Regulation of disease-associated gene expression in the 3D genome

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

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

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem Cell

Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming

(2016) Jonathan A. Beagan et al.   Cell Stem Cell

Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming

(2016) Peter Hugo Lodewijk Krijger et al.   Cell Stem Cell

The three-dimensional cancer genome

(2016) M Ryan Corces et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Gene regulation and chromatin organization: relevance of cohesin mutations to human disease

(2016) Erwan Watrin et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Shhand ZRS enhancer colocalisation is specific to the zone of polarising activity

(2016) Iain Williamson et al.   DEVELOPMENT

The second decade of 3C technologies: detailed insights into nuclear organization

(2016) Annette Denker et al.   GENES & DEVELOPMENT

Cause and Consequence of Tethering a SubTAD to Different Nuclear Compartments

(2016) Patrick J. Wijchers et al.   MOLECULAR CELL

Hierarchy within the mammary STAT5-driven Wap super-enhancer

(2016) Ha Youn Shin et al.   NATURE GENETICS

Genetic dissection of the α-globin super-enhancer in vivo

(2016) Deborah Hay et al.   NATURE GENETICS

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Breaking TADs: How Alterations of Chromatin Domains Result in Disease

(2016) Darío G. Lupiáñez et al.   TRENDS IN GENETICS

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq

(2015) Siddarth Selvaraj et al.   BMC GENOMICS

A Long-Distance Chromatin Affair

(2015) Annette Denker et al.   CELL

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

(2015) Fabian Grubert et al.   CELL

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak 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

Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis

(2015) Aaron D. Viny et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms

(2015) Jasper Mullenders et al.   JOURNAL OF EXPERIMENTAL MEDICINE

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

(2015) Denes Hnisz et al.   MOLECULAR CELL

Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism

(2015) Derek A. Oldridge et al.   NATURE

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano et al.   NATURE GENETICS

Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers

(2015) Xiaoyang Zhang et al.   NATURE GENETICS

CTCF/cohesin-binding sites are frequently mutated in cancer

(2015) Riku Katainen et al.   NATURE GENETICS

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Mediator complex: a central integrator of transcription

(2015) Benjamin L. Allen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

(2015) Melina Claussnitzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders

(2015) Carlos Gómez-Marín 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

Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome

(2015) Yu Gyoung Tak et al.   Epigenetics & Chromatin

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

(2015) Matteo Vietri Rudan et al.   Cell Reports

Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping

(2014) Wulan Deng et al.   CELL

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

(2014) Suhas S.P. Rao et al.   CELL

A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia

(2014) Stefan Gröschel et al.   CELL

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

(2014) Jill M. Dowen et al.   CELL

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Obesity-associated variants within FTO form long-range functional connections with IRX3

(2014) Scott Smemo et al.   NATURE

Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping

(2014) Paula J P de Vree et al.   NATURE BIOTECHNOLOGY

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

(2014) Jim R Hughes et al.   NATURE GENETICS

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis

(2014) Veli Vural Uslu et al.   NATURE GENETICS

CTCF: an architectural protein bridging genome topology and function

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

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells

(2014) Pierre Therizols et al.   SCIENCE

CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer

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

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

(2013) Kyong-Rim Kieffer-Kwon et al.   CELL

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

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

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

Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization

(2013) Matthew Denholtz et al.   Cell Stem Cell

Identical cells with different 3D genomes; cause and consequences?

(2013) Peter HL Krijger et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

An Integrated Holo-Enhancer Unit Defines Tissue and Gene Specificity of the Fgf8 Regulatory Landscape

(2013) Mirna Marinić et al.   DEVELOPMENTAL CELL

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

The pluripotent genome in three dimensions is shaped around pluripotency factors

(2013) Elzo de Wit et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms

(2013) Ayana Kon et al.   NATURE GENETICS

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Quantitative analysis of genomic element interactions by molecular colony technique

(2013) Alexey A. Gavrilov et al.   NUCLEIC ACIDS RESEARCH

GWAS3D: detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications

(2013) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Complex genomic rearrangement in theSOX95′ region in a patient with Pierre Robin sequence and hypoplastic left scapula

(2012) Maki Fukami et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor

(2012) Wulan Deng et al.   CELL

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

(2012) Guoliang Li et al.   CELL

Opposing Functions of the ETS Factor Family Define Shh Spatial Expression in Limb Buds and Underlie Polydactyly

(2012) Laura A. Lettice et al.   DEVELOPMENTAL CELL

HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter

(2012) M. Visser et al.   GENOME RESEARCH

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

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

(2012) Yin Shen et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

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

Robust 4C-seq data analysis to screen for regulatory DNA interactions

(2012) Harmen J G van de Werken et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Self-organization of domain structures by DNA-loop-extruding enzymes

(2012) E. Alipour 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

Impact of copy number variations (CNVs) on long-range gene regulation at the HoxD locus

(2012) T. Montavon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Regulation of the Probability of Mouse Odorant Receptor Gene Choice

(2011) Mona Khan et al.   CELL

Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila

(2011) Frédéric Bantignies et al.   CELL

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA

(2011) E. Splinter et al.   GENES & DEVELOPMENT

Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor

(2011) Sandra Ruf et al.   NATURE GENETICS

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Genome–nuclear lamina interactions and gene regulation

(2010) Jop Kind et al.   CURRENT OPINION IN CELL BIOLOGY

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

A cluster of three long-range enhancers directs regional Shh expression in the epithelial linings

(2009) T. Sagai et al.   DEVELOPMENT

A specific mutation in the distant sonic hedgehog (SHH)cis-regulator (ZRS) causes Werner mesomelic syndrome (WMS) while complete ZRS duplications underlie Haas type polysyndactyly and preaxial polydactyly (PPD) with or without triphalangeal thumb

(2009) Dagmar Wieczorek et al.   HUMAN MUTATION

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Inactivation of the Fto gene protects from obesity

(2009) Julia Fischer et al.   NATURE

Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence

(2009) Sabina Benko et al.   NATURE GENETICS

Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition

(2009) K. M. Lower et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms

(2008) Vania Parelho et al.   CELL

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

(2008) Helen Heath et al.   EMBO JOURNAL

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE