Enhancer DNA methylation: implications for gene regulation

Extensive Recovery of Embryonic Enhancer and Gene Memory Stored in Hypomethylated Enhancer DNA

(2019) Unmesh Jadhav et al.   MOLECULAR CELL

Retention of paternal DNA methylome in the developing zebrafish germline

(2019) Ksenia Skvortsova et al.   Nature Communications

EGR1 recruits TET1 to shape the brain methylome during development and upon neuronal activity

(2019) Zhixiong Sun et al.   Nature Communications

A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs

(2018) Christian Pflueger et al.   GENOME RESEARCH

Postnatal DNA demethylation and its role in tissue maturation

(2018) Yitzhak Reizel et al.   Nature Communications

FBXL19 recruits CDK-Mediator to CpG islands of developmental genes priming them for activation during lineage commitment

(2018) Emilia Dimitrova et al.   eLife

DNA methylation reprogramming of functional elements during mammalian embryonic development

(2018) Congru Li et al.   Cell Discovery

Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate

(2018) Jose Luis Sardina et al.   Cell Stem Cell

Amphioxus functional genomics and the origins of vertebrate gene regulation

(2018) Ferdinand Marlétaz et al.   NATURE

Functions and mechanisms of epigenetic inheritance in animals

(2018) Ksenia Skvortsova et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Orphan CpG islands define a novel class of highly active enhancers

(2017) Joshua S. K. Bell et al.   Epigenetics

Intragenic DNA methylation prevents spurious transcription initiation

(2017) Francesco Neri et al.   NATURE

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

(2017) Yimeng Yin et al.   SCIENCE

A screening system to identify transcription factors that induce binding site-directed DNA demethylation

(2017) Takahiro Suzuki et al.   Epigenetics & Chromatin

The SET1 Complex Selects Actively Transcribed Target Genes via Multivalent Interaction with CpG Island Chromatin

(2017) David A. Brown et al.   Cell Reports

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

(2016) Jessica Charlet et al.   MOLECULAR CELL

Isoform Switch of TET1 Regulates DNA Demethylation and Mouse Development

(2016) Wenhao Zhang et al.   MOLECULAR CELL

TET-mediated DNA demethylation controls gastrulation by regulating Lefty–Nodal signalling

(2016) Hai-Qiang Dai et al.   NATURE

Active DNA demethylation at enhancers during the vertebrate phylotypic period

(2016) Ozren Bogdanović et al.   NATURE GENETICS

Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility

(2016) Chan-Wang Lio et al.   eLife

Tex10 Coordinates Epigenetic Control of Super-Enhancer Activity in Pluripotency and Reprogramming

(2015) Junjun Ding et al.   Cell Stem Cell

FBXL10 protects Polycomb-bound genes from hypermethylation

(2015) Mathieu Boulard et al.   NATURE GENETICS

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

(2014) Sergei Khrapunov et al.   BIOCHEMISTRY

Hydroxymethylation of DNA influences nucleosomal conformation and stability in vitro

(2014) Agnes Mendonca et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Reprogramming the Methylome: Erasing Memory and Creating Diversity

(2014) Heather J. Lee et al.   Cell Stem Cell

5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation

(2014) Gary C. Hon et al.   MOLECULAR CELL

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Synthetic CpG islands reveal DNA sequence determinants of chromatin structure

(2014) Elisabeth Wachter et al.   eLife

High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions

(2014) Arnaud R Krebs et al.   eLife

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

TET enzymes, TDG and the dynamics of DNA demethylation

(2013) Rahul M. Kohli et al.   NATURE

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

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

(2013) Gary C Hon et al.   NATURE GENETICS

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

UHRF1 targets DNMT1 for DNA methylation through cooperative binding of hemi-methylated DNA and methylated H3K9

(2013) Xiaoli Liu et al.   Nature Communications

Transcription Factor Occupancy Can Mediate Active Turnover of DNA Methylation at Regulatory Regions

(2013) Angelika Feldmann et al.   PLoS Genetics

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

(2013) Hannah K Long et al.   eLife

Genome-wide and Caste-Specific DNA Methylomes of the Ants Camponotus floridanus and Harpegnathos saltator

(2012) Roberto Bonasio et al.   CURRENT BIOLOGY

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis

(2012) O. Bogdanovic et al.   GENOME RESEARCH

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation

(2012) Hideharu Hashimoto et al.   NUCLEIC ACIDS RESEARCH

DNA methylation status predicts cell type-specific enhancer activity

(2011) Malgorzata Wiench et al.   EMBO JOURNAL

CpG island chromatin

(2011) Neil P. Blackledge et al.   Epigenetics

CpG islands and the regulation of transcription

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

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

(2011) Michael B. Stadler et al.   NATURE

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

(2011) Hao Wu et al.   NATURE

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

(2011) Michael J. Ziller 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

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

(2010) John P. Thomson et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Targets and dynamics of promoter DNA methylation during early mouse development

(2010) Julie Borgel et al.   NATURE GENETICS

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

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

Lessons from comparative analysis of X-chromosome inactivation in mammals

(2009) Ikuhiro Okamoto et al.   CHROMOSOME RESEARCH

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

X Chromosome Dosage Compensation: How Mammals Keep the Balance

(2008) Bernhard Payer et al.   Annual Review of Genetics

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

(2008) Fabio Mohn et al.   MOLECULAR CELL