Organizational principles of 3D genome architecture

Establishment of DNA-DNA Interactions by the Cohesin Ring

(2018) Yasuto Murayama et al.   CELL

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

CTCF-Induced Circular DNA Complexes Observed by Atomic Force Microscopy

(2018) Matthew T. Mawhinney et al.   JOURNAL OF MOLECULAR BIOLOGY

Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization

(2018) Aleksandar Kojic et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A pathway for mitotic chromosome formation

(2018) Johan H. Gibcus et al.   SCIENCE

Real-time imaging of DNA loop extrusion by condensin

(2018) Mahipal Ganji et al.   SCIENCE

Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization

(2018) Aleksandar Kojic et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

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

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II

(2018) Huasong Lu et al.   NATURE

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

(2017) Jonathan A. Beagan et al.   GENOME RESEARCH

Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs

(2017) Yuan Lin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

3D Chromatin Architecture of Large Plant Genomes Determined by Local A/B Compartments

(2017) Pengfei Dong et al.   Molecular Plant

Bladder Cancer: 4 Big questions

(2017) Chris Berdik   NATURE

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl

(2017) Georg A. Busslinger 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

The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain

(2017) Kevin M. Harlen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes

(2017) Dusan Racko et al.   NUCLEIC ACIDS RESEARCH

Nonequilibrium Chromosome Looping via Molecular Slip Links

(2017) C. A. Brackley et al.   PHYSICAL REVIEW LETTERS

De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture

(2017) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacillus subtilis SMC complexes juxtapose chromosome arms as they travel from origin to terminus

(2017) Xindan Wang et al.   SCIENCE

The condensin complex is a mechanochemical motor that translocates along DNA

(2017) Tsuyoshi Terakawa et al.   SCIENCE

High-Throughput Imaging for the Discovery of Cellular Mechanisms of Disease

(2017) Gianluca Pegoraro et al.   TRENDS IN GENETICS

SMC Progressively Aligns Chromosomal Arms in Caulobacter crescentus but Is Antagonized by Convergent Transcription

(2017) Ngat T. Tran et al.   Cell Reports

Chromatin States in Mouse Sperm Correlate with Embryonic and Adult Regulatory Landscapes

(2017) Yoon Hee Jung et al.   Cell Reports

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA

(2016) Gergely Nagy et al.   BMC GENOMICS

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

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

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Genome-wide mapping and analysis of chromosome architecture

(2016) Anthony D. Schmitt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture

(2016) Caelin Cubeñas-Potts et al.   NUCLEIC ACIDS RESEARCH

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

(2016) Chris A. Brackley et al.   NUCLEIC ACIDS RESEARCH

Structural Insights into Ring Formation of Cohesin and Related Smc Complexes

(2016) Thomas Gligoris et al.   TRENDS IN CELL BIOLOGY

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

Evidence for cohesin sliding along budding yeast chromosomes

(2016) Maria Ocampo-Hafalla et al.   Open Biology

A CTCF Code for 3D Genome Architecture

(2015) Michael H. Nichols et al.   CELL

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

(2015) Zhonghui Tang et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

Architectural proteins, transcription, and the three-dimensional organization of the genome

(2015) Caelin Cubeñas-Potts et al.   FEBS LETTERS

The Hitchhiker’s guide to Hi-C analysis: Practical guidelines

(2015) Bryan R. Lajoie et al.   METHODS

An Overview of Genome Organization and How We Got There: from FISH to Hi-C

(2015) James Fraser et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing

(2015) Li Li et al.   MOLECULAR CELL

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

CTCF/cohesin-binding sites are frequently mutated in cancer

(2015) Riku Katainen et al.   NATURE GENETICS

Getting up to speed with transcription elongation by RNA polymerase II

(2015) Iris Jonkers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

(2015) Brian J. Beliveau et al.   Nature Communications

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

Classification of Intrinsically Disordered Regions and Proteins

(2014) Robin van der Lee et al.   CHEMICAL REVIEWS

The quantified cell

(2014) Avi Flamholz et al.   MOLECULAR BIOLOGY OF THE CELL

CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer

(2014) Christopher J. Kemp et al.   Cell Reports

De Novo Mutations in the Genome Organizer CTCF Cause Intellectual Disability

(2013) Anne Gregor et al.   AMERICAN JOURNAL OF HUMAN GENETICS

YY1 controls Igκ repertoire and B-cell development, and localizes with condensin on the Igκ locus

(2013) Xuan Pan et al.   EMBO JOURNAL

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

(2013) Takashi Nagano et al.   NATURE

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

(2013) J. Zuin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

(2013) T. B. K. Le et al.   SCIENCE

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

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

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

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