RNA contributions to the form and function of biomolecular condensates

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

FXR1 splicing is important for muscle development and biomolecular condensates in muscle cells

(2020) Jean A. Smith et al.   JOURNAL OF CELL BIOLOGY

Sequence-Independent Self-Assembly of Germ Granule mRNAs into Homotypic Clusters

(2020) Tatjana Trcek et al.   MOLECULAR CELL

Composition-dependent thermodynamics of intracellular phase separation

(2020) Joshua A. Riback et al.   NATURE

m6A-binding YTHDF proteins promote stress granule formation

(2020) Ye Fu et al.   Nature Chemical Biology

Recessive mutations in muscle-specific isoforms of FXR1 cause congenital multi-minicore myopathy

(2019) María Cristina Estañ et al.   Nature Communications

Phosphoregulated FMRP phase separation models activity-dependent translation through bidirectional control of mRNA granule formation

(2019) Brian Tsang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA structure maps across mammalian cellular compartments

(2019) Lei Sun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A gel phase promotes condensation of liquid P granules in Caenorhabditis elegans embryos

(2019) Andrea Putnam et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Arabidopsis FLL2 promotes liquid–liquid phase separation of polyadenylation complexes

(2019) Xiaofeng Fang et al.   NATURE

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

m6A enhances the phase separation potential of mRNA

(2019) Ryan J. Ries et al.   NATURE

The roles of structural dynamics in the cellular functions of RNAs

(2019) Laura R. Ganser et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2019) Ya-Cheng Liao et al.   CELL

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

(2019) Maria Hondele et al.   NATURE

Reading, writing and erasing mRNA methylation

(2019) Sara Zaccara et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA base-pairing complexity in living cells visualized by correlated chemical probing

(2019) Anthony M. Mustoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reentrant Phase Transitions and Non-Equilibrium Dynamics in Membraneless Organelles

(2018) Anthony N. Milin et al.   BIOCHEMISTRY

P-Bodies: Composition, Properties, and Functions

(2018) Yang Luo et al.   BIOCHEMISTRY

Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism

(2018) Ying Yang et al.   CELL RESEARCH

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

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

A User’s Guide for Phase Separation Assays with Purified Proteins

(2018) Simon Alberti et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2018) Tomohiro Yamazaki et al.   MOLECULAR CELL

In-cell RNA structure probing with SHAPE-MaP

(2018) Matthew J Smola et al.   Nature Protocols

A brave new world of RNA-binding proteins

(2018) Matthias W. Hentze et al.   NATURE REVIEWS MOLECULAR CELL 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

DNA-induced liquid phase condensation of cGAS activates innate immune signaling

(2018) Mingjian Du et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis

(2018) Ryota Yamagami et al.   Nature Communications

A New Lens for RNA Localization: Liquid-Liquid Phase Separation

(2018) Erin M. Langdon et al.   Annual Review of Microbiology

Emerging Roles for Intermolecular RNA-RNA Interactions in RNP Assemblies

(2018) Briana Van Treeck et al.   CELL

Methods for Physical Characterization of Phase-Separated Bodies and Membrane-less Organelles

(2018) Diana M. Mitrea et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2018) Huasong Lu et al.   NATURE

Kinase-controlled phase transition of membraneless organelles in mitosis

(2018) Arpan Kumar Rai et al.   NATURE

Fragile X mental retardation 1 gene enhances the translation of large autism-related proteins

(2018) Ethan J. Greenblatt et al.   SCIENCE

pH-Driven RNA Strand Separation under Prebiotically Plausible Conditions

(2018) Angelica Mariani et al.   BIOCHEMISTRY

TDP-43 and RNA form amyloid-like myo-granules in regenerating muscle

(2018) Thomas O. Vogler et al.   NATURE

RNA-binding proteins in neurodegeneration: mechanisms in aggregate

(2017) Erin G. Conlon et al.   GENES & DEVELOPMENT

Isolation of yeast and mammalian stress granule cores

(2017) Joshua R. Wheeler et al.   METHODS

P-Body Purification Reveals the Condensation of Repressed mRNA Regulons

(2017) Arnaud Hubstenberger et al.   MOLECULAR CELL

The Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules

(2017) Anthony Khong et al.   MOLECULAR CELL

RNA phase transitions in repeat expansion disorders

(2017) Ankur Jain et al.   NATURE

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

(2017) Lukasz Galganski et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Ruohan Li et al.   RNA

The RNA modification landscape in human disease

(2017) Nicky Jonkhout et al.   RNA

RNA modifications go viral

(2017) Nandan S. Gokhale et al.   PLoS Pathogens

Is Tau Aggregation Toxic or Protective?

(2017) Erin E. Congdon et al.   JOURNAL OF ALZHEIMERS DISEASE

Amyloid-like Self-Assembly of a Cellular Compartment

(2016) Elvan Boke et al.   CELL

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

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

(2016) Shambaditya Saha et al.   CELL

Nucleation by rRNA Dictates the Precision of Nucleolus Assembly

(2016) Hanieh Falahati et al.   CURRENT BIOLOGY

Simultaneous multicolor detection of RNA and proteins using super-resolution microscopy

(2016) Mari Mito et al.   METHODS

RNA Remodeling Activity of DEAD Box Proteins Tuned by Protein Concentration, RNA Length, and ATP

(2016) Younghoon Kim et al.   MOLECULAR CELL

Global Mapping of Human RNA-RNA Interactions

(2016) Eesha Sharma et al.   MOLECULAR CELL

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

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

Messenger RNA modifications: Form, distribution, and function

(2016) W. V. Gilbert et al.   SCIENCE

The APOBEC Protein Family: United by Structure, Divergent in Function

(2016) Jason D. Salter et al.   TRENDS IN BIOCHEMICAL SCIENCES

Principles and Properties of Stress Granules

(2016) David S.W. Protter et al.   TRENDS IN CELL BIOLOGY

A pH-driven transition of the cytoplasm from a fluid- to a solid-like state promotes entry into dormancy

(2016) Matthias Christoph Munder et al.   eLife

ATPase activity of the DEAD-box protein Dhh1 controls processing body formation

(2016) Christopher Frederick Mugler et al.   eLife

Metal Cations in G-Quadruplex Folding and Stability

(2016) Debmalya Bhattacharyya et al.   Frontiers in Chemistry

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

(2015) Amandine Molliex et al.   CELL

A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation

(2015) Avinash Patel et al.   CELL

PolyQ-dependent RNA–protein assemblies control symmetry breaking

(2015) ChangHwan Lee et al.   JOURNAL OF CELL BIOLOGY

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

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

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

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis

(2015) Matthew J Smola et al.   Nature Protocols

ALS/FTD Mutation-Induced Phase Transition of FUS Liquid Droplets and Reversible Hydrogels into Irreversible Hydrogels Impairs RNP Granule Function

(2015) Tetsuro Murakami et al.   NEURON

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

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

Differential effects of Ydj1 and Sis1 on Hsp70-mediated clearance of stress granules inSaccharomyces cerevisiae

(2015) Robert W. Walters et al.   RNA

When bigger is better: the role of polyploidy in organogenesis

(2015) Terry L. Orr-Weaver   TRENDS IN GENETICS

Drosophila germ granules are structured and contain homotypic mRNA clusters

(2015) Tatjana Trcek et al.   Nature Communications

RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

(2014) Jesse M. Engreitz et al.   CELL

P granules

(2014) Jennifer T. Wang et al.   CURRENT BIOLOGY

The lncRNA Neat1 is required for corpus luteum formation and the establishment of pregnancy in a subpopulation of mice

(2014) S. Nakagawa et al.   DEVELOPMENT

Multistep process of FUS aggregation in the cell cytoplasm involves RNA-dependent and RNA-independent mechanisms

(2014) Tatyana A. Shelkovnikova et al.   HUMAN MOLECULAR GENETICS

WTAP is a novel oncogenic protein in acute myeloid leukemia

(2014) H Bansal et al.   LEUKEMIA

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

The dynamic epitranscriptome: N6-methyladenosine and gene expression control

(2014) Kate D. Meyer et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme

(2014) Hui-Ting Lee et al.   NUCLEIC ACIDS RESEARCH

Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics

(2014) N. F. Dupuis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The long noncoding RNA Neat1 is required for mammary gland development and lactation

(2014) Laura Standaert et al.   RNA

Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions

(2014) C. A. Strulson et al.   RNA

The multifunctional Staufen proteins: conserved roles from neurogenesis to synaptic plasticity

(2014) Jacki E. Heraud-Farlow et al.   TRENDS IN NEUROSCIENCES

Dual Specificity Kinase DYRK3 Couples Stress Granule Condensation/Dissolution to mTORC1 Signaling

(2013) Frank Wippich et al.   CELL

Protein Aggregation Behavior Regulates Cyclin Transcript Localization and Cell-Cycle Control

(2013) ChangHwan Lee et al.   DEVELOPMENTAL CELL

Endosomal transport of septin mRNA and protein indicates local translation on endosomes and is required for correct septin filamentation

(2013) Sebastian Baumann et al.   EMBO REPORTS

Deficiency of G3BP1, the stress granules assembly factor, results in abnormal synaptic plasticity and calcium homeostasis in neurons

(2013) Sophie Martin et al.   JOURNAL OF NEUROCHEMISTRY

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Hexanucleotide Repeats in ALS/FTD Form Length-Dependent RNA Foci, Sequester RNA Binding Proteins, and Are Neurotoxic

(2013) Youn-Bok Lee et al.   Cell Reports

Cell-free Formation of RNA Granules: Bound RNAs Identify Features and Components of Cellular Assemblies

(2012) Tina W. Han et al.   CELL

Kinesin-3 and dynein mediate microtubule-dependent co-transport of mRNPs and endosomes

(2012) S. Baumann et al.   JOURNAL OF CELL SCIENCE

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   NATURE

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

Mutations in ADAR1 cause Aicardi-Goutières syndrome associated with a type I interferon signature

(2012) Gillian I Rice et al.   NATURE GENETICS

P-Bodies and Stress Granules: Possible Roles in the Control of Translation and mRNA Degradation

(2012) C. J. Decker et al.   Cold Spring Harbor Perspectives in Biology

The Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and Networks

(2011) Samuel E. Butcher et al.   ACCOUNTS OF CHEMICAL RESEARCH

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice

(2011) Shinichi Nakagawa et al.   JOURNAL OF CELL BIOLOGY

Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in Human Telomerase RNA

(2011) Natalia A. Denesyuk et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes

(2011) C. P. Brangwynne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Crowding Stabilizes Folded RNA Structure by the Excluded Volume Effect

(2010) Duncan Kilburn et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

The fungal RNA-binding protein Rrm4 mediates long-distance transport of ubi1 and rho3 mRNAs

(2009) Julian König et al.   EMBO JOURNAL

Facilitation of RNA Enzyme Activity in the Molecular Crowding Media of Cosolutes

(2009) Shu-ichi Nakano et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH