On the existence and functionality of topologically associating domains

Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations

(2019) Katerina Kraft et al.   NATURE CELL BIOLOGY

Visualizing DNA folding and RNA in embryos at single-cell resolution

(2019) Leslie J. Mateo et al.   NATURE

Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs

(2019) Magdalena Laugsch et al.   Cell Stem Cell

The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist

(2019) Joke G. van Bemmel et al.   NATURE GENETICS

Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity

(2019) Jeffrey M Alexander et al.   eLife

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

Functional dissection of the Sox9–Kcnj2 locus identifies nonessential and instructive roles of TAD architecture

(2019) Alexandra Despang et al.   NATURE GENETICS

LADL: light-activated dynamic looping for endogenous gene expression control

(2019) Ji Hun Kim et al.   NATURE METHODS

Preformed chromatin topology assists transcriptional robustness of Shh during limb development

(2019) Christina Paliou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Developmentally regulated Shh expression is robust to TAD perturbations

(2019) Iain Williamson et al.   DEVELOPMENT

Differential contribution of steady‐state RNA and active transcription in chromatin organization

(2019) A Rasim Barutcu et al.   EMBO REPORTS

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

(2019) Yanxiao Zhang et al.   NATURE GENETICS

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

Detecting hierarchical genome folding with network modularity

(2018) Heidi K Norton et al.   NATURE METHODS

Real-time imaging of DNA loop extrusion by condensin

(2018) Mahipal Ganji et al.   SCIENCE

Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries

(2018) James H. Sun et al.   CELL

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation

(2018) Sergi Cuartero et al.   NATURE IMMUNOLOGY

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

(2018) Bogdan Bintu et al.   SCIENCE

Crossed wires: 3D genome misfolding in human disease

(2017) Heidi K. Norton et al.   JOURNAL OF CELL BIOLOGY

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

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

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

(2017) Douglas H. Phanstiel et al.   MOLECULAR CELL

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map

(2017) Kyle P. Eagen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The condensin complex is a mechanochemical motor that translocates along DNA

(2017) Tsuyoshi Terakawa et al.   SCIENCE

Chromosome Compaction by Active Loop Extrusion

(2016) Anton Goloborodko et al.   BIOPHYSICAL JOURNAL

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

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

Rapid movement and transcriptional re‐localization of human cohesin on DNA

(2016) Iain F Davidson et al.   EMBO JOURNAL

Cohesin acetylation and Wapl‐Pds5 oppositely regulate translocation of cohesin along DNA

(2016) Mai Kanke et al.   EMBO JOURNAL

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Single-Molecule Imaging Reveals a Collapsed Conformational State for DNA-Bound Cohesin

(2016) Johannes Stigler et al.   Cell Reports

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

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

(2015) Zhonghui Tang 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

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

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

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

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

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

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

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

(2013) Takashi Nagano et al.   NATURE

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

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

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

(2012) E. Alipour et al.   NUCLEIC ACIDS RESEARCH

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

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

Cohesins localize with CTCF at the KSHV latency control region and at cellular c-myc and H19/Igf2 insulators

(2008) William Stedman et al.   EMBO JOURNAL

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE

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