Selective modulation of local linkages between active transcription and oxidative demethylation activity shapes cardiomyocyte-specific gene-body epigenetic status in mice

RNA Pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction

(2017) Nova Fong et al.   MOLECULAR CELL

Dnmt3a and Dnmt3b Associate with Enhancers to Regulate Human Epidermal Stem Cell Homeostasis

(2016) Lorenzo Rinaldi et al.   Cell Stem Cell

Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs

(2016) David Juan et al.   Cell Reports

Invasive Cell Fate Requires G1 Cell-Cycle Arrest and Histone Deacetylase-Mediated Changes in Gene Expression

(2015) David Q. Matus et al.   DEVELOPMENTAL CELL

Dynamic changes in the cardiac methylome during postnatal development

(2015) Choon Boon Sim et al.   FASEB JOURNAL

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

(2015) Tuncay Baubec et al.   NATURE

Repression of the Central Splicing Regulator RBFox2 Is Functionally Linked to Pressure Overload-Induced Heart Failure

(2015) Chaoliang Wei et al.   Cell Reports

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs

(2014) Long Jin et al.   BMC GENOMICS

BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones

(2014) Tomohiko Kanno et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation

(2014) Julie Dubois-Chevalier et al.   NUCLEIC ACIDS RESEARCH

Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease

(2014) Ralf Gilsbach et al.   Nature Communications

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

Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain

(2014) Lu Wen et al.   GENOME BIOLOGY

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

(2013) Chun-Xiao Song et al.   CELL

Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives

(2013) Cornelia G. Spruijt et al.   CELL

BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure

(2013) Priti Anand et al.   CELL

TET enzymes, TDG and the dynamics of DNA demethylation

(2013) Rahul M. Kohli et al.   NATURE

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Dynamics of 5-Hydroxymethylcytosine and Chromatin Marks in Mammalian Neurogenesis

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

MeCP2 Binds to 5hmC Enriched within Active Genes and Accessible Chromatin in the Nervous System

(2012) Marian Mellén et al.   CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome

(2011) M. Suzuki et al.   GENOME RESEARCH

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

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

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

Transient Regenerative Potential of the Neonatal Mouse Heart

(2011) E. R. Porrello et al.   SCIENCE

Quantification of the Sixth DNA Base Hydroxymethylcytosine in the Brain

(2010) Martin Münzel et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

(2010) Shinsuke Ito et al.   NATURE

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine

(2010) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

Cardiac Deletion of Smyd2 Is Dispensable for Mouse Heart Development

(2010) Florian Diehl et al.   PLoS One

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

(2010) Daniel Globisch et al.   PLoS One

Optimized design and data analysis of tag-based cytosine methylation assays

(2010) Masako Suzuki et al.   GENOME BIOLOGY

Cardiac Fibroblasts Regulate Myocardial Proliferation through β1 Integrin Signaling

(2009) Masaki Ieda et al.   DEVELOPMENTAL CELL

Nongenetic method for purifying stem cell–derived cardiomyocytes

(2009) Fumiyuki Hattori et al.   NATURE METHODS

The Colorful History of Active DNA Demethylation

(2008) Steen K.T. Ooi et al.   CELL

DNA methylation landscapes: provocative insights from epigenomics

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