Merging Established Mechanisms with New Insights: Condensates, Hubs, and the Regulation of RNA Polymerase II Transcription

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

(2021) Nils Schneider et al.   Science Advances

Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing

(2021) Tassa Saldi et al.   MOLECULAR CELL

Stress-induced nuclear condensation of NELF drives transcriptional downregulation

(2021) Prashant Rawat et al.   MOLECULAR CELL

Loci-specific phase separation of FET fusion oncoproteins promotes gene transcription

(2021) Linyu Zuo et al.   Nature Communications

Transcription organizes euchromatin via microphase separation

(2021) Lennart Hilbert et al.   Nature Communications

Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection

(2021) Yihan Wan et al.   CELL

The role of liquid–liquid phase separation in regulating enzyme activity

(2021) Brian G. O'Flynn et al.   CURRENT OPINION IN CELL BIOLOGY

Towards a ‘Spot On’ Understanding of Transcription in the Nucleus

(2021) Simona Patange et al.   JOURNAL OF MOLECULAR BIOLOGY

Transcription Regulation Through Nascent RNA Folding

(2021) Leonard Schärfen et al.   JOURNAL OF MOLECULAR BIOLOGY

HP1 drives de novo 3D genome reorganization in early Drosophila embryos

(2021) Fides Zenk et al.   NATURE

Phase Separation in Genome Organization across Evolution

(2021) Marina Feric et al.   TRENDS IN CELL BIOLOGY

Nascent RNA scaffolds contribute to chromosome territory architecture and counter chromatin compaction

(2021) Kevin Michael Creamer et al.   MOLECULAR CELL

Spatiotemporal coordination of transcription preinitiation complex assembly in live cells

(2021) Vu Q. Nguyen et al.   MOLECULAR CELL

Generic nature of the condensed states of proteins

(2021) Monika Fuxreiter et al.   NATURE CELL BIOLOGY

Mechanistic dissection of increased enzymatic rate in a phase-separated compartment

(2021) William Peeples et al.   Nature Chemical Biology

It’s not just a phase: function and characteristics of RNA-binding proteins in phase separation

(2021) Hannah J. Wiedner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2020) Fabian Erdel et al.   MOLECULAR CELL

HSF1 phase transition mediates stress adaptation and cell fate decisions

(2020) Giorgio Gaglia et al.   NATURE CELL BIOLOGY

Transcription in Living Cells: Molecular Mechanisms of Bursting

(2020) Joseph Rodriguez et al.   Annual Review of Biochemistry

Unblending of Transcriptional Condensates in Human Repeat Expansion Disease

(2020) Shaon Basu et al.   CELL

RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation

(2020) Jordina Guillén-Boixet et al.   CELL

Structure and mechanism of the RNA polymerase II transcription machinery

(2020) Allison C. Schier et al.   GENES & DEVELOPMENT

Composition-dependent thermodynamics of intracellular phase separation

(2020) Joshua A. Riback et al.   NATURE

The Sox2 transcription factor binds RNA

(2020) Zachariah E. Holmes et al.   Nature Communications

RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting

(2020) Porfirio Quintero-Cadena et al.   MOLECULAR CELL

Intrinsically Disordered Regions Direct Transcription Factor In Vivo Binding Specificity

(2020) Sagie Brodsky et al.   MOLECULAR CELL

MeCP2 links heterochromatin condensates and neurodevelopmental disease

(2020) Charles H. Li et al.   NATURE

Partitioning of cancer therapeutics in nuclear condensates

(2020) Isaac A. Klein et al.   SCIENCE

Biomolecular Condensates in the Nucleus

(2020) Benjamin R. Sabari et al.   TRENDS IN BIOCHEMICAL SCIENCES

Multivalent Proteins Rapidly and Reversibly Phase-Separate upon Osmotic Cell Volume Change

(2020) Ameya P. Jalihal 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

SON and SRRM2 are essential for nuclear speckle formation

(2020) İbrahim Avşar Ilik et al.   eLife

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

(2020) Hilmar Strickfaden et al.   CELL

Phase Separation as a Missing Mechanism for Interpretation of Disease Mutations

(2020) Brian Tsang et al.   CELL

RNA-Mediated Feedback Control of Transcriptional Condensates

(2020) Jonathan E. Henninger et al.   CELL

Biochemical Timekeeping Via Reentrant Phase Transitions

(2020) Bede Portz et al.   JOURNAL OF MOLECULAR BIOLOGY

Widespread occurrence of the droplet state of proteins in the human proteome

(2020) Maarten Hardenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Nuclear speckle fusion via long-range directional motion regulates speckle morphology after transcriptional inhibition

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

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

(2019) Simon Alberti et al.   CELL

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

(2019) Leighton Core et al.   GENES & DEVELOPMENT

Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation

(2019) David Trombley McSwiggen et al.   eLife

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

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

Liquid–Liquid Phase Separation in Disease

(2019) Simon Alberti et al.   Annual Review of Genetics

Interplay between Short-Range Attraction and Long-Range Repulsion Controls Reentrant Liquid Condensation of Ribonucleoprotein–RNA Complexes

(2019) Ibraheem Alshareedah et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Histone Modifications Regulate Chromatin Compartmentalization by Contributing to a Phase Separation Mechanism

(2019) Liang Wang et al.   MOLECULAR CELL

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

(2019) Diana A. Stavreva et al.   MOLECULAR CELL

Enhancer Features that Drive Formation of Transcriptional Condensates

(2019) Krishna Shrinivas et al.   MOLECULAR CELL

Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes

(2019) Alicia V. Zamudio et al.   MOLECULAR CELL

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

DEAD-box ATPases are global regulators of phase-separated organelles

(2019) Maria Hondele et al.   NATURE

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

Probing and engineering liquid-phase organelles

(2019) Dan Bracha et al.   NATURE BIOTECHNOLOGY

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

(2019) Danfeng Cai et al.   NATURE CELL BIOLOGY

New Roles for Canonical Transcription Factors in Repeat Expansion Diseases

(2019) Lindsey D. Goodman et al.   TRENDS IN GENETICS

Relationship of Sequence and Phase Separation in Protein Low-Complexity Regions

(2018) Erik W. Martin et al.   BIOCHEMISTRY

Theories for Sequence-Dependent Phase Behaviors of Biomolecular Condensates

(2018) Yi-Hsuan Lin et al.   BIOCHEMISTRY

Formation of Chromatin Subcompartments by Phase Separation

(2018) Fabian Erdel et al.   BIOPHYSICAL JOURNAL

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

(2018) Jie Wang et al.   CELL

Enhancer RNA profiling predicts transcription factor activity

(2018) Joseph G. Azofeifa et al.   GENOME RESEARCH

Advances in Understanding Stimulus-Responsive Phase Behavior of Intrinsically Disordered Protein Polymers

(2018) Kiersten M. Ruff et al.   JOURNAL OF MOLECULAR BIOLOGY

RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome

(2018) Briana Van Treeck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA buffers the phase separation behavior of prion-like RNA binding proteins

(2018) Shovamayee Maharana et al.   SCIENCE

mRNA structure determines specificity of a polyQ-driven phase separation

(2018) Erin M. Langdon et al.   SCIENCE

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

Protein Phase Separation: A New Phase in Cell Biology

(2018) Steven Boeynaems et al.   TRENDS IN CELL BIOLOGY

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

(2018) Robert McCoy Vernon et al.   eLife

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

(2018) Huasong Lu et al.   NATURE

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

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

(2018) Ann Boija et al.   CELL

Three-Dimensional Genome Organization and Function in Drosophila

(2017) Yuri B. Schwartz et al.   GENETICS

Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis

(2017) Hector L. Franco et al.   GENOME RESEARCH

Hypersensitive termination of the hypoxic response by a disordered protein switch

(2017) Rebecca B. Berlow et al.   NATURE

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

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Direct observation of structure and dynamics during phase separation of an elastomeric protein

(2017) Sean E. Reichheld et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications

(2017) Christopher C. Ebmeier et al.   Cell Reports

Three-Dimensional Genome Organization and Function in Drosophila

(2017) Yuri B. Schwartz et al.   GENETICS

Mechanisms and Consequences of Macromolecular Phase Separation

(2016) Louis-Philippe Bergeron-Sandoval et al.   CELL

The Structure and Dynamics of Higher-Order Assemblies: Amyloids, Signalosomes, and Granules

(2016) Hao Wu et al.   CELL

Coexisting Liquid Phases Underlie Nucleolar Subcompartments

(2016) Marina Feric et al.   CELL

Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters

(2016) Timothy J. Nott et al.   Nature Chemistry

RNA Controls PolyQ Protein Phase Transitions

(2015) Huaiying Zhang et al.   MOLECULAR CELL

Polymer physics of intracellular phase transitions

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

Intrinsically disordered proteins in cellular signalling and regulation

(2015) Peter E. Wright et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Mediator complex: a central integrator of transcription

(2015) Benjamin L. Allen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcription factor trapping by RNA in gene regulatory elements

(2015) A. A. Sigova et al.   SCIENCE

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Association of polyalanine and polyglutamine coiled coils mediates expansion disease-related protein aggregation and dysfunction

(2014) Ilaria Pelassa et al.   HUMAN MOLECULAR GENETICS

TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications

(2014) Hyeshik Chang et al.   MOLECULAR CELL

The amyloid state and its association with protein misfolding diseases

(2014) Tuomas P. J. Knowles et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

3D imaging of Sox2 enhancer clusters in embryonic stem cells

(2014) Zhe Liu et al.   eLife

Phosphorylation-Regulated Binding of RNA Polymerase II to Fibrous Polymers of Low-Complexity Domains

(2013) Ilmin Kwon et al.   CELL

In vivo live imaging of RNA polymerase II transcription factories in primary cells

(2013) A. Ghamari et al.   GENES & DEVELOPMENT

Kinetic Competition between Elongation Rate and Binding of NELF Controls Promoter-Proximal Pausing

(2013) Jian Li et al.   MOLECULAR CELL

Nucleation of nuclear bodies by RNA

(2011) Sergey P. Shevtsov et al.   NATURE CELL BIOLOGY

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Transcription factories are nuclear subcompartments that remain in the absence of transcription

(2008) J. A. Mitchell et al.   GENES & DEVELOPMENT

Human U2 snRNA Genes Exhibit a Persistently Open Transcriptional State and Promoter Disassembly at Metaphase

(2008) T. Pavelitz et al.   MOLECULAR AND CELLULAR BIOLOGY