Principles of genome folding into topologically associating domains

Super-resolution Imaging of Individual Human Subchromosomal Regions in Situ Reveals Nanoscopic Building Blocks of Higher-Order Structure

(2018) Ke Fang et al.   ACS Nano

Formation of Chromatin Subcompartments by Phase Separation

(2018) Fabian Erdel et al.   BIOPHYSICAL JOURNAL

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah 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

Epigenetic maintenance of topological domains in the highly rearranged gibbon genome

(2018) Nathan H. Lazar et al.   GENOME RESEARCH

Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development

(2018) Yuki Ogiyama et al.   MOLECULAR CELL

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

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice

(2018) Qianli Dong et al.   PLANT JOURNAL

Chromatin organization by an interplay of loop extrusion and compartmental segregation

(2018) Johannes Nuebler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements

(2018) Bo Gu 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

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells

(2018) Qi Wang et al.   Nature Communications

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

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

(2018) Quentin Szabo et al.   Science Advances

Evolutionary stability of topologically associating domains is associated with conserved gene regulation

(2018) Jan Krefting et al.   BMC BIOLOGY

Quantitative differences in TAD border strength underly the TAD hierarchy in Drosophila chromosomes

(2018) Artem V. Luzhin et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

In Vivo Evidence for ATPase-Dependent DNA Translocation by the Bacillus subtilis SMC Condensin Complex

(2018) Xindan Wang et al.   MOLECULAR CELL

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

(2018) Huasong Lu et al.   NATURE

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

Three-dimensional genome structures of single diploid human cells

(2018) Longzhi Tan et al.   SCIENCE

Super-Resolution Imaging of Higher-Order Chromatin Structures at Different Epigenomic States in Single Mammalian Cells

(2018) Jianquan Xu et al.   Cell Reports

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

(2018) Bogdan Bintu et al.   SCIENCE

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

(2018) Guy Nir et al.   PLoS Genetics

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

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

Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes

(2017) Yinxiu Zhan et al.   GENOME RESEARCH

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation

(2017) Sharmistha Kundu et al.   MOLECULAR CELL

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging

(2017) Tadasu Nozaki et al.   MOLECULAR CELL

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

(2017) Pengfei Dong et al.   Molecular Plant

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   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

Comparison of computational methods for Hi-C data analysis

(2017) Mattia Forcato et al.   NATURE METHODS

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

Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe

(2017) Fabrizio Benedetti et al.   NUCLEIC ACIDS RESEARCH

Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map

(2017) Kyle P. Eagen 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

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

(2017) Horng D. Ou et al.   SCIENCE

Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation

(2017) Nathan Harmston et al.   Nature Communications

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

(2017) Diego I. Cattoni et al.   Nature Communications

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

(2017) Marie Trussart et al.   Nature Communications

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

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

Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo

(2017) Michael R Stadler et al.   eLife

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

Topologically associated domains: a successful scaffold for the evolution of gene regulation in animals

(2017) Rafael D. Acemel et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Condensin II is anchored by TFIIIC and H3K4me3 in the mammalian genome and supports the expression of active dense gene clusters

(2017) Kobe C. Yuen et al.   Science Advances

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Chromosome conformation capture technologies and their impact in understanding genome function

(2016) Satish Sati et al.   CHROMOSOMA

Neurosporachromosomes are organized by blocks of importin alpha-dependent heterochromatin that are largely independent of H3K9me3

(2016) Jonathan M. Galazka et al.   GENOME RESEARCH

Genome-wide analysis of chromatin packing inArabidopsis thalianaat single-gene resolution

(2016) Chang Liu et al.   GENOME RESEARCH

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

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

(2016) Alistair N. Boettiger et al.   NATURE

Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking

(2016) Joachim Weischenfeldt et al.   NATURE GENETICS

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

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

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

Breaking TADs: How Alterations of Chromatin Domains Result in Disease

(2016) Darío G. Lupiáñez et al.   TRENDS IN GENETICS

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

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

Stable Chromosome Condensation Revealed by Chromosome Conformation Capture

(2015) Kyle P. Eagen et al.   CELL

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh 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

Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo

(2015) Maria Aurelia Ricci et al.   CELL

Advanced microscopy methods for visualizing chromatin structure

(2015) Melike Lakadamyali et al.   FEBS LETTERS

Condensin promotes the juxtaposition of DNA flanking its loading site inBacillus subtilis

(2015) Xindan Wang et al.   GENES & DEVELOPMENT

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

(2015) Sergey V. Ulianov et al.   GENOME RESEARCH

Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging

(2015) Martial Marbouty et al.   MOLECULAR CELL

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

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

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

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

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

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

CTCF regulates the human p53 gene through direct interaction with its natural antisense transcript, Wrap53

(2014) R. Saldana-Meyer et al.   GENES & DEVELOPMENT

Genome-wide analysis of local chromatin packing inArabidopsis thaliana

(2014) Congmao Wang et al.   GENOME RESEARCH

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression

(2014) F. Ay et al.   GENOME RESEARCH

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila

(2014) Stefan Grob et al.   MOLECULAR CELL

Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis

(2014) Suhua Feng et al.   MOLECULAR CELL

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho et al.   NATURE

Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe

(2014) Takeshi Mizuguchi et al.   NATURE

Effects of supercoiling on enhancer–promoter contacts

(2014) Fabrizio Benedetti et al.   NUCLEIC ACIDS RESEARCH

Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci

(2014) Daniel Smeets et al.   Epigenetics & Chromatin

Super-resolution microscopy reveals decondensed chromatin structure at transcription sites

(2014) Yejun Wang et al.   Scientific Reports

Conservation and Divergence of Regulatory Strategies at Hox Loci and the Origin of Tetrapod Digits

(2014) Joost M. Woltering et al.   PLOS BIOLOGY

Insulator function and topological domain border strength scale with architectural protein occupancy

(2014) Kevin Van Bortle et al.   GENOME BIOLOGY

The Spatial Organization of the Human Genome

(2013) Wendy A. Bickmore   Annual Review of Genomics and Human Genetics

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

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

(2013) Takashi Nagano et al.   NATURE

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

(2013) T. B. K. Le et al.   SCIENCE

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

Cohesin and Polycomb Proteins Functionally Interact to Control Transcription at Silenced and Active Genes

(2013) Cheri A. Schaaf et al.   PLoS Genetics

Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations

(2012) Yu Zhang et al.   CELL

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

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Chromosome Territories

(2010) T. Cremer et al.   Cold Spring Harbor Perspectives in Biology

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

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

DNA dynamics vary according to macrodomain topography in theE. colichromosome

(2008) Olivier Espeli et al.   MOLECULAR MICROBIOLOGY