Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers

Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers

(2015) Michael Christoph Haffner et al.   Oncotarget

Cross species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites

(2011) Søren F Schmidt et al.   BMC GENOMICS

Mbd3/NURD Complex Regulates Expression of 5-Hydroxymethylcytosine Marked Genes in Embryonic Stem Cells

(2011) Ozlem Yildirim et al.   CELL

Tet1 and 5-hydroxymethylation

(2011) Hao Wu et al.   CELL CYCLE

DNA methylation status predicts cell type-specific enhancer activity

(2011) Malgorzata Wiench et al.   EMBO JOURNAL

Extensive chromatin remodelling and establishment of transcription factor ‘hotspots’ during early adipogenesis

(2011) Rasmus Siersbaek et al.   EMBO JOURNAL

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells

(2011) H. Wu et al.   GENES & DEVELOPMENT

Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers

(2011) A. A. Serandour et al.   GENOME RESEARCH

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

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

Genome-wide Regulation of 5hmC, 5mC, and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells

(2011) Yufei Xu et al.   MOLECULAR CELL

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams et al.   NATURE

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

(2011) William A. Pastor et al.   NATURE

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

(2011) Gabriella Ficz et al.   NATURE

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells

(2011) Hao Wu et al.   NATURE

5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging

(2011) Keith E Szulwach et al.   NATURE NEUROSCIENCE

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Forming functional fat: a growing understanding of adipocyte differentiation

(2011) Ana G. Cristancho et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CENTDIST: discovery of co-associated factors by motif distribution

(2011) Zhizhuo Zhang et al.   NUCLEIC ACIDS RESEARCH

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

Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells

(2011) Keith E. Szulwach et al.   PLoS Genetics

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells

(2011) Hume Stroud et al.   GENOME BIOLOGY

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

(2010) Aaron D. Goldberg et al.   CELL

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis

(2010) M. L. Conerly et al.   GENOME RESEARCH

Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns

(2010) J. R. Edwards et al.   GENOME RESEARCH

Proteasomal degradation of retinoid X receptor α reprograms transcriptional activity of PPARγ in obese mice and humans

(2010) Bruno Lefebvre et al.   JOURNAL OF CLINICAL INVESTIGATION

Cell-Specific Determinants of Peroxisome Proliferator-Activated Receptor   Function in Adipocytes and Macrophages

(2010) M. I. Lefterova et al.   MOLECULAR AND CELLULAR BIOLOGY

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

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

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine

(2010) Seung-Gi Jin et al.   NUCLEIC ACIDS RESEARCH

Evolution of the mammalian embryonic pluripotency gene regulatory network

(2010) B. Fernandez-Tresguerres et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

CEAS: cis-regulatory element annotation system

(2009) Hyunjin Shin et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers

(2009) J. Eeckhoute et al.   GENOME RESEARCH

Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity

(2009) C. Schmidl et al.   GENOME RESEARCH

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)

(2009) Paul G. Giresi et al.   METHODS

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

(2009) Chunyuan Jin et al.   NATURE GENETICS

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Genome-wide profiling of PPAR :RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis

(2008) R. Nielsen et al.   GENES & DEVELOPMENT

EsrrbActivatesOct4Transcription and Sustains Self-renewal and Pluripotency in Embryonic Stem Cells

(2008) Xiaofei Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY