RNA-binding and prion domains: the Yin and Yang of phase separation

Modulation of RNA Condensation by the DEAD-Box Protein eIF4A

(2020) Devin Tauber et al.   CELL

ALS-linked FUS mutations confer loss and gain of function in the nucleus by promoting excessive formation of dysfunctional paraspeckles

(2019) Haiyan An et al.   Acta Neuropathologica Communications

Molecular Mechanisms of TDP-43 Misfolding and Pathology in Amyotrophic Lateral Sclerosis

(2019) Archana Prasad et al.   Frontiers in Molecular Neuroscience

RNA Binding Antagonizes Neurotoxic Phase Transitions of TDP-43

(2019) Jacob R. Mann et al.   NEURON

RNA as a key factor in driving or preventing self-assembly of the TAR DNA-binding protein 43

(2019) Elsa Zacco et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2019) Simon Alberti et al.   CELL

AAA+ protein-based technologies to counter neurodegenerative disease

(2019) Zachary M. March et al.   BIOPHYSICAL JOURNAL

New roles for the de-ubiquitylating enzyme OTUD4 in an RNA-protein network and RNA granules

(2019) Richa Das et al.   JOURNAL OF CELL SCIENCE

Phase separation drives X-chromosome inactivation: a hypothesis

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

Protein aggregation mediates stoichiometry of protein complexes in aneuploid cells

(2019) Christopher M. Brennan et al.   GENES & DEVELOPMENT

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

RNA structure drives interaction with proteins

(2019) Natalia Sanchez de Groot et al.   Nature Communications

The mutational landscape of a prion-like domain

(2019) Benedetta Bolognesi et al.   Nature Communications

Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules

(2018) Sebastian Markmiller et al.   CELL

FUS Phase Separation Is Modulated by a Molecular Chaperone and Methylation of Arginine Cation-π Interactions

(2018) Seema Qamar 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

A brave new world of RNA-binding proteins

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

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

(2018) Yizhu Lin et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Shovamayee Maharana et al.   SCIENCE

Protein Phase Separation: A New Phase in Cell Biology

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

Different Material States of Pub1 Condensates Define Distinct Modes of Stress Adaptation and Recovery

(2018) Sonja Kroschwald et al.   Cell Reports

Intrinsically Disordered Regions Can Contribute Promiscuous Interactions to RNP Granule Assembly

(2018) David S.W. Protter et al.   Cell Reports

Multiple Modes of Protein–Protein Interactions Promote RNP Granule Assembly

(2018) Tanja Mittag et al.   JOURNAL OF MOLECULAR BIOLOGY

Controllable protein phase separation and modular recruitment to form responsive membraneless organelles

(2018) Benjamin S. Schuster et al.   Nature Communications

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Structure of Calcarisporiella thermophila Hsp104 Disaggregase that Antagonizes Diverse Proteotoxic Misfolding Events

(2018) Karolina Michalska et al.   STRUCTURE

An Integrative Study of Protein-RNA Condensates Identifies Scaffolding RNAs and Reveals Players in Fragile X-Associated Tremor/Ataxia Syndrome

(2018) Fernando Cid-Samper et al.   Cell Reports

The wisdom of crowds: regulating cell function through condensed states of living matter

(2017) Simon Alberti   JOURNAL OF CELL SCIENCE

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

(2017) Anthony Khong et al.   MOLECULAR CELL

Intracellular production of hydrogels and synthetic RNA granules by multivalent molecular interactions

(2017) Hideki Nakamura et al.   NATURE MATERIALS

Biomolecular condensates: organizers of cellular biochemistry

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

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

Identifying pathogenicity of human variants via paralog-based yeast complementation

(2017) Fan Yang et al.   PLoS Genetics

Are aberrant phase transitions a driver of cellular aging?

(2016) Simon Alberti et al.   BIOESSAYS

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

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

Intrinsic disorder in proteins involved in amyotrophic lateral sclerosis

(2016) Nikolas Santamaria et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Nucleation by rRNA Dictates the Precision of Nucleolus Assembly

(2016) Hanieh Falahati et al.   CURRENT BIOLOGY

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Two mutations G335D and Q343R within the amyloidogenic core region of TDP-43 influence its aggregation and inclusion formation

(2016) Lei-Lei Jiang et al.   Scientific Reports

A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression

(2016) Benedetta Bolognesi et al.   Cell Reports

Advances in the characterization of RNA-binding proteins

(2016) Domenica Marchese et al.   Wiley Interdisciplinary Reviews-RNA

Characterization of Amyloid Cores in Prion Domains

(2016) Ricardo Sant’Anna et al.   Scientific Reports

catRAPIDsignature: identification of ribonucleoproteins and RNA-binding regions

(2015) Carmen Maria Livi et al.   BIOINFORMATICS

Protein aggregation, structural disorder and RNA-binding ability: a new approach for physico-chemical and gene ontology classification of multiple datasets

(2015) Petr Klus et al.   BMC GENOMICS

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

(2015) Avinash Patel et al.   CELL

ALS mutant FUS proteins are recruited into stress granules in induced pluripotent stem cell-derived motoneurons

(2015) J. Lenzi et al.   Disease Models & Mechanisms

PolyQ-dependent RNA–protein assemblies control symmetry breaking

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

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

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

RNA Controls PolyQ Protein Phase Transitions

(2015) Huaiying Zhang et al.   MOLECULAR CELL

Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers

(2015) Felipe García Quiroz et al.   NATURE MATERIALS

ELM 2016—data update and new functionality of the eukaryotic linear motif resource

(2015) Holger Dinkel et al.   NUCLEIC ACIDS RESEARCH

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

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines

(2015) Mingcong Wang et al.   PROTEOMICS

The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs

(2015) Benedikt M. Beckmann et al.   Nature Communications

What Makes a Protein Sequence a Prion?

(2015) Raimon Sabate et al.   PLoS Computational Biology

PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition

(2014) A. K. Lancaster et al.   BIOINFORMATICS

The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities

(2014) Petr Klus et al.   BIOINFORMATICS

Stress Granule-Defective Mutants Deregulate Stress Responsive Transcripts

(2014) Xiaoxue Yang et al.   PLoS Genetics

Constitutive patterns of gene expression regulated by RNA-binding proteins

(2014) Davide Cirillo et al.   GENOME BIOLOGY

The long non-coding RNA nuclear-enriched abundant transcript 1_2 induces paraspeckle formation in the motor neuron during the early phase of amyotrophic lateral sclerosis

(2013) Yoshinori Nishimoto et al.   Molecular Brain

Evolutionary selection for protein aggregation

(2012) Natalia Sanchez de Groot et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels

(2012) Masato Kato et al.   CELL

Hsp104 Drives “Protein-Only” Positive Selection of Sup35 Prion Strains Encoding Strong [PSI+]

(2012) Morgan E. DeSantis et al.   CHEMISTRY & BIOLOGY

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   NATURE

Cellular Strategies for Regulating Functional and Nonfunctional Protein Aggregation

(2012) Jörg Gsponer et al.   Cell Reports

Amyloid-like Aggregates Sequester Numerous Metastable Proteins with Essential Cellular Functions

(2011) Heidi Olzscha et al.   CELL

The Effect of Amyloidogenic Peptides on Bacterial Aging Correlates with Their Intrinsic Aggregation Propensity

(2011) Anna Villar-Pique et al.   JOURNAL OF MOLECULAR BIOLOGY

Nucleation of nuclear bodies by RNA

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

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

A yeast functional screen predicts new candidate ALS disease genes

(2011) J. Couthouis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stress-specific composition, assembly and kinetics of stress granules in Saccharomyces cerevisiae

(2010) J. R. Buchan et al.   JOURNAL OF CELL SCIENCE

Prion-like disorders: blurring the divide between transmissibility and infectivity

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

Physicochemical Determinants of Chaperone Requirements

(2010) Gian Gaetano Tartaglia et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Translationally optimal codons associate with aggregation-prone sites in proteins

(2010) Yaelim Lee et al.   PROTEOMICS

A Systematic Survey Identifies Prions and Illuminates Sequence Features of Prionogenic Proteins

(2009) Simon Alberti et al.   CELL

Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation

(2009) C. P. Brangwynne et al.   SCIENCE

The Zyggregator method for predicting protein aggregation propensities

(2008) Gian Gaetano Tartaglia et al.   CHEMICAL SOCIETY REVIEWS

Prediction of Aggregation-Prone Regions in Structured Proteins

(2008) Gian Gaetano Tartaglia et al.   JOURNAL OF MOLECULAR BIOLOGY

Misfolded proteins partition between two distinct quality control compartments

(2008) Daniel Kaganovich et al.   NATURE

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY