Epigenetics of Modified DNA Bases: 5-Methylcytosine and Beyond

FACT complex is required for DNA demethylation at heterochromatin during reproduction inArabidopsis

(2018) Jennifer M. Frost et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Active N6-Methyladenine Demethylation by DMAD Regulates Gene Expression by Coordinating with Polycomb Protein in Neurons

(2018) Bing Yao et al.   MOLECULAR CELL

Dynamics of 5-carboxylcytosine during hepatic differentiation: Potential general role for active demethylation by DNA repair in lineage specification

(2017) Lara C. Lewis et al.   Epigenetics

Oxidized C5-methyl cytosine bases in DNA: 5-Hydroxymethylcytosine; 5-formylcytosine; and 5-carboxycytosine

(2017) Arne Klungland et al.   FREE RADICAL BIOLOGY AND MEDICINE

Live-cell analysis of DNA methylation during sexual reproduction inArabidopsisreveals context and sex-specific dynamics controlled by noncanonical RdDM

(2017) Mathieu Ingouff et al.   GENES & DEVELOPMENT

Epigenetics: History, present status and future perspective

(2017) Suresh Kumar et al.   INDIAN JOURNAL OF GENETICS AND PLANT BREEDING

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Exploiting induced and natural epigenetic variation for crop improvement

(2017) Nathan M. Springer et al.   NATURE REVIEWS GENETICS

Active DNA demethylation: mechanism and role in plant development

(2017) Yan Li et al.   PLANT CELL REPORTS

Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit

(2017) Zhaobo Lang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA N6-methyladenine is dynamically regulated in the mouse brain following environmental stress

(2017) Bing Yao et al.   Nature Communications

N6-methyladenine is an epigenetic marker of mammalian early life stress

(2017) Stacey L. Kigar et al.   Scientific Reports

Single-molecule quantification of 5-hydroxymethylcytosine for diagnosis of blood and colon cancers

(2017) Noa Gilat et al.   Clinical Epigenetics

Physiological, Biochemical, Epigenetic and Molecular Analyses of Wheat (Triticum aestivum) Genotypes with Contrasting Salt Tolerance

(2017) Suresh Kumar et al.   Frontiers in Plant Science

New Insights into 5hmC DNA Modification: Generation, Distribution and Function

(2017) Dong-Qiao Shi et al.   Frontiers in Genetics

Control of Foxp3 stability through modulation of TET activity

(2016) Xiaojing Yue et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

(2016) Jessica Charlet et al.   MOLECULAR CELL

Epigenetic modulators, modifiers and mediators in cancer aetiology and progression

(2016) Andrew P. Feinberg et al.   NATURE REVIEWS GENETICS

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function

(2016) Katherine E. Sloan et al.   RNA Biology

The cytosolic Fe-S cluster assembly component MET18 is required for the full enzymatic activity of ROS1 in active DNA demethylation

(2016) Xiaokang Wang et al.   Scientific Reports

DNA Methylation and Chromatin Regulation during Fleshy Fruit Development and Ripening

(2016) Philippe Gallusci et al.   Frontiers in Plant Science

A CRISPR-based approach for targeted DNA demethylation

(2016) Xingxing Xu et al.   Cell Discovery

Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification

(2015) Lakshminarayan M. Iyer et al.   BIOESSAYS

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

(2015) Jesse G. Zalatan et al.   CELL

DNA Methylation on N6-Adenine in C. elegans

(2015) Eric Lieberman Greer et al.   CELL

N6-Methyladenine DNA Modification in Drosophila

(2015) Guoqiang Zhang et al.   CELL

N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas

(2015) Ye Fu et al.   CELL

Functional coupling between writers, erasers and readers of histone and DNA methylation

(2015) Idelisse Ortiz Torres et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Making Sense of Optogenetics

(2015) Akash Guru et al.   INTERNATIONAL JOURNAL OF NEUROPSYCHOPHARMACOLOGY

Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes

(2015) Xi-liang Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2015) Tuncay Baubec et al.   NATURE

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

Transcriptional ‘memory’ of a stress: transient chromatin and memory (epigenetic) marks at stress-response genes

(2015) Zoya Avramova   PLANT JOURNAL

Epigenetic regulatory functions of DNA modifications: 5-methylcytosine and beyond

(2015) Achim Breiling et al.   Epigenetics & Chromatin

Determination of DNA adenine methylation in genomes of mammals and plants by liquid chromatography/mass spectrometry

(2015) Wei Huang et al.   RSC Advances

Loss of Tet Enzymes Compromises Proper Differentiation of Embryonic Stem Cells

(2014) Meelad M. Dawlaty et al.   DEVELOPMENTAL CELL

Role of Tet proteins in enhancer activity and telomere elongation

(2014) Falong Lu 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

Effects of Tet-induced oxidation products of 5-methylcytosine on Dnmt1- and DNMT3a-mediated cytosine methylation

(2014) Debin Ji et al.   Molecular BioSystems

Structural Basis for Hydroxymethylcytosine Recognition by the SRA Domain of UHRF2

(2014) Ting Zhou et al.   MOLECULAR CELL

Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA

(2014) Toni Pfaffeneder et al.   Nature Chemical Biology

5-Hydroxymethylcytosine is a predominantly stable DNA modification

(2014) Martin Bachman et al.   Nature Chemistry

DNA methylation: old dog, new tricks?

(2014) Cornelia G Spruijt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Epigenetic Regulation in Plants

(2014) C. S. Pikaard et al.   Cold Spring Harbor Perspectives in Biology

Transient Accumulation of 5-Carboxylcytosine Indicates Involvement of Active Demethylation in Lineage Specification of Neural Stem Cells

(2014) Lee M. Wheldon et al.   Cell Reports

5-Hydroxymethylcytosine Is Not Present in Appreciable Quantities in Arabidopsis DNA

(2014) Robert M. Erdmann et al.   G3-Genes Genomes Genetics

The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin

(2013) Assaf Zemach et al.   CELL

Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming

(2013) Chun-Xiao Song et al.   CELL

Combined Deficiency of Tet1 and Tet2 Causes Epigenetic Abnormalities but Is Compatible with Postnatal Development

(2013) Meelad M. Dawlaty et al.   DEVELOPMENTAL CELL

On how mammalian transcription factors recognize methylated DNA

(2013) Bethany A. Buck-Koehntop et al.   Epigenetics

The Intertwined Roles of Transcription and Repair Proteins

(2013) Yick W. Fong et al.   MOLECULAR CELL

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

(2013) William A. Pastor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA

(2013) Ye Fu et al.   Nature Communications

Dynamics of 5-Hydroxymethylcytosine and Chromatin Marks in Mammalian Neurogenesis

(2013) Maria A. Hahn et al.   Cell Reports

Biochemical Characterization of Recombinant β-Glucosyltransferase and Analysis of Global 5-Hydroxymethylcytosine in Unique Genomes

(2012) Jolyon Terragni et al.   BIOCHEMISTRY

Epigenetics

(2012) James R. Tollervey et al.   Epigenetics

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

(2012) J. I. Gent et al.   GENOME RESEARCH

5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary

(2012) Tarang Khare et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase

(2012) Eun-Ang Raiber et al.   GENOME BIOLOGY

Epigenetic control of gene regulation in plants

(2011) Massimiliano Lauria et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Deletion of Tet2 in mice leads to dysregulated hematopoietic stem cells and subsequent development of myeloid malignancies

(2011) Z. Li et al.   BLOOD

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

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

Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation

(2011) H. Wu et al.   GENES & DEVELOPMENT

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

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

The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes

(2011) Tian-Peng Gu et al.   NATURE

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

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

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification

(2010) Shinsuke Ito et al.   NATURE

Single base–resolution methylome of the silkworm reveals a sparse epigenomic map

(2010) Hui Xiang et al.   NATURE BIOTECHNOLOGY

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

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

Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates

(2010) Daniel Globisch et al.   PLoS One

Active DNA Demethylation Mediated by DNA Glycosylases

(2009) Jian-Kang Zhu   Annual Review of Genetics

Epigenetic regulation of stress responses in plants

(2009) Viswanathan Chinnusamy et al.   CURRENT OPINION IN PLANT BIOLOGY

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

(2009) M. Tahiliani et al.   SCIENCE

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE

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

(2009) S. Kriaucionis et al.   SCIENCE

Human AlkB Homolog 1 Is a Mitochondrial Protein That Demethylates 3-Methylcytosine in DNA and RNA

(2008) Marianne Pedersen Westbye et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE