DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries

Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells

(2018) Ioanna Pavlaki et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Pluripotency factors functionally premark cell-type-restricted enhancers in ES cells

(2018) Hong Sook Kim et al.   NATURE

DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts

(2018) Marco Catoni et al.   NUCLEIC ACIDS RESEARCH

Nascent DNA methylome mapping reveals inheritance of hemimethylation at CTCF/cohesin sites

(2018) Chenhuan Xu et al.   SCIENCE

Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver

(2018) Bryan J Matthews et al.   eLife

Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance

(2018) Anastasiya Kazachenka et al.   CELL

5-Formylcytosine organizes nucleosomes and forms Schiff base interactions with histones in mouse embryonic stem cells

(2018) Eun-Ang Raiber et al.   Nature Chemistry

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA

(2017) Hideharu Hashimoto et al.   MOLECULAR CELL

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

(2017) Jaime Abraham Castro-Mondragon et al.   NUCLEIC ACIDS RESEARCH

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

(2016) Matthias Merkenschlager et al.   Annual Review of Genomics and Human Genetics

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(2016) Pablo D Dans et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Transcription factors as readers and effectors of DNA methylation

(2016) Heng Zhu et al.   NATURE REVIEWS GENETICS

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability

(2016) Thuy T. M. Ngo et al.   Nature Communications

TET-catalyzed oxidation of intragenic 5-methylcytosine regulates CTCF-dependent alternative splicing

(2015) R. J. Marina et al.   EMBO JOURNAL

Tet1 and Tet2 Protect DNA Methylation Canyons against Hypermethylation

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

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke et al.   NATURE

Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale

(2015) Bo Xia et al.   NATURE METHODS

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Role of DNA Methylation in Modulating Transcription Factor Occupancy

(2015) Matthew T. Maurano et al.   Cell Reports

Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development

(2014) Vladimir B. Teif et al.   GENOME RESEARCH

5-Formylcytosine alters the structure of the DNA double helix

(2014) Eun-Ang Raiber et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Regulation of the Nucleosome Repeat Length In Vivo by the DNA Sequence, Protein Concentrations and Long-Range Interactions

(2014) Daria A. Beshnova et al.   PLoS Computational Biology

Genome-wide Analysis Reveals TET- and TDG-Dependent 5-Methylcytosine Oxidation Dynamics

(2013) Li Shen et al.   CELL

Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming

(2013) Chun-Xiao Song et al.   CELL

Combined Deficiency of Tet1 and Tet2 Causes Epigenetic Abnormalities but Is Compatible with Postnatal Development

(2013) Meelad M. Dawlaty et al.   DEVELOPMENTAL CELL

Large conserved domains of low DNA methylation maintained by Dnmt3a

(2013) Mira Jeong et al.   NATURE GENETICS

CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation

(2013) R. N. Plasschaert et al.   NUCLEIC ACIDS RESEARCH

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

Transcription Factor Occupancy Can Mediate Active Turnover of DNA Methylation at Regulatory Regions

(2013) Angelika Feldmann et al.   PLoS Genetics

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

(2012) Miao Yu et al.   CELL

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

Deletion of Tet2 in mice leads to dysregulated hematopoietic stem cells and subsequent development of myeloid malignancies

(2011) Z. Li et al.   BLOOD

Tet1 and Tet2 Regulate 5-Hydroxymethylcytosine Production and Cell Lineage Specification in Mouse Embryonic Stem Cells

(2011) Kian Peng Koh et al.   Cell Stem Cell

DNA-binding factors shape the mouse methylome at distal regulatory regions

(2011) Michael B. Stadler et al.   NATURE

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams et al.   NATURE

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

(2010) Yun Huang et al.   PLoS One

The PluriNetWork: An Electronic Representation of the Network Underlying Pluripotency in Mouse, and Its Applications

(2010) Anup Som et al.   PLoS One

VEZF1 Elements Mediate Protection from DNA Methylation

(2010) Jacqueline Dickson et al.   PLoS Genetics

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

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

Sequencing of natural strains of Arabidopsis thaliana with short reads

(2008) S. Ossowski et al.   GENOME RESEARCH

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

(2008) S. Cuddapah et al.   GENOME RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY