In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation

Nonlinear control of transcription through enhancer–promoter interactions

(2022) Jessica Zuin et al.   NATURE

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

(2021) Hui Huang et al.   NATURE GENETICS

Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

(2021) Ana Rita Amândio et al.   GENES & DEVELOPMENT

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

Developmentally regulated Shh expression is robust to TAD perturbations

(2019) Iain Williamson et al.   DEVELOPMENT

Polymer physics predicts the effects of structural variants on chromatin architecture

(2018) Simona Bianco et al.   NATURE GENETICS

Enhancer hubs and loop collisions identified from single-allele topologies

(2018) Amin Allahyar et al.   NATURE GENETICS

TADs are 3D structural units of higher-order chromosome organization in Drosophila

(2018) Quentin Szabo et al.   Science Advances

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

(2018) Bogdan Bintu et al.   SCIENCE

TheHoxDcluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes

(2017) Eddie Rodríguez-Carballo et al.   GENES & DEVELOPMENT

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

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano 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

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long 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

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding

(2016) Guillaume Andrey et al.   GENOME RESEARCH

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

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

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

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation

(2015) J. Fraser et al.   Molecular Systems Biology

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

(2015) Christian Schmidl et al.   NATURE METHODS

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

Deletions, Inversions, Duplications: Engineering of Structural Variants using CRISPR/Cas in Mice

(2015) Katerina Kraft et al.   Cell Reports

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

(2014) Suhas S.P. Rao et al.   CELL

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

A decade of 3C technologies: insights into nuclear organization

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

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

(2012) Yin Shen et al.   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

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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