Membraneless nuclear organelles and the search for phases within phases

Reentrant Phase Transitions and Non-Equilibrium Dynamics in Membraneless Organelles

(2018) Anthony N. Milin et al.   BIOCHEMISTRY

Dynamics and Function of Nuclear Bodies during Embryogenesis

(2018) Dahyana Arias Escayola et al.   BIOCHEMISTRY

The physical forces mediating self-association and phase-separation in the C-terminal domain of TDP-43

(2018) Hao-Ru Li et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Do Cellular Condensates Accelerate Biochemical Reactions? Lessons from Microdroplet Chemistry

(2018) Wylie Stroberg 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

PML nuclear bodies: from architecture to function

(2018) Valérie Lallemand-Breitenbach et al.   CURRENT OPINION IN CELL BIOLOGY

Crystal structure of a SFPQ/PSPC1 heterodimer provides insights into preferential heterodimerization of human DBHS family proteins

(2018) Jie Huang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation

(2018) Tomohiro Yamazaki et al.   MOLECULAR CELL

Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture

(2018) Yizhu Lin et al.   NUCLEIC ACIDS RESEARCH

Integrator subunit 4 is a ‘Symplekin-like’ scaffold that associates with INTS9/11 to form the Integrator cleavage module

(2018) Todd R Albrecht et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Shovamayee Maharana 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

Self-interaction of NPM1 modulates multiple mechanisms of liquid–liquid phase separation

(2018) Diana M. Mitrea et al.   Nature Communications

RING tetramerization is required for nuclear body biogenesis and PML sumoylation

(2018) Pengran Wang et al.   Nature Communications

Liquid-Liquid Phase Separation of Patchy Particles Illuminates Diverse Effects of Regulatory Components on Protein Droplet Formation

(2018) Valery Nguemaha et al.   Scientific Reports

Dual roles for ATP in the regulation of phase separated protein aggregates in Xenopus oocyte nucleoli

(2018) Michael H Hayes et al.   eLife

Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli

(2018) Elliot Dine et al.   Cell Systems

Intronless mRNAs transit through nuclear speckles to gain export competence

(2018) Ke Wang et al.   JOURNAL OF CELL BIOLOGY

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

(2018) Huasong Lu et al.   NATURE

Integrative structure and functional anatomy of a nuclear pore complex

(2018) Seung Joong Kim et al.   NATURE

RNA polymerase II clustering through carboxy-terminal domain phase separation

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

Phase separated microenvironments inside the cell nucleus are linked to disease and regulate epigenetic state, transcription and RNA processing

(2018) Iain A. Sawyer et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs

(2017) Yuan Lin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution

(2017) Jingyi Fei et al.   JOURNAL OF CELL SCIENCE

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

RNA phase transitions in repeat expansion disorders

(2017) Ankur Jain et al.   NATURE

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

(2017) Adam G. Larson et al.   NATURE

Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles

(2017) Ming-Tzo Wei et al.   Nature Chemistry

NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing

(2017) Li Jiang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Paraspeckles: nuclear nests helping to raise mature miRNAs

(2017) Jacek Krol   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Enrichment of dynamic chromosomal crosslinks drive phase separation of the nucleolus

(2017) Caitlin Hult et al.   NUCLEIC ACIDS RESEARCH

Nuclear speckles: molecular organization, biological function and role in disease

(2017) Lukasz Galganski et al.   NUCLEIC ACIDS RESEARCH

Coordinating cell cycle-regulated histone gene expression through assembly and function of the Histone Locus Body

(2017) Robert J. Duronio et al.   RNA Biology

Functional dissection of NEAT1 using genome editing reveals substantial localization of the NEAT1_1 isoform outside paraspeckles

(2017) Ruohan Li et al.   RNA

ATP controls the crowd

(2017) Allyson M. Rice et al.   SCIENCE

ATP as a biological hydrotrope

(2017) Avinash Patel et al.   SCIENCE

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing

(2017) Li Jiang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Paraspeckles: nuclear nests helping to raise mature miRNAs

(2017) Jacek Krol   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Survival of Motor Neuron Protein Acts as a Molecular Chaperone for mRNP Assembly

(2017) Paul G. Donlin-Asp et al.   Cell Reports

Ribonucleoprotein bodies are phased in

(2016) Aristeidis P. Sfakianos et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Cajal body function in genome organization and transcriptome diversity

(2016) Iain A. Sawyer et al.   BIOESSAYS

Passive Noise Filtering by Cellular Compartmentalization

(2016) Thomas Stoeger et al.   CELL

Polar Positioning of Phase-Separated Liquid Compartments in Cells Regulated by an mRNA Competition Mechanism

(2016) Shambaditya Saha et al.   CELL

ATPase-Modulated Stress Granules Contain a Diverse Proteome and Substructure

(2016) Saumya Jain et al.   CELL

Compositional Control of Phase-Separated Cellular Bodies

(2016) Salman F. Banani et al.   CELL

Toxic PR Poly-Dipeptides Encoded by the C9orf72 Repeat Expansion Target LC Domain Polymers

(2016) Yi Lin 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

Nucleation by rRNA Dictates the Precision of Nucleolus Assembly

(2016) Hanieh Falahati et al.   CURRENT BIOLOGY

Cycling in the nucleus: regulation of RNA 3′ processing and nuclear organization of replication-dependent histone genes

(2016) Valentina Romeo et al.   CURRENT OPINION IN CELL BIOLOGY

Higher‐order oligomerization promotes localization of SPOP to liquid nuclear speckles

(2016) Melissa R Marzahn et al.   EMBO JOURNAL

Droplet organelles?

(2016) Edward M Courchaine et al.   EMBO JOURNAL

Nucleolar organizer regions: genomic ‘dark matter’ requiring illumination

(2016) Brian McStay   GENES & DEVELOPMENT

The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL

(2016) Taro Mannen et al.   JOURNAL OF CELL BIOLOGY

Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization

(2016) Jason A. West et al.   JOURNAL OF CELL BIOLOGY

Concentrating pre-mRNA processing factors in the histone locus body facilitates efficient histone mRNA biogenesis

(2016) Deirdre C. Tatomer et al.   JOURNAL OF CELL BIOLOGY

Nuclear bodies: Built to boost

(2016) Iain A. Sawyer et al.   JOURNAL OF CELL BIOLOGY

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

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

p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

(2016) Carmen Adriaens et al.   NATURE MEDICINE

Structure of the human 26S proteasome at a resolution of 3.9 Å

(2016) Andreas Schweitzer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Cajal body and the nucleolus: “In a relationship” or “It's complicated”?

(2016) Laura Trinkle-Mulcahy et al.   RNA Biology

Specific genomic cues regulate Cajal body assembly

(2016) Iain A. Sawyer et al.   RNA Biology

Towards an understanding of regulating Cajal body activity by protein modification

(2016) Michael D. Hebert et al.   RNA Biology

Activation of transcription enforces the formation of distinct nuclear bodies in zebrafish embryos

(2016) Patricia Heyn et al.   RNA Biology

Cajal bodies are linked to genome conformation

(2016) Qiuyan Wang et al.   Nature Communications

Hierarchical Size Scaling during Multicellular Growth and Development

(2016) Sravanti Uppaluri et al.   Cell Reports

In Vivo Formation of Vacuolated Multi-phase Compartments Lacking Membranes

(2016) Hermann Broder Schmidt et al.   Cell Reports

Distinct stages in stress granule assembly and disassembly

(2016) Joshua R Wheeler et al.   eLife

Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization

(2015) Amandine Molliex et al.   CELL

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles

(2015) Sven Hennig et al.   JOURNAL OF CELL BIOLOGY

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

(2015) Yuan Lin et al.   MOLECULAR CELL

Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles

(2015) Timothy J. Nott et al.   MOLECULAR CELL

Transcriptome-wide dynamics of RNA pseudouridylation

(2015) John Karijolich et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

SWI/SNF chromatin-remodeling complexes function in noncoding RNA-dependent assembly of nuclear bodies

(2015) Tetsuya Kawaguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA transcription modulates phase transition-driven nuclear body assembly

(2015) Joel Berry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coilin: The first 25 years

(2015) Martin Machyna et al.   RNA Biology

The RNA-binding protein Sam68 regulates expression and transcription function of the androgen receptor splice variant AR-V7

(2015) Jacqueline Stockley et al.   Scientific Reports

SART3-Dependent Accumulation of Incomplete Spliceosomal snRNPs in Cajal Bodies

(2015) Ivan Novotný et al.   Cell Reports

Classification of Intrinsically Disordered Regions and Proteins

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

The Coilin Interactome Identifies Hundreds of Small Noncoding RNAs that Traffic through Cajal Bodies

(2014) Martin Machyna et al.   MOLECULAR CELL

PML isoforms in response to arsenic: high-resolution analysis of PML body structure and degradation

(2013) K. J. Hands et al.   JOURNAL OF CELL SCIENCE

Dynamics in Cytoplasm, Nucleus, and Lipid Droplet of a Live CHO Cell: Time-Resolved Confocal Microscopy

(2013) Shirsendu Ghosh et al.   LANGMUIR

NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies

(2013) Tetsuro Hirose et al.   MOLECULAR BIOLOGY OF THE CELL

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

Paraspeckle formation during the biogenesis of long non-coding RNAs

(2013) Takao Naganuma et al.   RNA Biology

RNA Seeds Higher-Order Assembly of FUS Protein

(2013) Jacob C. Schwartz et al.   Cell Reports

Differential Roles of PML Isoforms

(2013) Sébastien Nisole et al.   Frontiers in Oncology

JC Virus Intranuclear Inclusions Associated with PML-NBs

(2012) Yukiko Shishido-Hara et al.   AMERICAN JOURNAL OF PATHOLOGY

Post-translational modifications induce significant yet not extreme changes to protein structure

(2012) Fuxiao Xin et al.   BIOINFORMATICS

Crowding Effects on the Formation and Maintenance of Nuclear Bodies: Insights from Molecular-Dynamics Simulations of Simple Spherical Model Particles

(2012) Eun Jin Cho et al.   BIOPHYSICAL JOURNAL

Nuclear bodies: multifunctional companions of the genome

(2012) Miroslav Dundr   CURRENT OPINION IN CELL BIOLOGY

Reorganization of Cajal bodies and nucleolar targeting of coilin in motor neurons of type I spinal muscular atrophy

(2012) Olga Tapia et al.   HISTOCHEMISTRY AND CELL BIOLOGY

SRSF1 regulates the assembly of pre-mRNA processing factors in nuclear speckles

(2012) Vidisha Tripathi et al.   MOLECULAR BIOLOGY OF THE CELL

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   NATURE

Malat1 is not an essential component of nuclear speckles in mice

(2012) S. Nakagawa et al.   RNA

Compound sessile drops

(2012) Michael J. Neeson et al.   Soft Matter

Dynamic force-induced direct dissociation of protein complexes in a nuclear body in living cells

(2012) Yeh-Chuin Poh et al.   Nature Communications

Seed and grow: a two-step model for nuclear body biogenesis: Figure 1.

(2011) Miroslav Dundr   JOURNAL OF CELL BIOLOGY

Nucleation of nuclear bodies by RNA

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

Soft active aggregates: mechanics, dynamics and self-assembly of liquid-like intracellular protein bodies

(2011) Clifford P. Brangwynne   Soft Matter

SR and SR-related proteins redistribute to segregated fibrillar components of nucleoli in a response to DNA damage

(2011) Eiji Sakashita et al.   Nucleus

Sam68 sequestration and partial loss of function are associated with splicing alterations in FXTAS patients

(2010) Chantal Sellier et al.   EMBO JOURNAL

The splicing regulator Sam68 binds to a novel exonic splicing silencer and functions in SMN2 alternative splicing in spinal muscular atrophy

(2010) Simona Pedrotti et al.   EMBO JOURNAL

Three-dimensional organization of promyelocytic leukemia nuclear bodies

(2010) M. Lang et al.   JOURNAL OF CELL SCIENCE

Highly Ordered Spatial Organization of the Structural Long Noncoding NEAT1 RNAs within Paraspeckle Nuclear Bodies

(2010) Sylvie Souquere et al.   MOLECULAR BIOLOGY OF THE CELL

Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs

(2010) Yuntao S. Mao et al.   NATURE CELL BIOLOGY

Paraspeckles

(2010) A. H. Fox et al.   Cold Spring Harbor Perspectives in Biology

Biogenesis of Nuclear Bodies

(2010) M. Dundr et al.   Cold Spring Harbor Perspectives in Biology

Alternative Splicing of the Cyclin D1 Proto-Oncogene Is Regulated by the RNA-Binding Protein Sam68

(2009) M. P. Paronetto et al.   CANCER RESEARCH

Coilin phosphorylation mediates interaction with SMN and SmB′

(2009) Cory G. Toyota et al.   CHROMOSOMA

Nuclear Bodies: Random Aggregates of Sticky Proteins or Crucibles of Macromolecular Assembly?

(2009) A. Gregory Matera et al.   DEVELOPMENTAL CELL

Identification of a Sam68 Ribonucleoprotein Complex Regulated by Epidermal Growth Factor

(2009) Marc-Étienne Huot et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cajal-body formation correlates with differential coilin phosphorylation in primary and transformed cell lines

(2009) S. M. Hearst et al.   JOURNAL OF CELL SCIENCE

An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles

(2009) Christine M. Clemson et al.   MOLECULAR CELL

MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles

(2009) Yasnory T. F. Sasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data

(2009) Yvonne JK Edwards et al.   GENOME BIOLOGY

MEN  /  nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles

(2008) H. Sunwoo et al.   GENOME RESEARCH

De Novo Formation of a Subnuclear Body

(2008) T. E. Kaiser et al.   SCIENCE