Early de novo DNA methylation and prolonged demethylation in the muscle lineage

DNA Methylation Plasticity of Human Adipose-Derived Stem Cells in Lineage Commitment

(2012) María Berdasco et al.   AMERICAN JOURNAL OF PATHOLOGY

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

(2012) Jolyon Terragni et al.   BIOCHEMISTRY

Acute Exercise Remodels Promoter Methylation in Human Skeletal Muscle

(2012) Romain Barrès et al.   Cell Metabolism

Sim2 prevents entry into the myogenic program by repressing MyoD transcription during limb embryonic myogenesis

(2012) E. Havis et al.   DEVELOPMENT

Biallelic expression of Tbx1 protects the embryo from developmental defects caused by increased receptor tyrosine kinase signaling

(2012) Subreena Simrick et al.   DEVELOPMENTAL DYNAMICS

Chromatin and epigenetic regulation of pre-mRNA processing

(2012) S. J. Brown et al.   HUMAN MOLECULAR GENETICS

Tbx1 is a negative modulator of Mef2c

(2012) Luna Simona Pane et al.   HUMAN MOLECULAR GENETICS

Deciphering transcription dysregulation in FSH muscular dystrophy

(2012) Melanie Ehrlich et al.   JOURNAL OF HUMAN GENETICS

Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA

(2012) Liang Zhang et al.   Nature Chemical Biology

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Understanding the language of Lys36 methylation at histone H3

(2012) Eric J. Wagner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation

(2012) Hideharu Hashimoto et al.   NUCLEIC ACIDS RESEARCH

Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers

(2012) Aurélien A. Sérandour et al.   NUCLEIC ACIDS RESEARCH

AID Enzymatic Activity Is Inversely Proportional to the Size of Cytosine C5 Orbital Cloud

(2012) Gopinath Rangam et al.   PLoS One

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

(2012) M. J. Booth et al.   SCIENCE

Parallel mechanisms of epigenetic reprogramming in the germline

(2012) Jamie A. Hackett et al.   TRENDS IN GENETICS

Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster

(2012) Michael T. Bocker et al.   Nature Communications

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

(2012) Yoichiro Shibata et al.   PLoS Genetics

Differential PAX3 functions in normal skin melanocytes and melanoma cells

(2011) Sandra Medic et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Detecting 22q11.2 deletion in Chinese children with conotruncal heart defects and single nucleotide polymorphisms in the haploid TBX1 locus

(2011) Yue-Juan Xu et al.   BMC Medical Genetics

Gene expression during normal and FSHD myogenesis

(2011) Koji Tsumagari et al.   BMC Medical Genomics

5-Hydroxymethylcytosine Is Strongly Depleted in Human Cancers but Its Levels Do Not Correlate with IDH1 Mutations

(2011) S.-G. Jin et al.   CANCER RESEARCH

Mechanisms of T-box gene function in the developing heart

(2011) F. Greulich et al.   CARDIOVASCULAR RESEARCH

Thymine DNA Glycosylase Is Essential for Active DNA Demethylation by Linked Deamination-Base Excision Repair

(2011) Salvatore Cortellino et al.   CELL

Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain

(2011) Junjie U. Guo et al.   CELL

Emerging roles of TET proteins and 5-hydroxymethylcytosines in active DNA demethylation and beyond

(2011) Junjie U. Guo et al.   CELL CYCLE

H3K4 tri-methylation provides an epigenetic signature of active enhancers

(2011) Aleksandra Pekowska et al.   EMBO JOURNAL

Epigenetics: DNA demethylation promotes skeletal myotube maturation

(2011) Marlinda Hupkes et al.   FASEB JOURNAL

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation

(2011) Allison M. Cotton et al.   HUMAN GENETICS

Regulation of Synapse Structure and Function by Distinct Myosin II Motors

(2011) M. D. Rubio et al.   JOURNAL OF NEUROSCIENCE

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

(2011) Gabriella Ficz et al.   NATURE

Genomic mapping of 5-hydroxymethylcytosine in the human brain

(2011) Seung-Gi Jin et al.   NUCLEIC ACIDS RESEARCH

Elevated miR-499 Levels Blunt the Cardiac Stress Response

(2011) Joseph T. C. Shieh et al.   PLoS One

DNA Methylation Profiling of Embryonic Stem Cell Differentiation into the Three Germ Layers

(2011) Takayuki Isagawa et al.   PLoS One

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

Extensive epigenetic reprogramming in human somatic tissues between fetus and adult

(2011) Ryan KC Yuen et al.   Epigenetics & Chromatin

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Analysis of DNA Methylation in a Three-Generation Family Reveals Widespread Genetic Influence on Epigenetic Regulation

(2011) Jason Gertz et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The embryonic genes Dkk3, Hoxd8, Hoxd9 and Tbx1 identify muscle types in a diet-independent and fiber-type unrelated way

(2010) Janneke de Wilde et al.   BMC GENOMICS

Early demethylation of non-CpG, CpC-rich, elements in the myogenin 5’-flanking region

(2010) Andrea Fuso et al.   CELL CYCLE

Muscle stem cells in developmental and regenerative myogenesis

(2010) Jong-Sun Kang et al.   CURRENT OPINION IN CLINICAL NUTRITION AND METABOLIC CARE

Distinct enhancers at the Pax3 locus can function redundantly to regulate neural tube and neural crest expressions

(2010) Karl R. Degenhardt et al.   DEVELOPMENTAL BIOLOGY

Bmp Signaling Regulates Myocardial Differentiation from Cardiac Progenitors Through a MicroRNA-Mediated Mechanism

(2010) Jun Wang et al.   DEVELOPMENTAL CELL

Manipulation of endogenous regulatory elements and transgenic analyses of the Tbx1 gene

(2010) Zhen Zhang et al.   MAMMALIAN GENOME

Uncoupling of Expression of an Intronic MicroRNA and Its Myosin Host Gene by Exon Skipping

(2010) M. L. Bell et al.   MOLECULAR AND CELLULAR BIOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2010) Daniel Globisch et al.   PLoS One

CpG island clusters and pro-epigenetic selection for CpGs in protein-coding exons of HOX and other transcription factors

(2010) S. Branciamore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular coupling of DNA methylation and histone methylation

(2010) Hideharu Hashimoto et al.   Epigenomics

CCCTC-binding factor: to loop or to bridge

(2009) J. Zlatanova et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

A Family of microRNAs Encoded by Myosin Genes Governs Myosin Expression and Muscle Performance

(2009) Eva van Rooij et al.   DEVELOPMENTAL CELL

Muscle Giants: Molecular Scaffolds in Sarcomerogenesis

(2009) Aikaterini Kontrogianni-Konstantopoulos et al.   PHYSIOLOGICAL REVIEWS

Integrated Functions of Pax3 and Pax7 in the Regulation of Proliferation, Cell Size and Myogenic Differentiation

(2009) Charlotte A. Collins et al.   PLoS One

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

(2009) S. Kriaucionis et al.   SCIENCE

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources

(2009) Chunlei Wu et al.   GENOME BIOLOGY

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

DNA methylation profiling of pseudogene–parental gene pairs and two gene families

(2008) Rene Cortese et al.   GENOMICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Characterization of Ayu17-449 gene expression and resultant kidney pathology in a knockout mouse model

(2008) Hua Tang et al.   TRANSGENIC RESEARCH