Gene regulation during development in the light of topologically associating domains

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

(2015) Darío G. Lupiáñez et al.   CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

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

(2015) Borbala Mifsud et al.   NATURE GENETICS

The contribution of cohesin-SA1 to gene expression and chromatin architecture in two murine tissues

(2015) Ana Cuadrado et al.   NUCLEIC ACIDS RESEARCH

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

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

(2015) Matteo Vietri Rudan et al.   Cell Reports

A Discrete Transition Zone Organizes the Topological and Regulatory Autonomy of the Adjacent Tfap2c and Bmp7 Genes

(2015) Taro Tsujimura et al.   PLoS Genetics

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti et al.   CELL

3D Trajectories Adopted by Coding and Regulatory DNA Elements: First-Passage Times for Genomic Interactions

(2014) Joseph S. Lucas et al.   CELL

Enhancer Interaction Networks as a Means for Singular Olfactory Receptor Expression

(2014) Eirene Markenscoff-Papadimitriou 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

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

(2014) Jill M. Dowen et al.   CELL

The architecture of gene expression: integrating dispersed cis-regulatory modules into coherent regulatory domains

(2014) Wibke Schwarzer et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Development of five digits is controlled by a bipartite long-range cis-regulator

(2014) L. A. Lettice et al.   DEVELOPMENT

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

(2014) Iain Williamson et al.   GENES & DEVELOPMENT

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

(2014) François Le Dily et al.   GENES & DEVELOPMENT

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila

(2014) Stefan Grob et al.   MOLECULAR CELL

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

(2014) Muhammad A. Zabidi et al.   NATURE

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Enhancer loops appear stable during development and are associated with paused polymerase

(2014) Yad Ghavi-Helm et al.   NATURE

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

(2014) Evgeny Z. Kvon et al.   NATURE

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

(2014) Takeshi Mizuguchi et al.   NATURE

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

(2014) Jim R Hughes et al.   NATURE GENETICS

CTCF: an architectural protein bridging genome topology and function

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

Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci

(2014) N. Lonfat et al.   SCIENCE

In search of the determinants of enhancer–promoter interaction specificity

(2014) Joris van Arensbergen et al.   TRENDS IN CELL BIOLOGY

Disruption of Autoregulatory Feedback by a Mutation in a Remote, Ultraconserved PAX6 Enhancer Causes Aniridia

(2013) Shipra Bhatia et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?

(2013) Elphège P. Nora et al.   BIOESSAYS

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

Developmentally Regulated Subnuclear Genome Reorganization Restricts Neural Progenitor Competence in Drosophila

(2013) Minoree Kohwi et al.   CELL

A High-Resolution Enhancer Atlas of the Developing Telencephalon

(2013) Axel Visel et al.   CELL

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

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

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

CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets

(2013) Matthias Merkenschlager 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

Transcription Factories: Genome Organization and Gene Regulation

(2013) Argyris Papantonis et al.   CHEMICAL REVIEWS

Large-scale chromatin organization: the good, the surprising, and the still perplexing

(2013) Andrew S Belmont   CURRENT OPINION IN CELL BIOLOGY

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

(2013) Mirna Marinić et al.   DEVELOPMENTAL CELL

Cohesin-mediated interactions organize chromosomal domain architecture

(2013) Sevil Sofueva et al.   EMBO JOURNAL

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

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

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

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

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

(2013) Fulai Jin et al.   NATURE

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

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

(2013) Catherine Naughton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Functional implications of genome topology

(2013) Giacomo Cavalli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes

(2013) Fabrizio Benedetti et al.   NUCLEIC ACIDS RESEARCH

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

(2013) C. A. Brackley 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

Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers

(2013) C. Attanasio et al.   SCIENCE

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

(2013) G. Andrey et al.   SCIENCE

Multiple Enhancers Regulate Hoxd Genes and the Hotdog LncRNA during Cecum Budding

(2013) Saskia Delpretti et al.   Cell Reports

Clustering of Tissue-Specific Sub-TADs Accompanies the Regulation of HoxA Genes in Developing Limbs

(2013) Soizik Berlivet et al.   PLoS Genetics

Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture

(2013) Stefan Grob et al.   GENOME BIOLOGY

DNA Sequence-Dependent Compartmentalization and Silencing of Chromatin at the Nuclear Lamina

(2012) Joseph M. Zullo et al.   CELL

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

(2012) Wulan Deng et al.   CELL

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

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

(2012) Guoliang Li et al.   CELL

Higher-order chromatin structure: bridging physics and biology

(2012) Geoffrey Fudenberg et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Insulators, long-range interactions, and genome function

(2012) Jingping Yang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

3C-based technologies to study the shape of the genome

(2012) Wouter de Laat et al.   METHODS

Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation

(2012) Erik Splinter et al.   METHODS

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

(2012) Chunhui Hou et al.   MOLECULAR CELL

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

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

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(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

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

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

Complexity of chromatin folding is captured by the strings and binders switch model

(2012) M. Barbieri 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

Shadow enhancers: Frequently asked questions about distributed cis-regulatory information and enhancer redundancy

(2011) Scott Barolo   BIOESSAYS

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements

(2011) O. Hakim et al.   GENOME RESEARCH

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Variegated gene expression caused by cell-specific long-range DNA interactions

(2011) Daan Noordermeer et al.   NATURE CELL BIOLOGY

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

(2011) Sandra Ruf et al.   NATURE GENETICS

DNaseI Hypersensitivity and Ultraconservation Reveal Novel, Interdependent Long-Range Enhancers at the Complex Pax6 Cis-Regulatory Region

(2011) David J. McBride et al.   PLoS One

CCCTC-binding factor (CTCF) and cohesin influence the genomic architecture of the Igh locus and antisense transcription in pro-B cells

(2011) S. C. Degner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Cell type specificity of chromatin organization mediated by CTCF and cohesin

(2010) Chunhui Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cohesin: Its Roles and Mechanisms

(2009) Kim Nasmyth et al.   Annual Review of Genetics

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

(2009) T. Sagai et al.   DEVELOPMENT

Long-range regulation at the SOX9 locus in development and disease

(2009) C T Gordon et al.   JOURNAL OF MEDICAL GENETICS

Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus

(2009) Suzana Hadjur et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

A transposon-based chromosomal engineering method to survey a large cis-regulatory landscape in mice

(2009) Chikara Kokubu et al.   NATURE GENETICS

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

(2009) Sabina Benko et al.   NATURE GENETICS

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

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

Multiple modular promoter elements drive graded brinker expression in response to the Dpp morphogen gradient

(2008) L.-C. Yao et al.   DEVELOPMENT

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE

Transcriptional repression mediated by repositioning of genes to the nuclear lamina

(2008) K. L. Reddy et al.   NATURE

Ripples from neighbouring transcription

(2008) Miki Ebisuya et al.   NATURE CELL BIOLOGY

Maintenance of Long-Range DNA Interactions after Inhibition of Ongoing RNA Polymerase II Transcription

(2008) Robert-Jan Palstra et al.   PLoS One

CTCF physically links cohesin to chromatin

(2008) E. D. Rubio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping

(2008) Vijay K Tiwari et al.   PLOS BIOLOGY

Recruitment to the Nuclear Periphery Can Alter Expression of Genes in Human Cells

(2008) Lee E. Finlan et al.   PLoS Genetics