Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes

Nonlinear control of transcription through enhancer–promoter interactions

(2022) Jessica Zuin et al.   NATURE

Genome-wide enhancer maps link risk variants to disease genes

(2021) Joseph Nasser et al.   NATURE

Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression

(2021) Erica S.M. Vos et al.   MOLECULAR CELL

Defining genome architecture at base-pair resolution

(2021) Peng Hua et al.   NATURE

Enhancer release and retargeting activates disease-susceptibility genes

(2021) Soohwan Oh et al.   NATURE

How subtle changes in 3D structure can create large changes in transcription

(2021) Jordan Yupeng Xiao et al.   eLife

The structural basis for cohesin–CTCF-anchored loops

(2020) Yan Li et al.   NATURE

Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers

(2020) Michiel J. Thiecke et al.   Cell Reports

Single-gene imaging links genome topology, promoter–enhancer communication and transcription control

(2020) Jieru Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation

(2020) Ning Qing Liu et al.   NATURE GENETICS

Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

(2019) Bo Zhou et al.   GENOME RESEARCH

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

(2019) Yongdae Shin et al.   CELL

DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

(2019) Josef Redolfi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2019) Jeffrey M Alexander et al.   eLife

4C-seq from start to end: a detailed protocol for sample preparation and data analysis

(2019) Peter H.L. Krijger et al.   METHODS

Enhancer accessibility and CTCF occupancy underlie asymmetric TAD architecture and cell type specific genome topology

(2019) Christopher Barrington et al.   Nature Communications

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers

(2019) Laila El Khattabi et al.   CELL

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

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

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

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

(2018) Ralph Stadhouders et al.   NATURE GENETICS

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

(2018) Benjamin R. Sabari et al.   SCIENCE

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian 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

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   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

Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells

(2017) Paula Freire-Pritchett et al.   eLife

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

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

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

(2016) Annette Denker et al.   GENES & DEVELOPMENT

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Divisive suppression explains high-precision firing and contrast adaptation in retinal ganglion cells

(2016) Yuwei Cui et al.   eLife

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

(2015) Darío G. Lupiáñez et al.   CELL

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

(2015) Elizabeth Ing-Simmons et al.   GENOME RESEARCH

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

Genomic discovery of potent chromatin insulators for human gene therapy

(2015) Mingdong Liu et al.   NATURE BIOTECHNOLOGY

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

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

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

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions

(2014) Boryana Doyle et al.   PLoS Computational Biology

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

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

A noncytotoxic DsRed variant for whole-cell labeling

(2008) Rita L Strack et al.   NATURE METHODS