Tissue-specific epigenetics in gene neighborhoods: myogenic transcription factor genes

Chitinase-3-like protein 1 protects skeletal muscle from TNFα-induced inflammation and insulin resistance

(2014) Sven W. Görgens et al.   BIOCHEMICAL JOURNAL

Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model

(2014) Robin Andersson   BIOESSAYS

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

Long Noncoding RNAs in Cell-Fate Programming and Reprogramming

(2014) Ryan A. Flynn et al.   Cell Stem Cell

Notch signaling genes

(2014) Jolyon Terragni et al.   Epigenetics

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer

(2014) Phillippa C. Taberlay et al.   GENOME RESEARCH

DNA methylation analysis of human myoblasts during in vitro myogenic differentiation: de novo methylation of promoters of muscle-related genes and its involvement in transcriptional down-regulation

(2014) Kohei Miyata et al.   HUMAN MOLECULAR GENETICS

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

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

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Dissecting the dynamic changes of 5-hydroxymethylcytosine in T-cell development and differentiation

(2014) A. Tsagaratou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Uncoupling Transcription from Covalent Histone Modification

(2014) Hesheng Zhang et al.   PLoS Genetics

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

(2014) Lu Wen et al.   GENOME BIOLOGY

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

(2013) Kyong-Rim Kieffer-Kwon et al.   CELL

Direct molecular regulation of the myogenic determination gene Myf5 by Pax3, with modulation by Six1/4 factors, is exemplified by the −111kb-Myf5 enhancer

(2013) Philippe Daubas et al.   DEVELOPMENTAL BIOLOGY

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

(2013) Koji Tsumagari et al.   Epigenetics

Dial M(RF) for myogenesis

(2013) Natalia Moncaut et al.   FEBS Journal

Dynamic DNA methylation across diverse human cell lines and tissues

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

eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

(2013) Kambiz Mousavi et al.   MOLECULAR CELL

Chromatin and epigenetic features of long-range gene regulation

(2013) N. Harmston et al.   NUCLEIC ACIDS RESEARCH

Six1 Regulates MyoD Expression in Adult Muscle Progenitor Cells

(2013) Yubing Liu et al.   PLoS One

DNA methylation and differentiation: HOX genes in muscle cells

(2013) Koji Tsumagari et al.   Epigenetics & Chromatin

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

(2012) Jolyon Terragni et al.   BIOCHEMISTRY

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

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

Transcriptional Dominance of Pax7 in Adult Myogenesis Is Due to High-Affinity Recognition of Homeodomain Motifs

(2012) Vahab D. Soleimani et al.   DEVELOPMENTAL CELL

Genome-wide identification of enhancers in skeletal muscle: the role of MyoD1

(2012) R. Blum et al.   GENES & DEVELOPMENT

Coding exons function as tissue-specific enhancers of nearby genes

(2012) Ramon Y. Birnbaum et al.   GENOME RESEARCH

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Endothelial PI3K-C2α, a class II PI3K, has an essential role in angiogenesis and vascular barrier function

(2012) Kazuaki Yoshioka et al.   NATURE MEDICINE

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

(2012) Cole Trapnell et al.   Nature Protocols

Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome

(2012) Hebing Chen et al.   PLoS One

Lysine methyltransferase G9a methylates the transcription factor MyoD and regulates skeletal muscle differentiation

(2012) B. M. T. Ling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene expression during normal and FSHD myogenesis

(2011) Koji Tsumagari et al.   BMC Medical Genomics

H3K4 tri-methylation provides an epigenetic signature of active enhancers

(2011) Aleksandra Pekowska et al.   EMBO JOURNAL

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

(2011) Jason Ernst et al.   NATURE

Genome-wide remodeling of the epigenetic landscape during myogenic differentiation

(2011) P. Asp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011)   PLOS BIOLOGY

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

(2010) Andrea Fuso et al.   CELL CYCLE

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

(2010) Yi Cao et al.   DEVELOPMENTAL CELL

Regulation of gene expression in vertebrate skeletal muscle

(2010) Jaime J. Carvajal et al.   EXPERIMENTAL CELL RESEARCH

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

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA

(2010) Aleksandra Szwagierczak et al.   NUCLEIC ACIDS RESEARCH

MyoD- and nerve-dependent maintenance of MyoD expression in mature muscle fibres acts through the DRR/PRR element

(2008) Sophie B Charge et al.   BMC DEVELOPMENTAL BIOLOGY

Global transcriptional regulation of the locus encoding the skeletal muscle determination genes Mrf4 and Myf5

(2008) J. J. Carvajal et al.   GENES & DEVELOPMENT

A highly conserved molecular switch binds MSY-3 to regulate myogenin repression in postnatal muscle

(2008) L. Berghella et al.   GENES & DEVELOPMENT

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE