatric symptoms are prevalent in individuals withMeCP2duplication syndrome

(2009) Melissa B. Ramocki et al.   ANNALS OF NEUROLOGY

UHRF1 recruits the histone acetyltransferase Tip60 and controls its expression and activity

(2009) Mayada Achour et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Genetic characterization of TET1, TET2, and TET3 alterations in myeloid malignancies

(2009) O. Abdel-Wahab et al.   BLOOD

Np95 interacts with de novo DNA methyltransferases, Dnmt3a and Dnmt3b, and mediates epigenetic silencing of the viral CMV promoter in embryonic stem cells

(2009) Daniela Meilinger et al.   EMBO REPORTS

Let-7a elevates p21WAF1levels by targeting of NIRF and suppresses the growth of A549 lung cancer cells

(2009) Xiaoyan He et al.   FEBS LETTERS

P052 Acquired mutations in TET2 are common in myelodysplastic syndromes

(2009) S. Langemeijer et al.   LEUKEMIA RESEARCH

The multi-domain protein Np95 connects DNA methylation and histone modification

(2009) Andrea Rottach et al.   NUCLEIC ACIDS RESEARCH

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

Complications in the Assignment of 14 and 28 Da Mass Shift Detected by Mass Spectrometry as in Vivo Methylation from Endogenous Proteins

(2008) Sung Yun Jung et al.   ANALYTICAL CHEMISTRY

Kaiso Contributes to DNA Methylation-Dependent Silencing of Tumor Suppressor Genes in Colon Cancer Cell Lines

(2008) E. C. Lopes et al.   CANCER RESEARCH

Zbtb4 represses transcription of P21CIP1 and controls the cellular response to p53 activation

(2008) Axel Weber et al.   EMBO JOURNAL

Methyl-CpG-binding protein 2 polymorphisms and vulnerability to autism

(2008) C. S. Loat et al.   GENES BRAIN AND BEHAVIOR

Regulation of DNA methylation activity through Dnmt3L promoter methylation by Dnmt3 enzymes in embryonic development

(2008) Ye-Guang Hu et al.   HUMAN MOLECULAR GENETICS

The PHD Domain of Np95 (mUHRF1) Is Involved in Large-Scale Reorganization of Pericentromeric Heterochromatin

(2008) Roberto Papait et al.   MOLECULAR BIOLOGY OF THE CELL

DNMT3b overexpression contributes to a hypermethylator phenotype in human breast cancer cell lines

(2008) J Devon Roll et al.   Molecular Cancer

The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix

(2008) Hideharu Hashimoto et al.   NATURE

Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism

(2008) Kyohei Arita et al.   NATURE

Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1

(2008) George V. Avvakumov et al.   NATURE

UHRF1 binds G9a and participates in p21 transcriptional regulation in mammalian cells

(2008) Jong Kyong Kim et al.   NUCLEIC ACIDS RESEARCH

MeCP2, a Key Contributor to Neurological Disease, Activates and Represses Transcription

(2008) M. Chahrour et al.   SCIENCE