Association of 5-hydroxymethylation and 5-methylation of DNA cytosine with tissue-specific gene expression

Hydroxymethylation is uniquely distributed within term placenta, and is associated with gene expression

(2016) Benjamin B. Green et al.   FASEB JOURNAL

Role of TET enzymes in DNA methylation, development, and cancer

(2016) Kasper Dindler Rasmussen et al.   GENES & DEVELOPMENT

Tumour hypoxia causes DNA hypermethylation by reducing TET activity

(2016) Bernard Thienpont et al.   NATURE

Systematic identification of protein combinations mediating chromatin looping

(2016) Kai Zhang et al.   Nature Communications

The Influence of Hydroxylation on Maintaining CpG Methylation Patterns: A Hidden Markov Model Approach

(2016) Pascal Giehr et al.   PLoS Computational Biology

DNA Methylation in Skeletal Muscle Stem Cell Specification, Proliferation, and Differentiation

(2016) Rhianna C. Laker et al.   Stem Cells International

Heterozygous deletion of α-neurexin I or α-neurexin II results in behaviors relevant to autism and schizophrenia.

(2015) James Dachtler et al.   BEHAVIORAL NEUROSCIENCE

Characterizing 5-hydroxymethylcytosine in human prefrontal cortex at single base resolution

(2015) Jeffrey A. Gross et al.   BMC GENOMICS

Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer

(2015) Ke Chen et al.   CELL RESEARCH

The interplay of histone modifications - writers that read

(2015) T. Zhang et al.   EMBO REPORTS

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

(2015) Sruti Chandra et al.   HUMAN MOLECULAR GENETICS

Modulation of satellite cells activity and MyoD in rat thyroarytenoid muscle after reinnervation

(2015) Haruka Kodama et al.   LARYNGOSCOPE

Tet1 and Tet2 Protect DNA Methylation Canyons against Hypermethylation

(2015) Laura Wiehle et al.   MOLECULAR AND CELLULAR BIOLOGY

Bhlhe40 Represses PGC-1α Activity on Metabolic Gene Promoters in Myogenic Cells

(2015) Shih Ying Chung et al.   MOLECULAR AND CELLULAR BIOLOGY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Inter-individual variability contrasts with regional homogeneity in the human brain DNA methylome

(2015) Robert S. Illingworth et al.   NUCLEIC ACIDS RESEARCH

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

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The alternative role of DNA methylation in splicing regulation

(2015) Galit Lev Maor et al.   TRENDS IN GENETICS

DNA demethylation by 5-aza-2′-deoxycytidine is imprinted, targeted to euchromatin, and has limited transcriptional consequences

(2015) María-Paz Ramos et al.   Epigenetics & Chromatin

TET3 Is Recruited by REST for Context-Specific Hydroxymethylation and Induction of Gene Expression

(2015) Arshan Perera et al.   Cell Reports

On the presence and role of human gene-body DNA methylation

(2015) Daudi Jjingo et al.   Oncotarget

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

Redox Regulation by Pitx2 and Pitx3 Is Critical for Fetal Myogenesis

(2014) Aurore L’honoré et al.   DEVELOPMENTAL CELL

An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training

(2014) Maléne E Lindholm et al.   Epigenetics

Notch signaling genes

(2014) Jolyon Terragni et al.   Epigenetics

Greater organ involution in highly proliferative tissues associated with the early onset and acceleration of ageing in humans

(2014) Richard B. Richardson et al.   EXPERIMENTAL GERONTOLOGY

Pitx2 and Pitx3 transcription factors: two key regulators of the redox state in adult skeletal muscle stem cells and muscle regeneration

(2014) Aurore L'honoré et al.   FREE RADICAL BIOLOGY AND MEDICINE

New themes in the biological functions of 5-methylcytosine and 5-hydroxymethylcytosine

(2014) Erika L. Moen et al.   IMMUNOLOGICAL REVIEWS

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

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

TET1 is a maintenance DNA demethylase that prevents methylation spreading in differentiated cells

(2014) C. Jin et al.   NUCLEIC ACIDS RESEARCH

Architectural proteins CTCF and cohesin have distinct roles in modulating the higher order structure and expression of the CFTR locus

(2014) N. Gosalia 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

DNA cytosine methylation and hydroxymethylation at the borders

(2014) Melanie Ehrlich et al.   Epigenomics

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

(2014) Lu Wen et al.   GENOME BIOLOGY

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

(2013) Cornelia G. Spruijt et al.   CELL

Pitx genes are redeployed in adult myogenesis where they can act to promote myogenic differentiation in muscle satellite cells

(2013) Paul Knopp et al.   DEVELOPMENTAL BIOLOGY

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

Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription

(2013) Sílvia Carvalho et al.   NUCLEIC ACIDS RESEARCH

IL1RAPL1 Associated with Mental Retardation and Autism Regulates the Formation and Stabilization of Glutamatergic Synapses of Cortical Neurons through RhoA Signaling Pathway

(2013) Takashi Hayashi et al.   PLoS One

A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics

(2013) Qiang Song et al.   PLoS One

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Modeling, simulation and analysis of methylation profiles from reduced representation bisulfite sequencing experiments

(2013) Michelle R. Lacey et al.   Statistical Applications in Genetics and Molecular Biology

DNA methylation and differentiation: HOX genes in muscle cells

(2013) Koji Tsumagari et al.   Epigenetics & Chromatin

Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells

(2013) Francesco Neri et al.   GENOME BIOLOGY

Cadherins and neuropsychiatric disorders

(2012) Christoph Redies et al.   BRAIN RESEARCH

Diametrically opposite methylome-transcriptome relationships in high- and low-CpG promoter genes in postmitotic neural rat tissue

(2012) Theresa Hartung et al.   Epigenetics

Protection against De Novo Methylation Is Instrumental in Maintaining Parent-of-Origin Methylation Inherited from the Gametes

(2012) Charlotte Proudhon et al.   MOLECULAR CELL

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

(2012) J. Wang et al.   NUCLEIC ACIDS RESEARCH

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

(2012) M. J. Booth et al.   SCIENCE

The NIH Roadmap Epigenomics Program data resource

(2012) Lisa Helbling Chadwick   Epigenomics

Cell type-specific DNA methylation at intragenic CpG islands in the immune system

(2011) A. M. Deaton et al.   GENOME RESEARCH

Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes

(2011) C. E. Nestor et al.   GENOME RESEARCH

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

(2011) L. Song et al.   GENOME RESEARCH

O2 Regulates Skeletal Muscle Progenitor Differentiation through Phosphatidylinositol 3-Kinase/AKT Signaling

(2011) A. J. Majmundar et al.   MOLECULAR AND CELLULAR BIOLOGY

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

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

(2011)   PLOS BIOLOGY

Myogenic regulatory factors regulate M-cadherin expression by targeting its proximal promoter elements

(2010) Sheng Pin Hsiao et al.   BIOCHEMICAL JOURNAL

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

(2010) Yi Cao et al.   DEVELOPMENTAL CELL

Conserved role of intragenic DNA methylation in regulating alternative promoters

(2010) Alika K. Maunakea et al.   NATURE

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

(2010) Daniel Globisch et al.   PLoS One

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

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

(2009) S. Kriaucionis et al.   SCIENCE

Identification of a Novel Pool of Extracellular Pro-myostatin in Skeletal Muscle

(2008) Sarah B. Anderson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE