CTCF and cohesin regulate chromatin loop stability with distinct dynamics

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

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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

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

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

(2016) Iain F Davidson et al.   EMBO JOURNAL

CTCF: making the right connections

(2016) Rodolfo Ghirlando et al.   GENES & DEVELOPMENT

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

(2016) Guillaume Andrey et al.   GENOME RESEARCH

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

Bright photoactivatable fluorophores for single-molecule imaging

(2016) Jonathan B Grimm et al.   NATURE METHODS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang 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

Of Rings and Rods: Regulating Cohesin Entrapment of DNA to Generate Intra- and Intermolecular Tethers

(2016) Robert V. Skibbens   PLoS Genetics

A dynamic mode of mitotic bookmarking by transcription factors

(2016) Sheila S Teves et al.   eLife

Optimal Drift Correction for Superresolution Localization Microscopy with Bayesian Inference

(2015) Ahmed Elmokadem et al.   BIOPHYSICAL JOURNAL

Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes

(2015) Jiazhi Hu 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

A general method to improve fluorophores for live-cell and single-molecule microscopy

(2015) Jonathan B Grimm et al.   NATURE METHODS

Bayesian cluster identification in single-molecule localization microscopy data

(2015) Patrick Rubin-Delanchy et al.   NATURE METHODS

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

Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher

(2015) Davide Normanno et al.   Nature Communications

Steady-state cross-correlations for live two-colour super-resolution localization data sets

(2015) Matthew B. Stone et al.   Nature Communications

MXS-Chaining: A Highly Efficient Cloning Platform for Imaging and Flow Cytometry Approaches in Mammalian Systems

(2015) Hanna L. Sladitschek et al.   PLoS One

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

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

(2014) Suhas S.P. Rao et al.   CELL

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

(2014) Iain Williamson et al.   GENES & DEVELOPMENT

Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm

(2014) Yina Wang et al.   OPTICS EXPRESS

Characterization of a DNA exit gate in the human cohesin ring

(2014) P. J. Huis in 't Veld et al.   SCIENCE

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

(2013) Fulai Jin et al.   NATURE

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

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

(2013) Fabrizio Benedetti et al.   NUCLEIC ACIDS RESEARCH

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code

(2013) Hirotaka Nakahashi et al.   Cell Reports

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

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

A benchmark for chromatin binding measurements in live cells

(2012) Davide Mazza et al.   NUCLEIC ACIDS RESEARCH

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(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity

(2011) Anja Nitzsche et al.   PLoS One

FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know?

(2010) Florian Mueller et al.   CURRENT OPINION IN CELL BIOLOGY

Detection of Mycoplasma in cell cultures

(2010) Lesley Young et al.   Nature Protocols

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Statistical Analysis of Lateral Diffusion and Multistate Kinetics in Single-Molecule Imaging

(2009) Satomi Matsuoka et al.   BIOPHYSICAL JOURNAL

How a protein searches for its site on DNA: the mechanism of facilitated diffusion

(2009) Leonid Mirny et al.   Journal of Physics A-Mathematical and Theoretical

Agouti C57BL/6N embryonic stem cells for mouse genetic resources

(2009) Stephen J Pettitt et al.   NATURE METHODS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Evidence for a Common Mode of Transcription Factor Interaction with Chromatin as Revealed by Improved Quantitative Fluorescence Recovery after Photobleaching

(2008) Florian Mueller et al.   BIOPHYSICAL JOURNAL

Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms

(2008) Vania Parelho et al.   CELL

Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression

(2008) Asako Sakaue-Sawano et al.   CELL

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE

Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes

(2008) Arnauld Sergé et al.   NATURE METHODS

Highly inclined thin illumination enables clear single-molecule imaging in cells

(2008) Makio Tokunaga et al.   NATURE METHODS

High-density mapping of single-molecule trajectories with photoactivated localization microscopy

(2008) Suliana Manley et al.   NATURE METHODS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY