Regulation and function of mammalian DNA methylation patterns: a genomic perspective

Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

(2011) Antoine Molaro et al.   CELL

Tet1 and 5-hydroxymethylation

(2011) Hao Wu et al.   CELL CYCLE

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

(2011) Luisa Cimmino 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

RNA templating the epigenome

(2011) Robert C. Spitale et al.   Epigenetics

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

CpG islands and the regulation of transcription

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

Large-scale methylation domains mark a functional subset of neuronally expressed genes

(2011) D. I. Schroeder et al.   GENOME RESEARCH

Directional DNA Methylation Changes and Complex Intermediate States Accompany Lineage Specificity in the Adult Hematopoietic Compartment

(2011) Emily Hodges 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

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

(2011) Sanjeev Shukla et al.   NATURE

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

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

(2011) Hao Wu et al.   NATURE

DNMT3A mutations in acute myeloid leukemia

(2011) Mrinal Y Shah et al.   NATURE GENETICS

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

(2011) Benjamin P Berman et al.   NATURE GENETICS

Dnmt3a is essential for hematopoietic stem cell differentiation

(2011) Grant A Challen et al.   NATURE GENETICS

Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia

(2011) Xiao-Jing Yan et al.   NATURE GENETICS

Identification of genetic elements that autonomously determine DNA methylation states

(2011) Florian Lienert et al.   NATURE GENETICS

Dnmt3a silences hematopoietic stem cell self-renewal

(2011) Jennifer J Trowbridge et al.   NATURE GENETICS

Neuronal activity modifies the DNA methylation landscape in the adult brain

(2011) Junjie U Guo et al.   NATURE NEUROSCIENCE

Deletion of the de novo DNA methyltransferase Dnmt3a promotes lung tumor progression

(2011) Q. Gao 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

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

Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

(2010) Till Bartke et al.   CELL

Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis

(2010) M. L. Conerly et al.   GENOME RESEARCH

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

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

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

Comprehensive methylome map of lineage commitment from haematopoietic progenitors

(2010) Hong Ji et al.   NATURE

CpG islands influence chromatin structure via the CpG-binding protein Cfp1

(2010) John P. Thomson et al.   NATURE

Epigenetic memory in induced pluripotent stem cells

(2010) K. Kim 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

Conserved role of intragenic DNA methylation in regulating alternative promoters

(2010) Alika K. Maunakea et al.   NATURE

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

(2010) R Alan Harris et al.   NATURE BIOTECHNOLOGY

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

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Active DNA demethylation: many roads lead to Rome

(2010) Susan C. Wu et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2010) Seung-Gi Jin et al.   NUCLEIC ACIDS RESEARCH

Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail

(2010) Yingying Zhang et al.   NUCLEIC ACIDS RESEARCH

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

(2010) Yun Huang et al.   PLoS One

Genome-wide analysis reveals methyl-CpG-binding protein 2-dependent regulation of microRNAs in a mouse model of Rett syndrome

(2010) H. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dnmt3a-Dependent Nonpromoter DNA Methylation Facilitates Transcription of Neurogenic Genes

(2010) H. Wu et al.   SCIENCE

Epigenetic Reprogramming in Plant and Animal Development

(2010) Suhua Feng et al.   SCIENCE

Molecular coupling of DNA methylation and histone methylation

(2010) Hideharu Hashimoto et al.   Epigenomics

Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX–DNMT3–DNMT3L domain

(2009) Junji Otani et al.   EMBO REPORTS

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

(2009) E. Hodges et al.   GENOME RESEARCH

Selective Anchoring of DNA Methyltransferases 3A and 3B to Nucleosomes Containing Methylated DNA

(2009) S. Jeong et al.   MOLECULAR AND CELLULAR BIOLOGY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints

(2009) David N. Ciccone et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

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

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

Linking DNA methylation and histone modification: patterns and paradigms

(2009) Howard Cedar et al.   NATURE REVIEWS GENETICS

PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing

(2009) Quan Zhao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A human B cell methylome at 100−base pair resolution

(2009) Tibor A. Rauch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neuronal Activity-Induced Gadd45b Promotes Epigenetic DNA Demethylation and Adult Neurogenesis

(2009) D. K. Ma 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

Reversing DNA Methylation: New Insights from Neuronal Activity-Induced Gadd45b in Adult Neurogenesis

(2009) H. Wu et al.   Science Signaling

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

(2008) Ryan Lister 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

DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity

(2008) Kevin B Dong et al.   EMBO JOURNAL

G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription

(2008) Makoto Tachibana et al.   EMBO JOURNAL

DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes

(2008) S. Kuramochi-Miyagawa et al.   GENES & DEVELOPMENT

Comprehensive high-throughput arrays for relative methylation (CHARM)

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

MILI, a PIWI-interacting RNA-binding Protein, Is Required for Germ Line Stem Cell Self-renewal and Appears to Positively Regulate Translation

(2008) Yingdee Unhavaithaya et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors

(2008) Fabio Mohn et al.   MOLECULAR CELL

Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks

(2008) Daniel Zilberman et al.   NATURE

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

(2008) Toshiaki Watanabe et al.   NATURE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation

(2008) Yutaka Kondo et al.   NATURE GENETICS

Epigenetic events in mammalian germ-cell development: reprogramming and beyond

(2008) Hiroyuki Sasaki et al.   NATURE REVIEWS GENETICS

DNA methylation landscapes: provocative insights from epigenomics

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

De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes

(2008) Silvina Epsztejn-Litman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line

(2008) E. N. Gal-Yam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci

(2008) Robert Illingworth et al.   PLOS BIOLOGY

Antagonism between DNA and H3K27 Methylation at the Imprinted Rasgrf1 Locus

(2008) Anders M. Lindroth et al.   PLoS Genetics