Weak interactions in higher-order chromatin organization

Mouse Heterochromatin Adopts Digital Compaction States without Showing Hallmarks of HP1-Driven Liquid-Liquid Phase Separation

(2020) Fabian Erdel et al.   MOLECULAR CELL

RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

(2020) Alessandro Bonetti et al.   Nature Communications

RNA: Nuclear Glue for Folding the Genome

(2019) Ryu-Suke Nozawa et al.   TRENDS IN CELL BIOLOGY

Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly

(2019) Sreejith J. Nair et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Visualizing DNA folding and RNA in embryos at single-cell resolution

(2019) Leslie J. Mateo et al.   NATURE

Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms

(2019) Andrés M. Cardozo Gizzi et al.   MOLECULAR CELL

Xist Deletional Analysis Reveals an Interdependency between Xist RNA and Polycomb Complexes for Spreading along the Inactive X

(2019) David Colognori et al.   MOLECULAR CELL

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

(2019) Elizabeth H. Finn et al.   CELL

Heterochromatin protein HP1α gelation dynamics revealed by solid-state NMR spectroscopy

(2019) Bryce E Ackermann et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Disordered domains in chromatin-binding proteins

(2019) Matthew Watson et al.   Essays in Biochemistry

Transcription factors and 3D genome conformation in cell-fate decisions

(2019) Ralph Stadhouders et al.   NATURE

Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation

(2019) David Trombley McSwiggen et al.   eLife

Role of nuclear RNA in regulating chromatin structure and transcription

(2019) Davide Michieletto et al.   CURRENT OPINION IN CELL BIOLOGY

Genome organization around nuclear speckles

(2019) Yu Chen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma

(2019) Michael J. Johnston et al.   GENOME RESEARCH

The role of 3D genome organization in development and cell differentiation

(2019) Hui Zheng et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A New Portrait of Constitutive Heterochromatin: Lessons from Drosophila melanogaster

(2019) René M. Marsano et al.   TRENDS IN GENETICS

Disruption of nuclear speckles reduces chromatin interactions in active compartments

(2019) Shibin Hu et al.   Epigenetics & Chromatin

Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase?

(2019) Mustafa Mir et al.   DEVELOPMENT

Enhancer Features that Drive Formation of Transcriptional Condensates

(2019) Krishna Shrinivas et al.   MOLECULAR CELL

Mechanisms of Interplay between Transcription Factors and the 3D Genome

(2019) Seungsoo Kim et al.   MOLECULAR CELL

Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF

(2019) Anders S. Hansen et al.   MOLECULAR CELL

RNA Interactions Are Essential for CTCF-Mediated Genome Organization

(2019) Ricardo Saldaña-Meyer et al.   MOLECULAR CELL

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   CELL

Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences

(2019) David T. McSwiggen et al.   GENES & DEVELOPMENT

The Significance of the Intrinsically Disordered Regions for the Functions of the bHLH Transcription Factors

(2019) Aneta Tarczewska et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Gene expression amplification by nuclear speckle association

(2019) Jiah Kim et al.   JOURNAL OF CELL BIOLOGY

The liquid nucleome – phase transitions in the nucleus at a glance

(2019) Amy R. Strom et al.   JOURNAL OF CELL SCIENCE

The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation

(2019) Xiangru Huo 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

A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome

(2019) William H. Gittens et al.   Nature Communications

Compaction of Single-Molecule Megabase-Long Chromatin under the Influence of Macromolecular Crowding

(2018) Anatoly Zinchenko et al.   BIOPHYSICAL JOURNAL

Formation of Chromatin Subcompartments by Phase Separation

(2018) Fabian Erdel et al.   BIOPHYSICAL JOURNAL

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

(2018) Sofia A. Quinodoz et al.   CELL

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

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

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong 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

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

(2018) Qi Wang et al.   Nature Communications

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts

(2018) Jason C Bell et al.   eLife

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

(2018) Quentin Szabo et al.   Science Advances

Primary transcripts: from the discovery of RNA processing to current concepts of gene expression - Review

(2018) Klaus Scherrer   EXPERIMENTAL CELL RESEARCH

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

(2018) Yu Chen et al.   JOURNAL OF CELL BIOLOGY

RNA polymerase II clustering through carboxy-terminal domain phase separation

(2018) Marc Boehning et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations

(2018) Peter R Cook et al.   NUCLEIC ACIDS RESEARCH

Phase separated microenvironments inside the cell nucleus are linked to disease and regulate epigenetic state, transcription and RNA processing

(2018) Iain A. Sawyer et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Phase Separation, Protein Disorder, and Enhancer Function

(2018) Steven Hahn   CELL

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

(2018) Ann Boija et al.   CELL

Global transcriptional activity dynamics reveal functional enhancer RNAs

(2018) Yoon Jung Kim et al.   GENOME RESEARCH

Nuclear condensates of the Polycomb protein chromobox 2 (CBX2) assemble through phase separation

(2018) Roubina Tatavosian et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

Are TADs supercoiled?

(2018) Dusan Racko et al.   NUCLEIC ACIDS RESEARCH

Highly disordered histone H1−DNA model complexes and their condensates

(2018) Abigail L. Turner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Bogdan Bintu et al.   SCIENCE

The nuclear matrix protein HNRNPU maintains 3D genome architecture globally in mouse hepatocytes

(2017) Hui Fan et al.   GENOME RESEARCH

Regulation of Nucleosome Stacking and Chromatin Compaction by the Histone H4 N-Terminal Tail–H2A Acidic Patch Interaction

(2017) Qinming Chen et al.   JOURNAL OF MOLECULAR BIOLOGY

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

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

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

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

(2017) Adam G. Larson et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

GRID-seq reveals the global RNA–chromatin interactome

(2017) Xiao Li et al.   NATURE BIOTECHNOLOGY

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

(2017) Maxwell R Mumbach et al.   NATURE GENETICS

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

Form and function of topologically associating genomic domains in budding yeast

(2017) Umut Eser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intrinsically Disordered Proteome of Human Membrane-Less Organelles

(2017) April L. Darling et al.   PROTEOMICS

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

(2017) Horng D. Ou et al.   SCIENCE

cis -Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture

(2017) Jennifer Yihong Tan et al.   Cell Reports

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

(2017) Yoon Hee Jung et al.   Cell Reports

Architectural RNAs (arcRNAs): A class of long noncoding RNAs that function as the scaffold of nuclear bodies

(2016) Takeshi Chujo et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Nucleosomal arrays self‐assemble into supramolecular globular structures lacking 30‐nm fibers

(2016) Kazuhiro Maeshima et al.   EMBO JOURNAL

Mediator Undergoes a Compositional Change during Transcriptional Activation

(2016) Natalia Petrenko et al.   MOLECULAR CELL

Structural organization of the inactive X chromosome in the mouse

(2016) Luca Giorgetti et al.   NATURE

Mapping 3D genome architecture through in situ DNase Hi-C

(2016) Vijay Ramani et al.   Nature Protocols

Breaking TADs: How Alterations of Chromatin Domains Result in Disease

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

Cajal bodies are linked to genome conformation

(2016) Qiuyan Wang et al.   Nature Communications

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh et al.   CELL

Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo

(2015) Maria Aurelia Ricci et al.   CELL

RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity

(2015) Evangelos Pefanis et al.   CELL

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

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

Compartmentalization and Functionality of Nuclear Disorder: Intrinsic Disorder and Protein-Protein Interactions in Intra-Nuclear Compartments

(2015) Fanchi Meng et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Integrator mediates the biogenesis of enhancer RNAs

(2015) Fan Lai et al.   NATURE

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Evolution of disorder in Mediator complex and its functional relevance

(2015) Malini Nagulapalli et al.   NUCLEIC ACIDS RESEARCH

The Role of Crowding Forces in Juxtaposing β-Globin Gene Domain Remote Regulatory Elements in Mouse Erythroid Cells

(2015) Arkadiy K. Golov et al.   PLoS One

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

ASAR15, A cis-Acting Locus that Controls Chromosome-Wide Replication Timing and Stability of Human Chromosome 15

(2015) Nathan Donley et al.   PLoS Genetics

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

(2014) Suhas S.P. Rao et al.   CELL

Chromatin as dynamic 10-nm fibers

(2014) Kazuhiro Maeshima et al.   CHROMOSOMA

Chromatin regulates DNA torsional energy via topoisomerase II-mediated relaxation of positive supercoils

(2014) X. Fernandez et al.   EMBO JOURNAL

Chromatin without the 30-nm fiber

(2014) Sergey V Razin et al.   Epigenetics

Genome-wide analysis of local chromatin packing inArabidopsis thaliana

(2014) Congmao Wang et al.   GENOME RESEARCH

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Chromatin structure revealed by X-ray scattering analysis and computational modeling

(2014) Kazuhiro Maeshima et al.   METHODS

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

(2014) Ezgi Hacisuleyman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Effects of supercoiling on enhancer–promoter contacts

(2014) Fabrizio Benedetti et al.   NUCLEIC ACIDS RESEARCH

Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation

(2014) C.-L. Hsieh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovering the complexity of the metazoan transcriptome

(2014) Matthew J Hangauer et al.   GENOME BIOLOGY

New Mechanistic and Functional Insights into DNA Topoisomerases

(2013) Stefanie Hartman Chen et al.   Annual Review of Biochemistry

Intra- and inter-nucleosome interactions of the core histone tail domains in higher-order chromatin structure

(2013) Sharon Pepenella et al.   CHROMOSOMA

Supercoiling in DNA and chromatin

(2013) Nick Gilbert et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Communication of genome regulatory elements in a folded chromosome

(2013) Sergey V. Razin et al.   FEBS LETTERS

Crowded chromatin is not sufficient for heterochromatin formation and not required for its maintenance

(2013) Andreas Walter et al.   JOURNAL OF STRUCTURAL BIOLOGY

The role of the nucleosome acidic patch in modulating higher order chromatin structure

(2013) A. A. Kalashnikova et al.   Journal of the Royal Society Interface

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

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

(2013) Fulai Jin et al.   NATURE

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

(2013) Catherine Naughton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-generated torsional stress destabilizes nucleosomes

(2013) Sheila S Teves et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-dependent dynamic supercoiling is a short-range genomic force

(2013) Fedor Kouzine et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2013) Fabrizio Benedetti et al.   NUCLEIC ACIDS RESEARCH

Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub

(2013) Alexey A. Gavrilov et al.   NUCLEIC ACIDS RESEARCH

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

A biophysical model for transcription factories

(2013) Ana Z Canals-Hamann et al.   BMC Biophysics

Asynchronous Replication, Mono-Allelic Expression, and Long Range Cis-Effects of ASAR6

(2013) Nathan Donley et al.   PLoS Genetics

Crowding Effects on the Formation and Maintenance of Nuclear Bodies: Insights from Molecular-Dynamics Simulations of Simple Spherical Model Particles

(2012) Eun Jin Cho et al.   BIOPHYSICAL JOURNAL

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal 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

Local Nucleosome Dynamics Facilitate Chromatin Accessibility in Living Mammalian Cells

(2012) Saera Hihara et al.   Cell Reports

Transcriptional regulation and spatial organisation of the human AML1/RUNX1 gene

(2011) Elena N. Markova et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Transcription factories in the context of the nuclear and genome organization

(2011) S. V. Razin et al.   NUCLEIC ACIDS RESEARCH

Role of Direct Interactions between the Histone H4 Tail and the H2A Core in Long Range Nucleosome Contacts

(2010) Divya Sinha et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A method for genome-wide analysis of DNA helical tension by means of psoralen–DNA photobinding

(2010) Ignacio Bermúdez et al.   NUCLEIC ACIDS RESEARCH

The effects of histone H4 tail acetylations on cation-induced chromatin folding and self-association

(2010) Abdollah Allahverdi et al.   NUCLEIC ACIDS RESEARCH

Transcription factories: gene expression in unions?

(2009) Heidi Sutherland et al.   NATURE REVIEWS GENETICS

Isolation of Cell Nuclei Using Inert Macromolecules to Mimic the Crowded Cytoplasm

(2009) Ronald Hancock et al.   PLoS One

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

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

Transcription factories

(2008) David R.F. Carter et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Macromolecular crowding and its potential impact on nuclear function

(2008) Karsten Richter et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Self-association of polynucleosome chains by macromolecular crowding

(2008) Ronald Hancock   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Association between active genes occurs at nuclear speckles and is modulated by chromatin environment

(2008) Jill M. Brown et al.   JOURNAL OF CELL BIOLOGY