Transcriptional condensates and phase separation: condensing information across scales and mechanisms

Imaging transcription elongation dynamics by new technologies unveils the organization of initiation and elongation in transcription factories

(2022) Hiroshi Kimura et al.   CURRENT OPINION IN CELL BIOLOGY

On the role of phase separation in the biogenesis of membraneless compartments

(2022) Andrea Musacchio   EMBO JOURNAL

Sequence-dependent surface condensation of a pioneer transcription factor on DNA

(2022) Jose A. Morin et al.   Nature Physics

SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding

(2022) Sofia A. Quinodoz et al.   Nature Protocols

Function moves biomolecular condensates in phase space

(2022) Marina Feric et al.   BIOESSAYS

Transcription activation is enhanced by multivalent interactions independent of phase separation

(2022) Jorge Trojanowski et al.   MOLECULAR CELL

Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription

(2022) Shasha Chong et al.   MOLECULAR CELL

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

(2022) Wenmeng Wang et al.   NUCLEIC ACIDS RESEARCH

Modulating gene regulation function by chemically controlled transcription factor clustering

(2022) Jiegen Wu et al.   Nature Communications

Phase Separation Properties in Transcriptional Organization

(2022) Chenghao Guo et al.   BIOCHEMISTRY

Enhancer-gene specificity in development and disease

(2022) Tomás Pachano et al.   DEVELOPMENT

Genetic variation associated with condensate dysregulation in disease

(2022) Salman F. Banani et al.   DEVELOPMENTAL CELL

Phase-separation antagonists potently inhibit transcription and broadly increase nucleosome density

(2022) Rajyalakshmi Meduri et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A conceptual framework for understanding phase separation and addressing open questions and challenges

(2022) Tanja Mittag et al.   MOLECULAR CELL

Hijacking of transcriptional condensates by endogenous retroviruses

(2022) Vahid Asimi et al.   NATURE GENETICS

Modulating biomolecular condensates: a novel approach to drug discovery

(2022) Diana M. Mitrea et al.   NATURE REVIEWS DRUG DISCOVERY

Long-distance association of topological boundaries through nuclear condensates

(2022) Amir Gamliel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics

(2022) Veer I. P. Keizer et al.   SCIENCE

Chromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA

(2022) Tuan Nguyen et al.   Nature Communications

Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer

(2022) Lele Song et al.   MOLECULAR CELL

Inducible transcriptional condensates drive 3D genome reorganization in the heat shock response

(2022) Surabhi Chowdhary et al.   MOLECULAR CELL

Targeting androgen receptor phase separation to overcome antiandrogen resistance

(2022) Jingjing Xie et al.   Nature Chemical Biology

ShareLoc — an open platform for sharing localization microscopy data

(2022) Wei Ouyang et al.   NATURE METHODS

Mechanisms governing target search and binding dynamics of hypoxia-inducible factors

(2022) Yu Chen et al.   eLife

A brief guideline for studies of phase-separated biomolecular condensates

(2022) Yifei Gao et al.   Nature Chemical Biology

Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1

(2022) Tsung-Han S. Hsieh et al.   NATURE GENETICS

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

(2022) Fan Zhang et al.   NUCLEIC ACIDS RESEARCH

Detecting and quantifying liquid–liquid phase separation in living cells by model-free calibrated half-bleaching

(2022) Fernando Muzzopappa et al.   Nature Communications

Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription

(2022) Isabel N. Goronzy et al.   Cell Reports

Fixation can change the appearance of phase separation in living cells

(2022) Shawn Irgen-Gioro et al.   eLife

Designer Condensates: A Toolkit for the Biomolecular Architect

(2021) Renee L. Hastings et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Interferon-γ induces tumor resistance to anti-PD-1 immunotherapy by promoting YAP phase separation

(2021) Man Yu et al.   MOLECULAR CELL

Stress-induced nuclear condensation of NELF drives transcriptional downregulation

(2021) Prashant Rawat et al.   MOLECULAR CELL

Biomolecular Condensates and Their Links to Cancer Progression

(2021) Danfeng Cai et al.   TRENDS IN BIOCHEMICAL SCIENCES

Transcription organizes euchromatin via microphase separation

(2021) Lennart Hilbert et al.   Nature Communications

1,6-hexanediol rapidly immobilizes and condenses chromatin in living human cells

(2021) Yuji Itoh et al.   Life Science Alliance

UTX condensation underlies its tumour-suppressive activity

(2021) Bi Shi et al.   NATURE

Phase separation drives aberrant chromatin looping and cancer development

(2021) Jeong Hyun Ahn et al.   NATURE

Testing the super-enhancer concept

(2021) Gerd A. Blobel et al.   NATURE REVIEWS GENETICS

Nuclear compartmentalization as a mechanism of quantitative control of gene expression

(2021) Prashant Bhat et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

The Role of rDNA Clusters in Global Epigenetic Gene Regulation

(2021) Nickolai A. Tchurikov et al.   Frontiers in Genetics

RNA promotes the formation of spatial compartments in the nucleus

(2021) Sofia A. Quinodoz et al.   CELL

Live imaging of transcription sites using an elongating RNA polymerase II–specific probe

(2021) Satoshi Uchino et al.   JOURNAL OF CELL BIOLOGY

The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus

(2020) Thomas Cremer et al.   BIOESSAYS

Phase separation provides a mechanism to reduce noise in cells

(2020) A. Klosin et al.   SCIENCE

Unblending of Transcriptional Condensates in Human Repeat Expansion Disease

(2020) Shaon Basu et al.   CELL

YAP/TAZ phase separation for transcription

(2020) J. Matthew Franklin et al.   NATURE CELL BIOLOGY

CDK-Regulated Phase Separation Seeded by Histone Genes Ensures Precise Growth and Function of Histone Locus Bodies

(2020) Woonyung Hur et al.   DEVELOPMENTAL CELL

Human organoids: model systems for human biology and medicine

(2020) Jihoon Kim et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Partitioning of cancer therapeutics in nuclear condensates

(2020) Isaac A. Klein et al.   SCIENCE

Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin

(2020) Ezequiel Miron et al.   Science Advances

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

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

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

Matter over mind: Liquid phase separation and neurodegeneration

(2019) Shana Elbaum-Garfinkle   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2019) Simon Alberti et al.   CELL

Enhancer long-range contacts: The multi-adaptor protein LDB1 is the tie that binds

(2019) Guoyou Liu et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Liquid–Liquid Phase Separation in Disease

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

Developmentally regulated Shh expression is robust to TAD perturbations

(2019) Iain Williamson et al.   DEVELOPMENT

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

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 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

Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma

(2019) Berkley E. Gryder et al.   NATURE GENETICS

To boldly go where no cell has gone before

(2019) Ashley York   NATURE REVIEWS MICROBIOLOGY

Intravital Imaging Techniques for Biomedical and Clinical Research

(2019) Anouchka Coste et al.   CYTOMETRY PART A

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

(2019) Danfeng Cai et al.   NATURE CELL BIOLOGY

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

(2018) Sofia A. Quinodoz et al.   CELL

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

Epichromatin and chromomeres: a ‘fuzzy’ perspective

(2018) Donald E. Olins et al.   Open 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

Super-Resolution Imaging of Higher-Order Chromatin Structures at Different Epigenomic States in Single Mammalian Cells

(2018) Jianquan Xu et al.   Cell Reports

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

(2018) Ann Boija et al.   CELL

Method of the Year 2018: Imaging in freely behaving animals

(2018)   NATURE METHODS

Biomolecular condensates: organizers of cellular biochemistry

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

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

(2015) Denes Hnisz et al.   MOLECULAR CELL

Liquid-Liquid Phase Separation in Biology

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

Assemblages: Functional units formed by cellular phase separation

(2014) Jeffrey A. Toretsky et al.   JOURNAL OF CELL BIOLOGY

Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci

(2014) Daniel Smeets et al.   Epigenetics & Chromatin

Dealing with Pervasive Transcription

(2013) Torben Heick Jensen et al.   MOLECULAR CELL