DNA methylation: roles in mammalian development

Dynamics and Memory of Heterochromatin in Living Cells

(2012) Nathaniel A. Hathaway et al.   CELL

Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline

(2012) J. A. Hackett et al.   DEVELOPMENT

Smchd1-Dependent and -Independent Pathways Determine Developmental Dynamics of CpG Island Methylation on the Inactive X Chromosome

(2012) Anne-Valerie Gendrel et al.   DEVELOPMENTAL CELL

Trophoblast-specific DNA methylation occurs after the segregation of the trophectoderm and inner cell mass in the mouse periimplantation embryo

(2012) Momo O. Nakanishi et al.   Epigenetics

Cfp1 integrates both CpG content and gene activity for accurate H3K4me3 deposition in embryonic stem cells

(2012) T. Clouaire et al.   GENES & DEVELOPMENT

Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites

(2012) A. Hogart et al.   GENOME RESEARCH

Global profiling of DNA methylation erasure in mouse primordial germ cells

(2012) S. Guibert 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

DNA Methylation Dynamics during In Vivo Differentiation of Blood and Skin Stem Cells

(2012) Christoph Bock et al.   MOLECULAR CELL

Tet2 Facilitates the Derepression of Myeloid Target Genes during CEBPα-Induced Transdifferentiation of Pre-B Cells

(2012) Eric M. Kallin et al.   MOLECULAR CELL

The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells

(2012) Stefanie Seisenberger et al.   MOLECULAR CELL

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

(2012) Paul A. Ginno et al.   MOLECULAR CELL

A unique regulatory phase of DNA methylation in the early mammalian embryo

(2012) Zachary D. Smith et al.   NATURE

Mouse ooplasm confers context-specific reprogramming capacity

(2012) Michelle M Chan et al.   NATURE GENETICS

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

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

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

(2012) Scott B Rothbart 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

Trim28 Is Required for Epigenetic Stability During Mouse Oocyte to Embryo Transition

(2012) D. M. Messerschmidt et al.   SCIENCE

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

(2012) M. J. Booth et al.   SCIENCE

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

(2012) Julia Arand et al.   PLoS Genetics

Contribution of Intragenic DNA Methylation in Mouse Gametic DNA Methylomes to Establish Oocyte-Specific Heritable Marks

(2012) Hisato Kobayashi et al.   PLoS Genetics

Gene Reactivation by 5-Aza-2′-Deoxycytidine–Induced Demethylation Requires SRCAP–Mediated H2A.Z Insertion to Establish Nucleosome Depleted Regions

(2012) Xiaojing Yang et al.   PLoS Genetics

Histone H1 Depletion Impairs Embryonic Stem Cell Differentiation

(2012) Yunzhe Zhang et al.   PLoS Genetics

Genome-wide promoter DNA methylation dynamics of human hematopoietic progenitor cells during differentiation and aging

(2011) M. T. Bocker et al.   BLOOD

DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation

(2011) R. Shaknovich et al.   BLOOD

Epigenetic reprogramming and development: a unique heterochromatin organization in the preimplantation mouse embryo

(2011) A. Burton et al.   Briefings in Functional Genomics

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

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

(2011) Ozlem Yildirim et al.   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

DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs

(2011) Mohammad M. Karimi et al.   Cell Stem Cell

CpG islands and the regulation of transcription

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

Cell type-specific DNA methylation at intragenic CpG islands in the immune system

(2011) A. M. Deaton 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

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

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

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 is essential for hematopoietic stem cell differentiation

(2011) Grant A Challen et al.   NATURE GENETICS

Identification of genetic elements that autonomously determine DNA methylation states

(2011) Florian Lienert et al.   NATURE GENETICS

Dynamic CpG island methylation landscape in oocytes and preimplantation embryos

(2011) Sébastien A Smallwood et al.   NATURE GENETICS

Regulation of X-chromosome inactivation by the X-inactivation centre

(2011) Sandrine Augui et al.   NATURE REVIEWS GENETICS

PIWI-interacting small RNAs: the vanguard of genome defence

(2011) Mikiko C. Siomi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A promoter DNA demethylation landscape of human hematopoietic differentiation

(2011) Vincenzo Calvanese et al.   NUCLEIC ACIDS RESEARCH

Recognition of 5-Hydroxymethylcytosine by the Uhrf1 SRA Domain

(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

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

Lysine methyltransferase G9a is required for de novo DNA methylation and the establishment, but not the maintenance, of proviral silencing

(2011) D. C. Leung 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

Global DNA Demethylation During Mouse Erythropoiesis in Vivo

(2011) J. R. Shearstone et al.   SCIENCE

Role for piRNAs and Noncoding RNA in de Novo DNA Methylation of the Imprinted Mouse Rasgrf1 Locus

(2011) T. Watanabe et al.   SCIENCE

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

(2011) A. Inoue et al.   SCIENCE

De novo DNA methylation: a germ cell perspective

(2011) Sébastien A. Smallwood et al.   TRENDS IN GENETICS

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

(2011) Mark Wossidlo et al.   Nature Communications

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

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

Leukemic IDH1 and IDH2 Mutations Result in a Hypermethylation Phenotype, Disrupt TET2 Function, and Impair Hematopoietic Differentiation

(2010) Maria E. Figueroa et al.   CANCER CELL

Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

(2010) Till Bartke et al.   CELL

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

(2010) Mark Wossidlo et al.   EMBO JOURNAL

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

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

LSH and G9a/GLP complex are required for developmentally programmed DNA methylation

(2010) K. Myant et al.   GENOME RESEARCH

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe 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

Comprehensive methylome map of lineage commitment from haematopoietic progenitors

(2010) Hong Ji et al.   NATURE

L1 retrotransposition in neurons is modulated by MeCP2

(2010) Alysson R. Muotri et al.   NATURE

A role for the elongator complex in zygotic paternal genome demethylation

(2010) Yuki Okada et al.   NATURE

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

(2010) John P. Thomson et al.   NATURE

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

(2010) Toshiyuki Matsui 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

Targets and dynamics of promoter DNA methylation during early mouse development

(2010) Julie Borgel et al.   NATURE GENETICS

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Targeting of De Novo DNA Methylation Throughout the Oct-4 Gene Regulatory Region in Differentiating Embryonic Stem Cells

(2010) Rodoniki Athanasiadou et al.   PLoS One

Dnmt3b recruitment through E2F6 transcriptional repressor mediates germ-line gene silencing in murine somatic tissues

(2010) G. Velasco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MOV10L1 is necessary for protection of spermatocytes against retrotransposons by Piwi-interacting RNAs

(2010) R. J. A. Frost et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) P. Hajkova et al.   SCIENCE

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

(2010) J. Song et al.   SCIENCE

Epigenetic Reprogramming in Plant and Animal Development

(2010) Suhua Feng et al.   SCIENCE

DNMT1 Stability Is Regulated by Proteins Coordinating Deubiquitination and Acetylation-Driven Ubiquitination

(2010) Z. Du et al.   Science Signaling

Dynamic instability of genomic methylation patterns in pluripotent stem cells

(2010) Steen KT Ooi et al.   Epigenetics & Chromatin

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

(2010) Robert S. Illingworth et al.   PLoS Genetics

CTCF-Dependent Chromatin Bias Constitutes Transient Epigenetic Memory of the Mother at the H19-Igf2 Imprinting Control Region in Prospermatogonia

(2010) Dong-Hoon Lee et al.   PLoS Genetics

Active DNA demethylation in human postmitotic cells correlates with activating histone modifications, but not transcription levels

(2010) Maja Klug et al.   GENOME BIOLOGY

DNA Methyltransferase 1 Is Essential for and Uniquely Regulates Hematopoietic Stem and Progenitor Cells

(2009) Jennifer J. Trowbridge et al.   Cell Stem Cell

Germ cell specification in mice

(2009) Mitinori Saitou   CURRENT OPINION IN GENETICS & DEVELOPMENT

The TDRD9-MIWI2 Complex Is Essential for piRNA-Mediated Retrotransposon Silencing in the Mouse Male Germline

(2009) Masanobu Shoji et al.   DEVELOPMENTAL CELL

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

(2009) Junji Otani et al.   EMBO REPORTS

DNMT3B interacts with constitutive centromere protein CENP-C to modulate DNA methylation and the histone code at centromeric regions

(2009) Suhasni Gopalakrishnan et al.   HUMAN MOLECULAR GENETICS

Histone methylation is mechanistically linked to DNA methylation at imprinting control regions in mammals

(2009) Amandine Henckel et al.   HUMAN MOLECULAR GENETICS

Distribution of p53 binding protein 1 (53BP1) and phosphorylated H2A.X during mouse preimplantation development in the absence of DNA damage

(2009) Celine Ziegler-Birling et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Embryonic stem cells use ZFP809 to silence retroviral DNAs

(2009) Daniel Wolf et al.   NATURE

DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction

(2009) Ann-Marie Bröske et al.   NATURE GENETICS

Loss of the Mili-interacting Tudor domain–containing protein-1 activates transposons and alters the Mili-associated small RNA profile

(2009) Michael Reuter et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Regulation of DNMT1 stability through SET7-mediated lysine methylation in mammalian cells

(2009) P.-O. Esteve et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) M. Tahiliani et al.   SCIENCE

Requirement of Oct3/4 function for germ cell specification

(2008) Daiji Okamura et al.   DEVELOPMENTAL BIOLOGY

A Maternal-Zygotic Effect Gene, Zfp57, Maintains Both Maternal and Paternal Imprints

(2008) Xiajun Li et al.   DEVELOPMENTAL CELL

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

(2008) Kevin B Dong 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

Maternal and zygotic Dnmt1 are necessary and sufficient for the maintenance of DNA methylation imprints during preimplantation development

(2008) R. Hirasawa et al.   GENES & DEVELOPMENT

Complex genome-wide transcription dynamics orchestrated by Blimp1 for the specification of the germ cell lineage in mice

(2008) K. Kurimoto et al.   GENES & DEVELOPMENT

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

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

A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice

(2008) Alexei A. Aravin et al.   MOLECULAR CELL

Chromatin dynamics during epigenetic reprogramming in the mouse germ line

(2008) Petra Hajkova 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

Epigenetic restriction of embryonic cell lineage fate by methylation of Elf5

(2008) Ray Kit Ng et al.   NATURE CELL BIOLOGY

The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation

(2008) Jing Wang et al.   NATURE GENETICS

PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos

(2008) Mareike Puschendorf et al.   NATURE GENETICS

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

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

MLL protects CpG clusters from methylation within the Hoxa9 gene, maintaining transcript expression

(2008) F. E. Erfurth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Mapping of DNA Methylation in Mouse Promoters Reveals Epigenetic Reprogramming of Pluripotency Genes

(2008) Cassandra R. Farthing et al.   PLoS Genetics

Antagonism between DNA and H3K27 Methylation at the Imprinted Rasgrf1 Locus

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