To loop or not to loop: what is the role of TADs in enhancer function and gene regulation?

Visualizing the Role of Boundary Elements in Enhancer-Promoter Communication

(2020) Moe Yokoshi et al.   MOLECULAR CELL

On the existence and functionality of topologically associating domains

(2020) Jonathan A. Beagan et al.   NATURE GENETICS

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

(2020) Kadir C. Akdemir et al.   NATURE GENETICS

In situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila

(2020) Rodrigo G. Arzate-Mejía et al.   Nature Communications

A Dynamic Folded Hairpin Conformation Is Associated with α-Globin Activation in Erythroid Cells

(2020) Andrea M. Chiariello et al.   Cell Reports

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

(2020) Tsung-Han S. Hsieh et al.   MOLECULAR CELL

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

The emergence of genome architecture and zygotic genome activation

(2020) Antoine Vallot et al.   CURRENT OPINION IN CELL BIOLOGY

CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response

(2020) Grégoire Stik et al.   NATURE GENETICS

Regulation of single-cell genome organization into TADs and chromatin nanodomains

(2020) Quentin Szabo et al.   NATURE GENETICS

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

(2019) Elizabeth H. Finn et al.   CELL

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

Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping

(2019) Judith Hyle et al.   NUCLEIC ACIDS RESEARCH

Principles of genome folding into topologically associating domains

(2019) Quentin Szabo et al.   Science Advances

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

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

Large distances separate coregulated genes in living Drosophila embryos

(2019) Tyler Heist et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete reconstitution of bypass and blocking functions in a minimal artificial Fab-7 insulator from Drosophila bithorax complex

(2019) Olga Kyrchanova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multi-enhancer transcriptional hubs confer phenotypic robustness

(2019) Albert Tsai et al.   eLife

Developmentally regulated Shh expression is robust to TAD perturbations

(2019) Iain Williamson et al.   DEVELOPMENT

Enhancer Priming Enables Fast and Sustained Transcriptional Responses to Notch Signaling

(2019) Julia Falo-Sanjuan et al.   DEVELOPMENTAL CELL

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

(2019) Nezha S. Benabdallah et al.   MOLECULAR CELL

The Role of Insulation in Patterning Gene Expression

(2019) Özdemir et al.   Genes

TADs as the Caller Calls Them

(2019) Elzo de Wit   JOURNAL OF MOLECULAR BIOLOGY

Chromatin structure dynamics during the mitosis-to-G1 phase transition

(2019) Haoyue Zhang et al.   NATURE

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Human cohesin compacts DNA by loop extrusion

(2019) Yoori Kim et al.   SCIENCE

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

(2018) Sofia A. Quinodoz et al.   CELL

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

The Insulator Protein CTCF Is Required for CorrectHoxGene Expression, but Not for Embryonic Development inDrosophila

(2018) Maria Cristina Gambetta et al.   GENETICS

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Enhancer hubs and loop collisions identified from single-allele topologies

(2018) Amin Allahyar et al.   NATURE GENETICS

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong et al.   SCIENCE

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Real-time imaging of DNA loop extrusion by condensin

(2018) Mahipal Ganji et al.   SCIENCE

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

(2018) Lucas J.T. Kaaij et al.   Cell Reports

The Insulator Protein CTCF Is Required for CorrectHoxGene Expression, but Not for Embryonic Development inDrosophila

(2018) Maria Cristina Gambetta et al.   GENETICS

A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions

(2018) Jill M. Brown et al.   Nature Communications

Selective interactions between diverse STEs organize the ANT-C Hox cluster

(2018) Mo Li et al.   Scientific Reports

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

(2018) A. Marieke Oudelaar et al.   NATURE GENETICS

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

(2018) Bogdan Bintu et al.   SCIENCE

Boundaries mediate long-distance interactions between enhancers and promoters in the Drosophila Bithorax complex

(2018) Nikolay Postika et al.   PLoS Genetics

Three-Dimensional Genome Organization and Function in Drosophila

(2017) Yuri B. Schwartz et al.   GENETICS

The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries

(2017) Sarah C. Hsu et al.   MOLECULAR CELL

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie 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

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

Three-Dimensional Genome Organization and Function in Drosophila

(2017) Yuri B. Schwartz et al.   GENETICS

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

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

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz et al.   CELL

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   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

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

(2016) Caroline R. Bartman et al.   MOLECULAR CELL

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Determinants of Chromosome Architecture: Insulator Pairing in cis and in trans

(2016) Miki Fujioka et al.   PLoS Genetics

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

(2015) Darío G. Lupiáñez 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

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

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

(2014) Yad Ghavi-Helm et al.   NATURE

The Border Between the Ultrabithorax and abdominal-A Regulatory Domains in the Drosophila Bithorax Complex

(2013) W. Bender et al.   GENETICS

The Drosophila eve Insulator Homie Promotes eve Expression and Protects the Adjacent Gene from Repression by Polycomb Spreading

(2013) Miki Fujioka et al.   PLoS Genetics

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

(2012) Tom Sexton et al.   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

Orientation-dependent interaction between Drosophila insulators is a property of this class of regulatory elements

(2008) O. Kyrchanova et al.   NUCLEIC ACIDS RESEARCH

CTCF-dependent enhancer-blocking by alternative chromatin loop formation

(2008) C. Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA