Transcription factors as readers and effectors of DNA methylation

Bivalent Regions of Cytosine Methylation and H3K27 Acetylation Suggest an Active Role for DNA Methylation at Enhancers

(2016) Jessica Charlet et al.   MOLECULAR CELL

Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation

(2015) Jun Wan et al.   BMC GENOMICS

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

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

(2015) Zhiyi Sun et al.   MOLECULAR CELL

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome

(2015) Harrison W. Gabel et al.   NATURE

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke et al.   NATURE

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

(2015) Bo Xia et al.   NATURE METHODS

Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2

(2015) Benyam Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide profiling of DNA methylation provides insights into epigenetic regulation of fungal development in a plant pathogenic fungus, Magnaporthe oryzae

(2015) Junhyun Jeon et al.   Scientific Reports

Role of DNA Methylation in Modulating Transcription Factor Occupancy

(2015) Matthew T. Maurano et al.   Cell Reports

Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression

(2015) Ruslan Strogantsev et al.   GENOME BIOLOGY

Unusual Characteristics of the DNA Binding Domain of Epigenetic Regulatory Protein MeCP2 Determine Its Binding Specificity

(2014) Sergei Khrapunov et al.   BIOCHEMISTRY

Evolving insights on how cytosine methylation affects protein-DNA binding

(2014) A. C. Dantas Machado et al.   Briefings in Functional Genomics

Pioneer transcription factors in cell reprogramming

(2014) Makiko Iwafuchi-Doi et al.   GENES & DEVELOPMENT

Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity

(2014) S. Takayama et al.   GENOME RESEARCH

Direct ChIP-bisulfite sequencing reveals a role of H3K27me3 mediating aberrant hypermethylation of promoter CpG islands in cancer cells

(2014) Fei Gao et al.   GENOMICS

Paradoxical Role of DNA Methylation in Activation of FoxA2 Gene Expression during Endoderm Development

(2014) Keren Bahar Halpern et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Characterization of monoclonal antibody's binding kinetics using oblique-incidence reflectivity difference approach

(2014) Shuang Liu et al.   mAbs

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

(2014) Hao Wu et al.   NATURE BIOTECHNOLOGY

Structural basis for Klf4 recognition of methylated DNA

(2014) Y. Liu et al.   NUCLEIC ACIDS RESEARCH

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

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

(2013) Tuncay Baubec 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

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition

(2013) Alika K Maunakea et al.   CELL RESEARCH

CG methylated microarrays identify a novel methylated sequence bound by the CEBPB ATF4 heterodimer that is active in vivo

(2013) I. K. Mann et al.   GENOME RESEARCH

Cross-talk between Site-specific Transcription Factors and DNA Methylation States

(2013) Adam Blattler et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Developmentally Programmed 3′ CpG Island Methylation Confers Tissue- and Cell-Type-Specific Transcriptional Activation

(2013) Da-Hai Yu et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2013) Gary C Hon et al.   NATURE GENETICS

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

(2013) Housheng Hansen He et al.   NATURE METHODS

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

(2013) Junjie U Guo et al.   NATURE NEUROSCIENCE

Mechanisms and models of somatic cell reprogramming

(2013) Yosef Buganim et al.   NATURE REVIEWS GENETICS

Integrative analysis of tissue-specific methylation and alternative splicing identifies conserved transcription factor binding motifs

(2013) J. Wan et al.   NUCLEIC ACIDS RESEARCH

Probing DNA shape and methylation state on a genomic scale with DNase I

(2013) A. Lazarovici 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

ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes

(2013) Adam Blattler et al.   Epigenetics & Chromatin

PPARγ-induced PARylation promotes local DNA demethylation by production of 5-hydroxymethylcytosine

(2013) Katsunori Fujiki et al.   Nature Communications

Oncogenic Isocitrate Dehydrogenase Mutations: Mechanisms, Models, and Clinical Opportunities

(2013) R. A. Cairns et al.   Cancer Discovery

DNA methylation presents distinct binding sites for human transcription factors

(2013) Shaohui Hu et al.   eLife

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

(2013) Mario Iurlaro et al.   GENOME BIOLOGY

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

An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence

(2012) Y. Liu et al.   GENES & DEVELOPMENT

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

IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype

(2012) Sevin Turcan et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso

(2012) B. A. Buck-Koehntop 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

The Discovery of 5-Formylcytosine in Embryonic Stem Cell DNA

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

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

(2011) Wei Xu et al.   CANCER CELL

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

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

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

In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions

(2011) Simon Quenneville et al.   MOLECULAR CELL

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

Epigenome-wide association studies for common human diseases

(2011) Vardhman K. Rakyan et al.   NATURE REVIEWS GENETICS

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation

(2011) J. J. Li 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

Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma

(2010) Houtan Noushmehr et al.   CANCER CELL

Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

(2010) Till Bartke et al.   CELL

Chromatin remodelling during development

(2010) Lena Ho et al.   NATURE

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

CpG methylation of half-CRE sequences creates C/EBP  binding sites that activate some tissue-specific genes

(2010) V. Rishi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers

(2010) Frank Lyko et al.   PLOS BIOLOGY

Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling

(2009) Shaohui Hu et al.   CELL

Cancer-associated IDH1 mutations produce 2-hydroxyglutarate

(2009) Lenny Dang et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Sensitive digital quantification of DNA methylation in clinical samples

(2009) Meng Li et al.   NATURE BIOTECHNOLOGY

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

(2009) Akiko Doi et al.   NATURE GENETICS

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

(2009) Rafael A Irizarry et al.   NATURE GENETICS

Histone modifications, DNA methylation, and Schizophrenia

(2009) David P. Gavin et al.   NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS

IDH1andIDH2Mutations in Gliomas

(2009) Hai Yan et al.   NEW ENGLAND JOURNAL OF MEDICINE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

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

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

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

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

An Integrated Genomic Analysis of Human Glioblastoma Multiforme

(2008) D. W. Parsons et al.   SCIENCE

Methylated DNA Recognition during the Reversal of Epigenetic Silencing Is Regulated by Cysteine and Serine Residues in the Epstein-Barr Virus Lytic Switch Protein

(2008) Questa H. Karlsson et al.   PLoS Pathogens