DNA methylation and differentiation: silencing, upregulation and modulation of gene expression

The role of genetics in the establishment and maintenance of the epigenome

(2013) Covadonga Huidobro et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

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

(2013) Koji Tsumagari et al.   Epigenetics

Dynamic DNA methylation across diverse human cell lines and tissues

(2013) K. E. Varley et al.   GENOME RESEARCH

DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure

(2013) S. Gelfman et al.   GENOME RESEARCH

Developmentally Programmed 3′ CpG Island Methylation Confers Tissue- and Cell-Type-Specific Transcriptional Activation

(2013) Da-Hai Yu et al.   MOLECULAR AND CELLULAR BIOLOGY

Dissecting complex epigenetic alterations in human lupus

(2013) Dipak R Patel et al.   ARTHRITIS RESEARCH & THERAPY

DNA methylation and differentiation: HOX genes in muscle cells

(2013) Koji Tsumagari et al.   Epigenetics & Chromatin

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

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

Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values

(2012) B. S. Pedersen et al.   BIOINFORMATICS

Epigenetic features are significantly associated with alternative splicing

(2012) Yuanpeng Zhou et al.   BMC GENOMICS

H2A.Z Facilitates Access of Active and Repressive Complexes to Chromatin in Embryonic Stem Cell Self-Renewal and Differentiation

(2012) Gangqing Hu et al.   Cell Stem Cell

Turning on Myogenin in Muscle: A Paradigm for Understanding Mechanisms of Tissue-Specific Gene Expression

(2012) Herve Faralli et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

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

(2012) Subreena Simrick et al.   DEVELOPMENTAL DYNAMICS

PGE2 inducesinterleukin-8derepression in human astrocytoma through coordinated DNA demethylation and histone hyperacetylation

(2012) Isabella Venza et al.   Epigenetics

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human cerebellum

(2012) Tao Wang et al.   HUMAN MOLECULAR GENETICS

XPG and XPF Endonucleases Trigger Chromatin Looping and DNA Demethylation for Accurate Expression of Activated Genes

(2012) Nicolas Le May et al.   MOLECULAR CELL

CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization

(2012) Jesse D. Ziebarth et al.   NUCLEIC ACIDS RESEARCH

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

DNA methylation restricts spontaneous multi-lineage differentiation of mesenchymal progenitor cells, but is stable during growth factor-induced terminal differentiation

(2011) Marlinda Hupkes et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Gene expression during normal and FSHD myogenesis

(2011) Koji Tsumagari et al.   BMC Medical Genomics

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

(2011) Junjie U. Guo et al.   CELL

DNA Demethylation Dynamics

(2011) Nidhi Bhutani et al.   CELL

The methyl-CpG-binding protein CIBZ suppresses myogenic differentiation by directly inhibiting myogenin expression

(2011) Yu Oikawa et al.   CELL RESEARCH

Human Epigenome Data Reveal Increased CpG Methylation in Alternatively Spliced Sites and Putative Exonic Splicing Enhancers

(2011) Christina Anastasiadou et al.   DNA AND CELL BIOLOGY

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

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

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

(2011) Takayuki Isagawa et al.   PLoS One

Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences

(2011) Y. Tao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nicotine induced CpG methylation of Pax6 binding motif in StAR promoter reduces the gene expression and cortisol production

(2011) Tingting Wang et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Regulation of skeletal muscle stem cells through epigenetic mechanisms

(2011) Pedro Sousa-Victor et al.   TOXICOLOGY MECHANISMS AND METHODS

Extensive epigenetic reprogramming in human somatic tissues between fetus and adult

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

Genome-wide MyoD Binding in Skeletal Muscle Cells: A Potential for Broad Cellular Reprogramming

(2010) Yi Cao et al.   DEVELOPMENTAL CELL

Epigenetic regulation of vertebrateHoxgenes: A dynamic equilibrium

(2010) Natalia Soshnikova et al.   Epigenetics

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

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

Domain-Specific Response of Imprinted Genes to Reduced DNMT1

(2010) J. R. Weaver et al.   MOLECULAR AND CELLULAR BIOLOGY

Interplay between DNA Methylation and Transcription Factor Availability: Implications for Developmental Activation of the Mouse Myogenin Gene

(2010) D. Palacios et al.   MOLECULAR AND CELLULAR BIOLOGY

Conserved role of intragenic DNA methylation in regulating alternative promoters

(2010) Alika K. Maunakea et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Lsh Mediated RNA Polymerase II Stalling at HoxC6 and HoxC8 Involves DNA Methylation

(2010) Yongguang Tao et al.   PLoS One

CpG methylation of half-CRE sequences creates C/EBP  binding sites that activate some tissue-specific genes

(2010) V. Rishi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell type specificity of chromatin organization mediated by CTCF and cohesin

(2010) Chunhui Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effect of 5-Azacytidine: Evidence for Alteration of the Multipotent Ability of Mesenchymal Stem Cells

(2010) Ana-Maria Rosca et al.   STEM CELLS AND DEVELOPMENT

Finding distal regulatory elements in the human genome

(2009) Nathaniel D Heintzman et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

A human B cell methylome at 100−base pair resolution

(2009) Tibor A. Rauch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) S. Kriaucionis et al.   SCIENCE

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

(2008) Fabio Mohn et al.   MOLECULAR CELL

A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci

(2008) Robert Illingworth et al.   PLOS BIOLOGY

Global Mapping of DNA Methylation in Mouse Promoters Reveals Epigenetic Reprogramming of Pluripotency Genes

(2008) Cassandra R. Farthing et al.   PLoS Genetics