Transcription factor condensates and signaling driven transcription

Functional partitioning of transcriptional regulators by patterned charge blocks

(2023) Heankel Lyons et al.   CELL

NANOG prion-like assembly mediates DNA bridging to facilitate chromatin reorganization and activation of pluripotency

(2022) Kyoung-Jae Choi et al.   NATURE CELL BIOLOGY

A histidine cluster determines YY1-compartmentalized coactivators and chromatin elements in phase-separated enhancer clusters

(2022) Wenmeng Wang et al.   NUCLEIC ACIDS RESEARCH

Human cytomegalovirus forms phase-separated compartments at viral genomes to facilitate viral replication

(2022) Enrico Caragliano et al.   Cell Reports

Stochastic particle unbinding modulates growth dynamics and size of transcription factor condensates in living cells

(2022) Gorka Muñoz-Gil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Liquid Phase Partitioning in Virus Replication: Observations and Opportunities

(2022) Chao Wu et al.   Annual Review of Virology

Androgen receptor signaling and spatial chromatin organization in castration-resistant prostate cancer

(2022) Tianyi Zhou et al.   Frontiers in Medicine

SOX2 modulates the nuclear organization and transcriptional activity of the glucocorticoid receptor

(2022) Martin Stortz et al.   JOURNAL OF MOLECULAR BIOLOGY

Targeting androgen receptor phase separation to overcome antiandrogen resistance

(2022) Jingjing Xie et al.   Nature Chemical Biology

Dynamic phase separation of the androgen receptor and its coactivators key to regulate gene expression

(2022) Fan Zhang et al.   NUCLEIC ACIDS RESEARCH

Anomalous collapses of Nares Strait ice arches leads to enhanced export of Arctic sea ice

(2021) G. W. K. Moore et al.   Nature Communications

Transcription activation depends on the length of the RNA polymerase II C‐terminal domain

(2021) Anna Sawicka et al.   EMBO JOURNAL

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

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

Base-resolution models of transcription-factor binding reveal soft motif syntax

(2021) Žiga Avsec et al.   NATURE GENETICS

Evidence for additive and synergistic action of mammalian enhancers during cell fate determination

(2021) Jinmi Choi et al.   eLife

Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation

(2021) Joo-Hyung Lee et al.   MOLECULAR CELL

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

Local states of chromatin compaction at transcription start sites control transcription levels

(2021) Satoru Ishihara et al.   NUCLEIC ACIDS RESEARCH

Glucocorticoid receptor condensates link DNA-dependent receptor dimerization and transcriptional transactivation

(2021) Filipp Frank et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biomolecular condensates at sites of DNA damage: More than just a phase

(2021) Vincent Spegg et al.   DNA REPAIR

CTCF-mediated chromatin looping provides a topological framework for the formation of phase-separated transcriptional condensates

(2021) Ryanggeun Lee et al.   NUCLEIC ACIDS RESEARCH

RNA in formation and regulation of transcriptional condensates

(2021) Phillip A. Sharp et al.   RNA

Paraspeckle Protein NONO Promotes TAZ Phase Separation in the Nucleus to Drive the Oncogenic Transcriptional Program

(2021) Yiju Wei et al.   Advanced Science

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

(2020) Anisha Shakya et al.   BIOPHYSICAL JOURNAL

Modulation of RNA Condensation by the DEAD-Box Protein eIF4A

(2020) Devin Tauber et al.   CELL

Phase separation provides a mechanism to reduce noise in cells

(2020) A. Klosin et al.   SCIENCE

U1 snRNP regulates cancer cell migration and invasion in vitro

(2020) Jung-Min Oh et al.   Nature Communications

Ligand dependent gene regulation by transient ERα clustered enhancers

(2020) Bharath Saravanan et al.   PLoS Genetics

Unblending of Transcriptional Condensates in Human Repeat Expansion Disease

(2020) Shaon Basu et al.   CELL

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

(2020) Yi Lu et al.   NATURE CELL BIOLOGY

Unraveling the molecular interactions involved in phase separation of glucocorticoid receptor

(2020) Martin Stortz et al.   BMC BIOLOGY

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

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

Phase transition of RNA−protein complexes into ordered hollow condensates

(2020) Ibraheem Alshareedah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combinatorial Action of Temporally Segregated Transcription Factors

(2020) Julien Charest et al.   DEVELOPMENTAL CELL

Respiratory Syncytial Virus Sequesters NF-κB Subunit p65 to Cytoplasmic Inclusion Bodies To Inhibit Innate Immune Signaling

(2020) Fatoumatta Jobe et al.   JOURNAL OF VIROLOGY

Phase separation by ssDNA binding protein controlled via protein−protein and protein−DNA interactions

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

RNA-Mediated Feedback Control of Transcriptional Condensates

(2020) Jonathan E. Henninger et al.   CELL

Splicing at the phase-separated nuclear speckle interface: a model

(2020) Susan E Liao et al.   NUCLEIC ACIDS RESEARCH

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

Spontaneous driving forces give rise to protein−RNA condensates with coexisting phases and complex material properties

(2019) Steven Boeynaems et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2019) Jeffrey M Alexander et al.   eLife

Phase separation of 53 BP 1 determines liquid‐like behavior of DNA repair compartments

(2019) Sinan Kilic et al.   EMBO JOURNAL

FOXA1 mutations alter pioneering activity, differentiation and prostate cancer phenotypes

(2019) Elizabeth J. Adams et al.   NATURE

m6A enhances the phase separation potential of mRNA

(2019) Ryan J. Ries et al.   NATURE

RNA is a critical element for the sizing and the composition of phase-separated RNA–protein condensates

(2019) Marina Garcia-Jove Navarro et al.   Nature Communications

Multi-enhancer transcriptional hubs confer phenotypic robustness

(2019) Albert Tsai et al.   eLife

RNA Granules Hitchhike on Lysosomes for Long-Distance Transport, Using Annexin A11 as a Molecular Tether

(2019) Ya-Cheng Liao et al.   CELL

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

(2019) Liang Wang et al.   MOLECULAR CELL

Enhancer Features that Drive Formation of Transcriptional Condensates

(2019) Krishna Shrinivas et al.   MOLECULAR CELL

RNA Interactions Are Essential for CTCF-Mediated Genome Organization

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

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

(2019) Nezha S. Benabdallah 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

Birth of Nucleolar Compartments: Phase Separation-Driven Ribosomal RNA Sorting and Processing

(2019) Denis L.J. Lafontaine   MOLECULAR CELL

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

(2019) Danfeng Cai et al.   NATURE CELL BIOLOGY

Functional Implications of Intracellular Phase Transitions

(2018) Alex S. Holehouse et al.   BIOCHEMISTRY

Phase Separation of FUS Is Suppressed by Its Nuclear Import Receptor and Arginine Methylation

(2018) Mario Hofweber et al.   CELL

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

(2018) Jie Wang et al.   CELL

Prion-like low-complexity sequences: Key regulators of protein solubility and phase behavior

(2018) Titus Franzmann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RGG/RG Motif Regions in RNA Binding and Phase Separation

(2018) P. Andrew Chong et al.   JOURNAL OF MOLECULAR BIOLOGY

Quantitative imaging of chromatin decompaction in living cells

(2018) Elisa Dultz et al.   MOLECULAR BIOLOGY OF THE CELL

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

Paraspeckles: Where Long Noncoding RNA Meets Phase Separation

(2018) Archa H. Fox et al.   TRENDS IN BIOCHEMICAL SCIENCES

Protein Phase Separation: A New Phase in Cell Biology

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

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

(2018) Ann Boija et al.   CELL

Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity

(2018) Joseph Rodriguez et al.   CELL

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

RNA Chemical Proteomics Reveals the N6-Methyladenosine (m6A)-Regulated Protein–RNA Interactome

(2017) A. Emilia Arguello et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2017) Adam G. Larson et al.   NATURE

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes

(2017) Cedric R. Clapier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Biomolecular condensates: organizers of cellular biochemistry

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

Liquid–liquid phase separation of the microtubule-binding repeats of the Alzheimer-related protein Tau

(2017) Susmitha Ambadipudi et al.   Nature Communications

Pioneer factors and ATP-dependent chromatin remodeling factors interact dynamically: A new perspective

(2016) Erin E. Swinstead et al.   BIOESSAYS

Compositional Control of Phase-Separated Cellular Bodies

(2016) Salman F. Banani et al.   CELL

Phase separation in biology; functional organization of a higher order

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

Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes

(2016) Sakthi D. Moorthy et al.   GENOME RESEARCH

Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein

(2016) Chi W. Pak et al.   MOLECULAR CELL

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

Spatial genomic heterogeneity in diffuse intrinsic pontine and midline high-grade glioma: implications for diagnostic biopsy and targeted therapeutics

(2016) Lindsey M. Hoffman et al.   Acta Neuropathologica Communications

RNA Controls PolyQ Protein Phase Transitions

(2015) Huaiying Zhang et al.   MOLECULAR CELL

Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins

(2015) Yuan Lin et al.   MOLECULAR CELL

The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics

(2015) Shana Elbaum-Garfinkle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription factor trapping by RNA in gene regulatory elements

(2015) A. A. Sigova et al.   SCIENCE

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

Enhancer Activation Requires trans-Recruitment of a Mega Transcription Factor Complex

(2014) Zhijie Liu et al.   CELL

Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation

(2014) Kim Van Roey et al.   CHEMICAL REVIEWS

Classification of Intrinsically Disordered Regions and Proteins

(2014) Robin van der Lee et al.   CHEMICAL REVIEWS

Enhancer Function: Mechanistic and Genome-Wide Insights Come Together

(2014) Jennifer L. Plank et al.   MOLECULAR CELL

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

Discovery and Characterization of Super-Enhancer-Associated Dependencies in Diffuse Large B Cell Lymphoma

(2013) Bjoern Chapuy et al.   CANCER CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Defining the RGG/RG Motif

(2013) Palaniraja Thandapani et al.   MOLECULAR CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Androgen receptor driven transcription in molecular apocrine breast cancer is mediated by FoxA1

(2011) Jessica L L Robinson et al.   EMBO JOURNAL

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Nucleation of nuclear bodies by RNA

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

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Third-Party Bioluminescence Resonance Energy Transfer Indicates Constitutive Association of Membrane Proteins: Application to Class A G-Protein-Coupled Receptors and G-Proteins

(2010) Sudhakiranmayi Kuravi et al.   BIOPHYSICAL JOURNAL

Net charge per residue modulates conformational ensembles of intrinsically disordered proteins

(2010) A. H. Mao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear Speckles

(2010) D. L. Spector et al.   Cold Spring Harbor Perspectives in Biology

Searching DNA via a “Monkey Bar” Mechanism: The Significance of Disordered Tails

(2009) Dana Vuzman et al.   JOURNAL OF MOLECULAR BIOLOGY