DNA methylation: a historical perspective

Two competing mechanisms of DNMT3A recruitment regulate the dynamics of de novo DNA methylation at PRC1-targeted CpG islands

(2021) Daniel N. Weinberg et al.   NATURE GENETICS

QSER1 protects DNA methylation valleys from de novo methylation

(2021) Gary Dixon et al.   SCIENCE

DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation

(2021) Wendan Ren et al.   Nature Communications

BANP opens chromatin and activates CpG-island-regulated genes

(2021) Ralph S. Grand et al.   NATURE

Dnmt1 has de novo activity targeted to transposable elements

(2021) Chuck Haggerty et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineages

(2021) Daniel Andergassen et al.   DEVELOPMENTAL CELL

Interplay between chromatin marks in development and disease

(2021) Sanne M. Janssen et al.   NATURE REVIEWS GENETICS

A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity

(2020) Paul Adrian Ginno et al.   Nature Communications

Active turnover of genomic methylcytosine in pluripotent cells

(2020) Fabio Spada et al.   Nature Chemical Biology

Imprecise DNMT1 activity coupled with neighbor-guided correction enables robust yet flexible epigenetic inheritance

(2020) Qiujun Wang et al.   NATURE GENETICS

TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers

(2020) Jocelyn Charlton et al.   NATURE GENETICS

Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation

(2020) Wendan Ren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing

(2020) Kenjiro Shirane et al.   NATURE GENETICS

Active turnover of DNA methylation during cell fate decisions

(2020) Aled Parry et al.   NATURE REVIEWS GENETICS

SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development

(2019) Qianhua Xu et al.   NATURE GENETICS

The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape

(2019) Daniel N. Weinberg et al.   NATURE

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

DNA methylation loss in late-replicating domains is linked to mitotic cell division

(2018) Wanding Zhou et al.   NATURE GENETICS

Genetic determinants and epigenetic effects of pioneer-factor occupancy

(2018) Julie Donaghey et al.   NATURE GENETICS

Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding

(2018) Satyanarayan Rao et al.   Epigenetics & Chromatin

Genome-wide tracking of dCas9-methyltransferase footprints

(2018) Christina Galonska et al.   Nature Communications

BAH domains and a histone-like motif in DNA methyltransferase 1 (DNMT1) regulate de novo and maintenance methylation in vivo

(2018) Olya Yarychkivska et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Stella safeguards the oocyte methylome by preventing de novo methylation mediated by DNMT1

(2018) Yingfeng Li et al.   NATURE

The discovery and importance of genomic imprinting

(2018) Anne C Ferguson-Smith et al.   eLife

Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer

(2017) Zachary D. Smith et al.   NATURE

Intragenic DNA methylation prevents spurious transcription initiation

(2017) Francesco Neri et al.   NATURE

Maternal H3K27me3 controls DNA methylation-independent imprinting

(2017) Azusa Inoue et al.   NATURE

The DNA methyltransferase family: a versatile toolkit for epigenetic regulation

(2017) Frank Lyko   NATURE REVIEWS GENETICS

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes

(2017) Judith F. Kribelbauer et al.   Cell Reports

Methylated cis-regulatory elements mediate KLF4-dependent gene transactivation and cell migration

(2017) Jun Wan et al.   eLife

Editing DNA Methylation in the Mammalian Genome

(2016) X. Shawn Liu et al.   CELL

Targeted DNA demethylation in vivo using dCas9–peptide repeat and scFv–TET1 catalytic domain fusions

(2016) Sumiyo Morita et al.   NATURE BIOTECHNOLOGY

Editing the epigenome: technologies for programmable transcription and epigenetic modulation

(2016) Pratiksha I Thakore et al.   NATURE METHODS

Allosteric control of mammalian DNA methyltransferases – a new regulatory paradigm

(2016) Albert Jeltsch et al.   NUCLEIC ACIDS RESEARCH

The DNA methyltransferase DNMT3C protects male germ cells from transposon activity

(2016) Joan Barau et al.   SCIENCE

Epigenetic Determinants of Cancer

(2016) Stephen B. Baylin et al.   Cold Spring Harbor Perspectives in Biology

Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition

(2016) Jian Fang et al.   Nature Communications

Engineering of a Histone-Recognition Domain in Dnmt3a Alters the Epigenetic Landscape and Phenotypic Features of Mouse ESCs

(2015) Kyung-Min Noh et al.   MOLECULAR CELL

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke et al.   NATURE

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

(2015) Tuncay Baubec et al.   NATURE

DNA methylation pathways and their crosstalk with histone methylation

(2015) Jiamu Du et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

DNA methylation dynamics of the human preimplantation embryo

(2014) Zachary D. Smith et al.   NATURE

Structural insight into autoinhibition and histone H3-induced activation of DNMT3A

(2014) Xue Guo et al.   NATURE

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and Disease

(2013) Jeannie T. Lee et al.   CELL

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Large conserved domains of low DNA methylation maintained by Dnmt3a

(2013) Mira Jeong et al.   NATURE GENETICS

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

Base-Resolution Analyses of Sequence and Parent-of-Origin Dependent DNA Methylation in the Mouse Genome

(2012) Wei Xie et al.   CELL

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

(2012) Zachary D. Smith et al.   NATURE

Rate of de novo mutations and the importance of father’s age to disease risk

(2012) Augustine Kong 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

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

The Replication Focus Targeting Sequence (RFTS) Domain Is a DNA-competitive Inhibitor of Dnmt1

(2011) Farisa Syeda et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

DNA-binding factors shape the mouse methylome at distal regulatory regions

(2011) Michael B. Stadler et al.   NATURE

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

Dynamic CpG island methylation landscape in oocytes and preimplantation embryos

(2011) Sébastien A Smallwood et al.   NATURE GENETICS

Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1)

(2011) K. Takeshita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome

(2011) A. Colaneri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Dnmt3a PWWP Domain Reads Histone 3 Lysine 36 Trimethylation and Guides DNA Methylation

(2010) Arunkumar Dhayalan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Targets and dynamics of promoter DNA methylation during early mouse development

(2010) Julie Borgel et al.   NATURE GENETICS

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

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

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

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Rethinking how DNA methylation patterns are maintained

(2009) Peter A. Jones et al.   NATURE REVIEWS GENETICS

Identification of a region of the DNMT1 methyltransferase that regulates the maintenance of genomic imprints

(2009) E. Borowczyk 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

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

(2009) S. Kriaucionis et al.   SCIENCE

The Colorful History of Active DNA Demethylation

(2008) Steen K.T. Ooi et al.   CELL

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

(2008) Ryan Lister et al.   CELL

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

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

DNA methylation landscapes: provocative insights from epigenomics

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