Developing in 3D: the role of CTCF in cell differentiation

TheHoxDcluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes

(2017) Eddie Rodríguez-Carballo et al.   GENES & DEVELOPMENT

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

(2017) Jonathan A. Beagan et al.   GENOME RESEARCH

CTCFdeletion syndrome: clinical features and epigenetic delineation

(2017) Ikumi Hori et al.   JOURNAL OF MEDICAL GENETICS

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

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

(2017) Hideharu Hashimoto et al.   MOLECULAR CELL

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl

(2017) Georg A. Busslinger et al.   NATURE

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

(2017) Lars L. P. Hanssen et al.   NATURE CELL BIOLOGY

Composition and dosage of a multipartite enhancer cluster control developmental expression of Ihh (Indian hedgehog)

(2017) Anja J Will et al.   NATURE GENETICS

CTCF genetic alterations in endometrial carcinoma are pro-tumorigenic

(2017) A D Marshall et al.   ONCOGENE

CCCTC-Binding Factor Transcriptionally Targets Wdr5 to Mediate Somatic Cell Reprogramming

(2017) Feng Wang et al.   STEM CELLS AND DEVELOPMENT

The LDB1 Complex Co-opts CTCF for Erythroid Lineage-Specific Long-Range Enhancer Interactions

(2017) Jongjoo Lee et al.   Cell Reports

CTCF counter-regulates cardiomyocyte development and maturation programs in the embryonic heart

(2017) Melisa Gomez-Velazquez et al.   PLoS Genetics

CTCF participates in DNA damage response via poly(ADP-ribosyl)ation

(2017) Deqiang Han et al.   Scientific Reports

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

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

Chromosome Compaction by Active Loop Extrusion

(2016) Anton Goloborodko et al.   BIOPHYSICAL JOURNAL

Epigenetic silencing of miR-181c by DNA methylation in glioblastoma cell lines

(2016) Erandi Ayala-Ortega et al.   BMC CANCER

CTCF-mediated chromatin loops enclose inducible gene regulatory domains

(2016) Martin Oti et al.   BMC GENOMICS

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem Cell

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

CTCF-mediated topological boundaries during development foster appropriate gene regulation

(2016) Varun Narendra et al.   GENES & DEVELOPMENT

Neurosporachromosomes are organized by blocks of importin alpha-dependent heterochromatin that are largely independent of H3K9me3

(2016) Jonathan M. Galazka et al.   GENOME RESEARCH

Sperm is epigenetically programmed to regulate gene transcription in embryos

(2016) Marta Teperek et al.   GENOME RESEARCH

Genome-wide analysis of chromatin packing inArabidopsis thalianaat single-gene resolution

(2016) Chang Liu et al.   GENOME RESEARCH

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding

(2016) Guillaume Andrey et al.   GENOME RESEARCH

DNA methylation profiling in human Huntington's disease brain

(2016) Rebecca A.G. De Souza et al.   HUMAN MOLECULAR GENETICS

CTCF-mediated Chromatin Loop for the Posterior Hoxc Gene Expression in MEF Cells

(2016) Hyehyun Min et al.   IUBMB LIFE

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

Transcriptional programs that control expression of the autoimmune regulator gene Aire

(2016) Yonatan Herzig et al.   NATURE IMMUNOLOGY

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

CTCF contributes in a critical way to spermatogenesis and male fertility

(2016) Abrahan Hernández-Hernández et al.   Scientific Reports

Neuronal CTCF Is Necessary for Basal and Experience-Dependent Gene Regulation, Memory Formation, and Genomic Structure of BDNF and Arc

(2016) Dev Sharan Sams et al.   Cell Reports

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

CTCF-Mediated and Pax6-Associated Gene Expression in Corneal Epithelial Cell-Specific Differentiation

(2016) Shanli Tsui et al.   PLoS One

A transducible nuclear/nucleolar protein, mLLP, regulates neuronal morphogenesis and synaptic transmission

(2016) Nam-Kyung Yu et al.   Scientific Reports

Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes

(2015) Jiazhi Hu et al.   CELL

A CTCF Code for 3D Genome Architecture

(2015) Michael H. Nichols et al.   CELL

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh et al.   CELL

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

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

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

Structure, function and evolution of topologically associating domains (TADs) atHOXloci

(2015) Nicolas Lonfat et al.   FEBS LETTERS

A structural hierarchy mediated by multiple nuclear factors establishesIgHlocus conformation

(2015) Tatiana Gerasimova et al.   GENES & DEVELOPMENT

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

Locus-Specific Targeting to the X Chromosome Revealed by the RNA Interactome of CTCF

(2015) Johnny T. Kung et al.   MOLECULAR CELL

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

CTCF-binding elements 1 and 2 in theIghintergenic control region cooperatively regulate V(D)J recombination

(2015) Sherry G. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

CTCF Recruits Centromeric Protein CENP-E to the Pericentromeric/Centromeric Regions of Chromosomes through Unusual CTCF-Binding Sites

(2015) Tiaojiang Xiao et al.   Cell Reports

Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality

(2015) Ian C. Welsh et al.   Cell Reports

Role of DNA Methylation in Modulating Transcription Factor Occupancy

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

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

Chromatin features and the epigenetic regulation of pluripotency states in ESCs

(2014) W.-W. Tee et al.   DEVELOPMENT

The Left-Right Pitx2 Pathway Drives Organ-Specific Arterial and Lymphatic Development in the Intestine

(2014) Aparna Mahadevan et al.   DEVELOPMENTAL CELL

CTCF regulates the human p53 gene through direct interaction with its natural antisense transcript, Wrap53

(2014) R. Saldana-Meyer et al.   GENES & DEVELOPMENT

Population and single-cell genomics reveal theAiredependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia

(2014) Stephen N. Sansom et al.   GENOME RESEARCH

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression

(2014) F. Ay et al.   GENOME RESEARCH

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

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

Functional interplay between MyoD and CTCF in regulating long-range chromatin interactions during differentiation

(2014) C. Battistelli et al.   JOURNAL OF CELL SCIENCE

Dual Effect of CTCF Loss on Neuroprogenitor Differentiation and Survival

(2014) L. A. Watson et al.   JOURNAL OF NEUROSCIENCE

Functional Interactions between NURF and Ctcf Regulate Gene Expression

(2014) Zhijun Qiu et al.   MOLECULAR AND CELLULAR BIOLOGY

Oct-1 Regulates IL-17 Expression by Directing Interchromosomal Associations in Conjunction with CTCF in T Cells

(2014) Lark Kyun Kim et al.   MOLECULAR CELL

Nodal signalling determines biradial asymmetry in Hydra

(2014) Hiroshi Watanabe et al.   NATURE

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe

(2014) Takeshi Mizuguchi et al.   NATURE

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Analysis of neonatal brain lacking ATRX or MeCP2 reveals changes in nucleosome density, CTCF binding and chromatin looping

(2014) Kristin D. Kernohan et al.   NUCLEIC ACIDS RESEARCH

CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer

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

Conservation and Divergence of Regulatory Strategies at Hox Loci and the Origin of Tetrapod Digits

(2014) Joost M. Woltering et al.   PLOS BIOLOGY

Integrated Pathway-Based Approach Identifies Association between Genomic Regions at CTCF and CACNB2 and Schizophrenia

(2014) Dilafruz Juraeva et al.   PLoS Genetics

De Novo Mutations in the Genome Organizer CTCF Cause Intellectual Disability

(2013) Anne Gregor et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Jpx RNA Activates Xist by Evicting CTCF

(2013) Sha Sun et al.   CELL

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions

(2013) A. R. Prickett et al.   GENOME RESEARCH

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers

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

Brief report: miR-290-295 regulate embryonic stem cell differentiation propensities by repressing pax6

(2013) Haggai Kaspi et al.   STEM CELLS

Signaling and Transcriptional Networks in Heart Development and Regeneration

(2013) B. G. Bruneau   Cold Spring Harbor Perspectives in Biology

A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code

(2013) Hirotaka Nakahashi et al.   Cell Reports

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Epigenetic repression of cardiac progenitor gene expression by Ezh2 is required for postnatal cardiac homeostasis

(2012) Paul Delgado-Olguín et al.   NATURE GENETICS

γ-Protocadherins Control Cortical Dendrite Arborization by Regulating the Activity of a FAK/PKC/MARCKS Signaling Pathway

(2012) Andrew M. Garrett et al.   NEURON

MyoD regulates p57 kip2 expression by interacting with a distant cis -element and modifying a higher order chromatin structure

(2012) Anna Busanello et al.   NUCLEIC ACIDS RESEARCH

Loss of Maternal CTCF Is Associated with Peri-Implantation Lethality of Ctcf Null Embryos

(2012) James M. Moore et al.   PLoS One

Functional and Molecular Characterization of the Role of CTCF in Human Embryonic Stem Cell Biology

(2012) Sri Kripa Balakrishnan et al.   PLoS One

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

(2012) Hebing Chen et al.   PLoS One

Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of Protocadherin-  gene expression

(2012) K. Monahan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTCF/cohesin-mediated DNA looping is required for protocadherin   promoter choice

(2012) Y. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The chromatin insulator CTCF and the emergence of metazoan diversity

(2012) P. Heger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTCF Is Required for Neural Development and Stochastic Expression of Clustered Pcdh Genes in Neurons

(2012) Teruyoshi Hirayama et al.   Cell Reports

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

(2011) Zhe Liu et al.   CELL

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Neuron-specific impairment of inter-chromosomal pairing and transcription in a novel model of human 15q-duplication syndrome

(2011) Makiko Meguro-Horike et al.   HUMAN MOLECULAR GENETICS

CTCF Promotes Muscle Differentiation by Modulating the Activity of Myogenic Regulatory Factors

(2011) Paul Delgado-Olguín et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Specific Sites in the C Terminus of CTCF Interact with the SA2 Subunit of the Cohesin Complex and Are Required for Cohesin-Dependent Insulation Activity

(2011) T. Xiao et al.   MOLECULAR AND CELLULAR BIOLOGY

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

CTCF-binding elements mediate control of V(D)J recombination

(2011) Chunguang Guo et al.   NATURE

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

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

CTCF Regulates Ataxin-7 Expression through Promotion of a Convergently Transcribed, Antisense Noncoding RNA

(2011) Bryce L. Sopher et al.   NEURON

Restraint of angiogenesis by zinc finger transcription factor CTCF-dependent chromatin insulation

(2011) M. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Latent Pro-Survival Function for the Mir-290-295 Cluster in Mouse Embryonic Stem Cells

(2011) Grace X. Y. Zheng et al.   PLoS Genetics

Hox genes and regional patterning of the vertebrate body plan

(2010) Moises Mallo et al.   DEVELOPMENTAL BIOLOGY

Functional Analysis of CTCF During Mammalian Limb Development

(2010) Natalia Soshnikova et al.   DEVELOPMENTAL CELL

The miR-290-295 cluster promotes pluripotency maintenance by regulating cell cycle phase distribution in mouse embryonic stem cells

(2010) Zsuzsanna Lichner et al.   DIFFERENTIATION

Gene-specific repression of the p53 target gene PUMA via intragenic CTCF-Cohesin binding

(2010) N. P. Gomes et al.   GENES & DEVELOPMENT

An insulator embedded in the chicken α-globin locus regulates chromatin domain configuration and differential gene expression

(2010) Mayra Furlan-Magaril et al.   NUCLEIC ACIDS RESEARCH

The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting

(2009) Mary E. Donohoe et al.   NATURE

Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development

(2008) L.-B. Wan et al.   DEVELOPMENT

Transcription factors CTCF and Pax6 are segregated to different cell types during retinal cell differentiation

(2008) M. Valeria Canto-Soler et al.   DEVELOPMENTAL DYNAMICS

CTCF regulates cell cycle progression of αβ T cells in the thymus

(2008) Helen Heath et al.   EMBO JOURNAL

The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions

(2008) Parimal Majumder et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The CTCF Insulator Protein Is Posttranslationally Modified by SUMO

(2008) M. J. MacPherson et al.   MOLECULAR AND CELLULAR BIOLOGY