Phase separation in transcription factor dynamics and chromatin organization

Chromatin mechanics dictates subdiffusion and coarsening dynamics of embedded condensates

(2021) Daniel S. W. Lee et al.   Nature Physics

Liquid-liquid phase separation of light-inducible transcription factors increases transcription activation in mammalian cells and mice

(2021) Nils Schneider et al.   Science Advances

Co-condensation between transcription factor and coactivator p300 modulates transcriptional bursting kinetics

(2021) Liang Ma et al.   MOLECULAR CELL

An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors

(2021) David A. Garcia et al.   MOLECULAR CELL

Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model

(2021) David A Garcia et al.   NUCLEIC ACIDS RESEARCH

Mechanical Regulation of Transcription: Recent Advances

(2021) Kaustubh Wagh et al.   TRENDS IN CELL BIOLOGY

HP1 proteins compact DNA into mechanically and positionally stable phase separated domains

(2021) Madeline M Keenen et al.   eLife

Bridging-induced phase separation induced by cohesin SMC protein complexes

(2021) Je-Kyung Ryu et al.   Science Advances

Liquid-Liquid Phase Separation of Histone Proteins in Cells: Role in Chromatin Organization

(2020) Anisha Shakya et al.   BIOPHYSICAL JOURNAL

MINFLUX nanoscopy delivers 3D multicolor nanometer resolution in cells

(2020) Klaus C. Gwosch et al.   NATURE METHODS

Elastic ripening and inhibition of liquid–liquid phase separation

(2020) Kathryn A. Rosowski et al.   Nature Physics

CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention

(2020) Elena M. Pugacheva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Valence and patterning of aromatic residues determine the phase behavior of prion-like domains

(2020) Erik W. Martin et al.   SCIENCE

Phase separation provides a mechanism to reduce noise in cells

(2020) A. Klosin et al.   SCIENCE

Phase separation of TAZ compartmentalizes the transcription machinery to promote gene expression

(2020) Yi Lu et al.   NATURE CELL BIOLOGY

Multiple mechanisms regulate H3 acetylation of enhancers in response to thyroid hormone

(2020) Stine M. Præstholm et al.   PLoS Genetics

Unraveling the molecular interactions involved in phase separation of glucocorticoid receptor

(2020) Martin Stortz et al.   BMC BIOLOGY

Intrinsically Disordered Regions Direct Transcription Factor In Vivo Binding Specificity

(2020) Sagie Brodsky et al.   MOLECULAR CELL

Partitioning of cancer therapeutics in nuclear condensates

(2020) Isaac A. Klein et al.   SCIENCE

Transcription Factors and DNA Play Hide and Seek

(2020) David M. Suter   TRENDS IN CELL BIOLOGY

The Self-Organizing Genome: Principles of Genome Architecture and Function

(2020) Tom Misteli   CELL

Opposing Effects of Cohesin and Transcription on CTCF Organization Revealed by Super-resolution Imaging

(2020) Bo Gu et al.   MOLECULAR CELL

Nucleated transcriptional condensates amplify gene expression

(2020) Ming-Tzo Wei et al.   NATURE CELL BIOLOGY

Phase-Separated Transcriptional Condensates Accelerate Target-Search Process Revealed by Live-Cell Single-Molecule Imaging

(2020) Samantha Kent et al.   Cell Reports

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

(2020) Hilmar Strickfaden et al.   CELL

RNA-Mediated Feedback Control of Transcriptional Condensates

(2020) Jonathan E. Henninger et al.   CELL

Protein condensates as aging Maxwell fluids

(2020) Louise Jawerth et al.   SCIENCE

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

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

Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates

(2019) Simon Alberti et al.   CELL

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

(2019) Elizabeth H. Finn et al.   CELL

Heterochromatin drives compartmentalization of inverted and conventional nuclei

(2019) Martin Falk et al.   NATURE

Regulation of nuclear architecture, mechanics, and nucleocytoplasmic shuttling of epigenetic factors by cell geometric constraints

(2019) Farid Alisafaei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility

(2019) Ryan S. Stowers et al.   Nature Biomedical Engineering

Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility

(2019) Diana A. Stavreva 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

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   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

HP1 reshapes nucleosome core to promote phase separation of heterochromatin

(2019) S. Sanulli et al.   NATURE

Phase separation of YAP reorganizes genome topology for long-term YAP target gene expression

(2019) Danfeng Cai et al.   NATURE CELL BIOLOGY

A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins

(2018) Jie Wang et al.   CELL

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types

(2018) Anne Zirkel et al.   MOLECULAR CELL

YAP/TAZ upstream signals and downstream responses

(2018) Antonio Totaro et al.   NATURE CELL BIOLOGY

Physical principles of intracellular organization via active and passive phase transitions

(2018) Joel Berry et al.   REPORTS ON PROGRESS IN PHYSICS

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

Pi-Pi contacts are an overlooked protein feature relevant to phase separation

(2018) Robert McCoy Vernon et al.   eLife

RNA polymerase II clustering through carboxy-terminal domain phase separation

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

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

(2018) Ann Boija et al.   CELL

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

(2018) Yongdae Shin et al.   CELL

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

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

(2017) Adam G. Larson et al.   NATURE

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

Nuclear microenvironments modulate transcription from low-affinity enhancers

(2017) Albert Tsai et al.   eLife

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

Passive Noise Filtering by Cellular Compartmentalization

(2016) Thomas Stoeger et al.   CELL

Coexisting Liquid Phases Underlie Nucleolar Subcompartments

(2016) Marina Feric et al.   CELL

Phase separation in biology; functional organization of a higher order

(2016) Diana M. Mitrea et al.   Cell Communication and Signaling

Polymer physics of intracellular phase transitions

(2015) Clifford P. Brangwynne et al.   Nature Physics

Single cell visualization of transcription kinetics variance of highly mobile identical genes using 3D nanoimaging

(2015) Paolo Annibale et al.   Scientific Reports

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels

(2012) Masato Kato et al.   CELL

Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation

(2009) C. P. Brangwynne et al.   SCIENCE

Protein Phase Behavior in Aqueous Solutions: Crystallization, Liquid-Liquid Phase Separation, Gels, and Aggregates

(2007) André C. Dumetz et al.   BIOPHYSICAL JOURNAL