Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin

Formation of a multi‐layered 3‐dimensional structure of the heterochromatin compartment during early mammalian development

(2021) Rawin Poonperm et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Dynamic Nuclear Structure Emerges from Chromatin Cross-Links and Motors

(2021) Kuang Liu et al.   PHYSICAL REVIEW LETTERS

Interphase Chromatin Undergoes a Local Sol-Gel Transition upon Cell Differentiation

(2021) Iraj Eshghi et al.   PHYSICAL REVIEW LETTERS

Nucleation landscape of biomolecular condensates

(2021) Shunsuke F. Shimobayashi et al.   NATURE

PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency

(2021) Paula Dobrinić et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Monitoring the spatio-temporal organization and dynamics of the genome

(2020) Haitham A Shaban et al.   NUCLEIC ACIDS RESEARCH

Chromosome dynamics during interphase: a biophysical perspective

(2020) Maxime MC Tortora et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization

(2020) Joachim Wolff et al.   NUCLEIC ACIDS RESEARCH

Cohesin and condensin extrude DNA loops in a cell-cycle dependent manner

(2020) Stefan Golfier et al.   eLife

Fluid-like chromatin: Toward understanding the real chromatin organization present in the cell

(2020) Kazuhiro Maeshima et al.   CURRENT OPINION IN CELL BIOLOGY

Two-Parameter Mobility Assessments Discriminate Diverse Regulatory Factor Behaviors in Chromatin

(2020) Jonathan Lerner et al.   MOLECULAR CELL

Coupling chromatin structure and dynamics by live super-resolution imaging

(2020) R. Barth et al.   Science Advances

Regulation of single-cell genome organization into TADs and chromatin nanodomains

(2020) Quentin Szabo et al.   NATURE GENETICS

Condensed Chromatin Behaves like a Solid on the Mesoscale In Vitro and in Living Cells

(2020) Hilmar Strickfaden et al.   CELL

Reflections on the organization and the physical state of chromatin in eukaryotic cells.

(2020) Hilmar Strickfaden   GENOME

4D nucleome modeling

(2020) Marco Di Stefano et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Tracking and interpreting long-range chromatin interactions with super-resolution live-cell imaging

(2020) Hugo B. Brandão et al.   CURRENT OPINION IN CELL BIOLOGY

Condensin II Counteracts Cohesin and RNA Polymerase II in the Establishment of 3D Chromatin Organization

(2019) M. Jordan Rowley et al.   Cell Reports

The role of transcription in shaping the spatial organization of the genome

(2019) Bas van Steensel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Enhanced diffusion, swelling, and slow reconfiguration of a single chain in non-Gaussian active bath

(2019) Subhasish Chaki et al.   JOURNAL OF CHEMICAL PHYSICS

Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II

(2019) Ryosuke Nagashima et al.   JOURNAL OF CELL BIOLOGY

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

(2019) Elizabeth H. Finn et al.   CELL

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

(2019) Yongdae Shin et al.   CELL

Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes

(2019) Marius Socol et al.   NUCLEIC ACIDS RESEARCH

Polymer coil–globule phase transition is a universal folding principle of Drosophila epigenetic domains

(2019) Antony Lesage et al.   Epigenetics & Chromatin

Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity

(2019) Jeffrey M Alexander et al.   eLife

Principles of genome folding into topologically associating domains

(2019) Quentin Szabo et al.   Science Advances

Phase separation of Polycomb-repressive complex 1 is governed by a charged disordered region of CBX2

(2019) Aaron J. Plys et al.   GENES & DEVELOPMENT

Heterochromatin drives compartmentalization of inverted and conventional nuclei

(2019) Martin Falk et al.   NATURE

Chromosome dynamics near the sol-gel phase transition dictate the timing of remote genomic interactions

(2019) Nimish Khanna et al.   Nature Communications

Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers

(2019) O. Shukron et al.   Nature Communications

Determining cellular CTCF and cohesin abundances to constrain 3D genome models

(2019) Claudia Cattoglio et al.   eLife

Organization of fast and slow chromatin revealed by single-nucleosome dynamics

(2019) S. S. Ashwin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural and Dynamical Signatures of Local DNA Damage in Live Cells

(2019) Jonah A. Eaton et al.   BIOPHYSICAL JOURNAL

Formation of Chromatin Subcompartments by Phase Separation

(2018) Fabian Erdel et al.   BIOPHYSICAL JOURNAL

Capturing the Onset of PRC2-Mediated Repressive Domain Formation

(2018) Ozgur Oksuz et al.   MOLECULAR CELL

Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription

(2018) Haitham A Shaban et al.   NUCLEIC ACIDS RESEARCH

Epigenomics in 3D: importance of long-range spreading and specific interactions in epigenomic maintenance

(2018) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes

(2018) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes

(2018) Surya K. Ghosh et al.   PLoS Computational Biology

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

(2018) Quentin Szabo et al.   Science Advances

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

Interphase human chromosome exhibits out of equilibrium glassy dynamics

(2018) Guang Shi et al.   Nature Communications

Organizational principles of 3D genome architecture

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

Extensile motor activity drives coherent motions in a model of interphase chromatin

(2018) David Saintillan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci

(2018) Lei Liu et al.   PLoS Computational Biology

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

(2017) Tadasu Nozaki 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

Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

(2017) Michael H Hauer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

IC-Finder: inferring robustly the hierarchical organization of chromatin folding

(2017) Noelle Haddad et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Horng D. Ou et al.   SCIENCE

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

Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

(2017) Michael H Hauer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Visualization of Chromatin Decompaction and Break Site Extrusion as Predicted by Statistical Polymer Modeling of Single-Locus Trajectories

(2017) Assaf Amitai et al.   Cell Reports

Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data

(2017) Ofir Shukron et al.   PLoS Computational Biology

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

(2017) François Serra et al.   PLoS Computational Biology

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

Liquid-like behavior of chromatin

(2016) Kazuhiro Maeshima et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

(2016) Caroline R. Bartman et al.   MOLECULAR CELL

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

(2016) Alistair N. Boettiger et al.   NATURE

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo

(2015) Maria Aurelia Ricci et al.   CELL

Chromosome dynamics and folding in eukaryotes: Insights from live cell microscopy

(2015) Kerstin Bystricky   FEBS LETTERS

Two distinct modes for propagation of histone PTMs across the cell cycle

(2015) Constance Alabert et al.   GENES & DEVELOPMENT

Anomalous Diffusion in Fractal Globules

(2015) M. V. Tamm et al.   PHYSICAL REVIEW LETTERS

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

Loss of lamin A function increases chromatin dynamics in the nuclear interior

(2015) I. Bronshtein 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

On the time scale associated with Monte Carlo simulations

(2014) Kristof M. Bal et al.   JOURNAL OF CHEMICAL PHYSICS

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

(2014) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

SAM Domain Polymerization Links Subnuclear Clustering of PRC1 to Gene Silencing

(2013) Kyoichi Isono et al.   DEVELOPMENTAL CELL

High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome

(2013) Houssam Hajjoul et al.   GENOME RESEARCH

Micron-scale coherence in interphase chromatin dynamics

(2013) A. Zidovska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy

(2012) A. Soranno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic Monte Carlo versus Brownian dynamics: A comparison for self-diffusion and crystallization in colloidal fluids

(2010) E. Sanz et al.   JOURNAL OF CHEMICAL PHYSICS

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo 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