A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation

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

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

Cell-Specific Dysregulation of MicroRNA Expression in Obese White Adipose Tissue

(2014) Frédérik Oger et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

(2014) Jim R Hughes et al.   NATURE GENETICS

PPARγ and the global map of adipogenesis and beyond

(2014) Martina I. Lefterova et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Transcriptional and epigenetic regulation of PPARγ expression during adipogenesis

(2014) Ji-Eun Lee et al.   Cell and Bioscience

CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer

(2014) Christopher J. Kemp et al.   Cell Reports

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes

(2014) Petra C Schwalie et al.   GENOME BIOLOGY

Cross-enhancement of ANGPTL4 transcription by HIF1 alpha and PPAR beta/delta is the result of the conformational proximity of two response elements

(2014) Tsuyoshi Inoue et al.   GENOME BIOLOGY

Understanding the variegation of fat: Novel regulators of adipocyte differentiation and fat tissue biology

(2013) Elisabetta Mueller   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

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

(2013) Cornelia G. Spruijt et al.   CELL

The DNA-binding factor Ctcf critically controls gene expression in macrophages

(2013) Tatjana Nikolic et al.   Cellular & Molecular Immunology

Cohesin-mediated interactions organize chromosomal domain architecture

(2013) Sevil Sofueva et al.   EMBO JOURNAL

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

(2013) V. C. Seitan et al.   GENOME RESEARCH

Peroxisome Proliferator-activated Receptor γ Regulates Genes Involved in Insulin/Insulin-like Growth Factor Signaling and Lipid Metabolism during Adipogenesis through Functionally Distinct Enhancer Classes

(2013) Frédérik Oger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Simultaneously Learning DNA Motif Along with Its Position and Sequence Rank Preferences Through Expectation Maximization Algorithm

(2013) ZhiZhuo Zhang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Farnesoid X Receptor Inhibits the Transcriptional Activity of Carbohydrate Response Element Binding Protein in Human Hepatocytes

(2013) S. Caron et al.   MOLECULAR AND CELLULAR BIOLOGY

Distinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites

(2013) Jason Gertz et al.   MOLECULAR CELL

Acute Genome-Wide Effects of Rosiglitazone on PPARγ Transcriptional Networks in Adipocytes

(2013) Anders Kristian Haakonsson et al.   MOLECULAR ENDOCRINOLOGY

Effect of natural genetic variation on enhancer selection and function

(2013) S. Heinz et al.   NATURE

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

(2013) William A. Pastor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1

(2013) Thu-Hang Pham et al.   NUCLEIC ACIDS RESEARCH

A quality control system for profiles obtained by ChIP sequencing

(2013) Marco-Antonio Mendoza-Parra et al.   NUCLEIC ACIDS RESEARCH

Lipoatrophy and severe metabolic disturbance in mice with fat-specific deletion of PPAR 

(2013) F. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alteration of genic 5-hydroxymethylcytosine patterning in olfactory neurons correlates with changes in gene expression and cell identity

(2013) Bradley M. Colquitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

(2013) J. Zuin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PPARγ-induced PARylation promotes local DNA demethylation by production of 5-hydroxymethylcytosine

(2013) Katsunori Fujiki et al.   Nature Communications

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

(2013) Angelika Feldmann et al.   PLoS Genetics

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

Adipogenesis: From Stem Cell to Adipocyte

(2012) Qi Qun Tang et al.   Annual Review of Biochemistry

MeCP2 Binds to 5hmC Enriched within Active Genes and Accessible Chromatin in the Nervous System

(2012) Marian Mellén et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

CTCF: insights into insulator function during development

(2012) M. Herold et al.   DEVELOPMENT

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

Genome-wide Studies of CCCTC-binding Factor (CTCF) and Cohesin Provide Insight into Chromatin Structure and Regulation: FIGURE 1.

(2012) Bum-Kyu Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-Wide Profiling of Peroxisome Proliferator-Activated Receptor   in Primary Epididymal, Inguinal, and Brown Adipocytes Reveals Depot-Selective Binding Correlated with Gene Expression

(2012) M. S. Siersbaek et al.   MOLECULAR AND CELLULAR BIOLOGY

Integrative Genomics Identifies the Corepressor SMRT as a Gatekeeper of Adipogenesis through the Transcription Factors C/EBPβ and KAISO

(2012) Sunil K. Raghav et al.   MOLECULAR CELL

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

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

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

Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers

(2012) Aurélien A. Sérandour et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Hebing Chen et al.   PLoS One

Coordinated Regulation of PPAR Expression and Activity through Control of Chromatin Structure in Adipogenesis and Obesity

(2012) Jérôme Eeckhoute et al.   PPAR Research

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

CTCF function is modulated by neighboring DNA binding factors

(2011) Oliver Weth et al.   Biochemistry and Cell Biology

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions

(2011) Joseph K. Pickrell et al.   BIOINFORMATICS

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

(2011) Ozlem Yildirim et al.   CELL

Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3

(2011) Zhe Liu et al.   CELL

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

(2011) Rasmus Siersbaek et al.   EMBO JOURNAL

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

(2011) B.-K. Lee et al.   GENOME RESEARCH

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

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

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

(2011) Yufei Xu et al.   MOLECULAR CELL

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

(2011) Hao Wu et al.   NATURE

Forming functional fat: a growing understanding of adipocyte differentiation

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

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes

(2011) David Martin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CENTDIST: discovery of co-associated factors by motif distribution

(2011) Zhizhuo Zhang et al.   NUCLEIC ACIDS RESEARCH

Transcriptional networks and chromatin remodeling controlling adipogenesis

(2011) Rasmus Siersbæk et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation

(2011) Hironori Waki et al.   PLoS Genetics

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

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

Propagation of adipogenic signals through an epigenomic transition state

(2010) D. J. Steger et al.   GENES & DEVELOPMENT

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

ENCODE whole-genome data in the UCSC genome browser (2011 update)

(2010) Brian J. Raney et al.   NUCLEIC ACIDS RESEARCH

A Quantitative Model of Transcriptional Regulation Reveals the Influence of Binding Location on Expression

(2010) Kenzie D. MacIsaac et al.   PLoS Computational Biology

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

CTCF and its protein partners: divide and rule?

(2009) J. Zlatanova et al.   JOURNAL OF CELL SCIENCE

The Peroxisome Proliferator-Activated Receptor  /Retinoid X Receptor   Heterodimer Targets the Histone Modification Enzyme PR-Set7/Setd8 Gene and Regulates Adipogenesis through a Positive Feedback Loop

(2009) K.-i. Wakabayashi et al.   MOLECULAR AND CELLULAR BIOLOGY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

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

(2009) Da Wei Huang et al.   Nature Protocols

CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features

(2009) Kobby Essien et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

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

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

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

(2008) Yutao Fu et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY