Mechanisms and Regulation of RNA Condensation in RNP Granule Formation

Trends in Biochemical Sciences, Journal Year: 2020, Volume and Issue: 45(9), P. 764 - 778

Published: May 11, 2020

Intermolecular RNA–RNA interactions contribute to the formation, content, and biophysical properties of many RNP granules.Cells utilize both genetically programmed promiscuous in granules.RNA–protein modulate protein dynamics have evolved mechanisms regulate RNA condensation through chaperones.RNA chaperones can be influenced by post-translational modifications (PTMs). Ribonucleoprotein (RNP) granules are RNA–protein assemblies that involved multiple aspects metabolism linked memory, development, disease. Some form, part, formation intermolecular interactions. In vitro, such trans occurs readily, suggesting cells require RNA-based condensation. We assess how this phenomenon. propose control ATP-dependent processes, static buffering, dynamic mechanisms. Moreover, perturbations these This reveals cellular kinetic thermodynamic maintain proper distribution molecules between dispersed condensed forms. Eukaryotic contain a variety ribonucleoprotein (see Glossary). large non-membrane-bound present nucleus cytosol. Examples include nucleolus (the site rRNA biogenesis), stress (SGs; which form from untranslating RNAs [1.Buchan J.R. Parker R. granules: ins outs translation.Mol. Cell. 2009; 36: 932-941Abstract Full Text PDF PubMed Scopus (763) Google Scholar]), neuronal (that important for transport translation synaptic mRNAs plasticity [2.Bakthavachalu B. et al.RNP-granule assembly via ataxin-2 disordered domains is required long-term memory neurodegeneration.Neuron. 2018; 98: 754-766Abstract (26) Scholar]). members growing class biological referred as biomolecular condensates (reviewed [3.Shin Y. Brangwynne C.P. Liquid phase cell physiology disease.Science. 2017; 357eaaf4382Crossref (507) Biomolecular non-membranous multivalent their components. Condensates differ traditional diverse nature allows variable size lack any unique stoichiometry or stereospecificity. generally specific population enriched RNAs. As examples, SGs P-bodies (PBs) cytoplasmic RNAs, requires transcripts its organization [4.Berry J. al.RNA transcription modulates transition-driven nuclear body assembly.Proc. Natl. Acad. Sci. U. S. A. 2015; 112: E5237-E5245Crossref Scholar], paraspeckles NEAT1 long noncoding (lnc)RNA [5.Clemson C.M. al.An architectural role RNA: essential structure paraspeckles.Mol. 33: 717-726Abstract (769) Scholar]. also compartmentalize RNA-binding proteins (RBPs). For instance, distinct RBPs accumulate PBs, although they share some components [6.Buchan mRNP granules.RNA Biol. 2014; 11: 1019-1103Crossref (0) Scholar, 7.Kedersha N. al.Stress processing bodies dynamically sites remodeling.J. Cell 2005; 169: 871-884Crossref (883) 8.Jain al.ATPase-modulated proteome substructure.Cell. 2016; 164: 487-498Abstract (374) 9.Hubstenberger al.P-body purification repressed mrna regulons.Mol. 68: 144-157Abstract (140) 10.Youn J.Y. al.High-density proximity mapping subcellular mRNA-associated bodies.Mol. 69: 517-532Abstract (127) summation protein–protein RNPs (Figure 1). Protein–protein promote granule occur bound involve well-folded [11.Protter D.S.W. Principles granules.Trends 26: 668-679Abstract (332) example, G3BP1 bind mRNAs, then dimerization increase [12.Zhang P. al.Chronic optogenetic induction cytotoxic evolution ALS-FTD pathology.Elife. 2019; 8e39578Crossref Many intrinsically regions (IDRs) forming with domains, providing additional contacts, weak other IDRs Three general lines evidence argue driven, at least self-assembly/condensation. Specifically, detailed below, self-assembly vitro readily; biochemical changes inhibit correspondingly affect cells, cells. The robust suggests will coalesce into whenever there sufficiently high local concentration sequences interact. Cells appear taken advantage phenomenon build functions. impact on P-granules Caenorhabditis elegans segregation during development [13.Lee C.H. al.Recruitment P proteins.Elife. 2020; 9e52896Crossref correlates increased survival responses [14.Aulas al.Stress-specific differences composition related foci.J. 130: 927-937Crossref (69) review here developed function. highlight spontaneous process, process kinetically thermodynamically way chaperones, chaperone function engage drive vitro. yeast total extracts readily self-assemble under approximately physiological conditions [15.Van Treeck contributes defining transcriptome.Proc. 115: 2734-2739Crossref (84) UV crosslinking shows self-assembled engages [16.Tauber D. al.Modulation DEAD-box eIF4A.Cell. 180: 411-426Abstract addition, enhance higher salt concentrations screen phosphate backbone repulsion interactions, crowding agents strengthen excluded volume effect Thus, increasing facilitates Further, cations polyamines arginine-containing dipeptide repeat especially effective promoting Scholar,17.Aumiller W.M. al.RNA-based coacervates model membraneless organelles: properties, interfacial liposome assembly.Langmuir. 32: 10042-10053Crossref (63) 18.Langdon E.M. al.mRNA determines specificity polyQ-driven separation.Science. 360: 922-927Crossref (107) 19.Boeynaems al.Spontaneous driving forces give rise protein−RNA coexisting phases complex material properties.Proc. 116: 7889-7898Crossref efficient low 2 μg/ml across range (corresponding ~10–9–10–7 M, depending transcript length), lower than 0.5–10 mg/ml (typically ~10–6–10–4 M) used demonstrate [20.Van Emerging roles assemblies.Cell. 174: 791-802Abstract well below intracellular concentration, we note caveat assays often not directly comparable. addition Watson–Crick base pairs, types molecular condensation, including non-Watson–Crick base-pairing [21.Leontis N.B. al.The pairs associated isostericity matrices.Nucleic Acids Res. 2002; 30: 3497-3531Crossref Scholar,22.Leontis Westhof E. Geometric nomenclature classification pairs.RNA. 2001; 7: 499-512Crossref (623) Hence, all homopolymer undergo partition oligonucleotides 16.Tauber 17.Aumiller bridges, cation–π, π–π helical stacking, sufficient condense short double-stranded (dsRNA) liquid crystals [23.Yevdokimov Y.M. al.Liquid-crystalline dispersions nucleic acids.Liq. Cryst. 1992; 12: 1-16Crossref Scholar,24.Zanchetta G. al.Liquid crystal ordering DNA oligomers partially overlapping sequences.J. Phys. Condens. Matter. 2008; 20: 494214Crossref (31) an condensate determined strength underlying Although homopolymeric biological, utilized simple system elucidate rules governing assembly. polypyrimidines more polyA has capacity π By contrast, polyG mixtures polyU stable gels, presumably owing G-quadruplex Scholar,16.Tauber Different specificities homotypic clustering polyC spontaneously segregate interact surfaces patterns lead spatial within consistent observation two different fungi [18.Langdon Particular features repetitiveness, ensemble diversity number predicted structures RNA) may [19.Boeynaems Scholar,25.Jain Vale R.D. transitions expansion disorders.Nature. 546: 243-247Crossref (186) 26.Fay M.M. al.ALS/FTD-associated C9ORF72 promotes cells.Cell Rep. 21: 3573-3584Abstract 27.Zhang al.G-quadruplex trigger separation.Nucleic 47: 11746-11754PubMed 28.Ma W. al.Unstructured generate TIS networks.bioRxiv. (Published online February 18, 2020. https://doi.org/10.1101/2020.02.14.949503)Google effects folding problem (Box 1) interaction (a consequence folding) likely trapped interactions.Box 1The Folding Problem ChaperonesFor typical transcript, possible would similar free energy IA). These metastable dissociate very slow timescales. possesses rugged landscape where relatively probability being nonnative conformation, [138.Herschlag problem.J. Chem. 1995; 270: 20871-20874Crossref (568) Scholar] Put differently, best understood folds (often slow) equilibrium each [139.Ganser L.R. structural RNAs.Nat. Rev. Mol. 474-489Crossref resolve actions [137.Jarmoskaite I. Russell helicase remodelers.Annu. Biochem. 83: 697-725Crossref Scholar,140.Rajkowitcsh annealers, helicases.RNA 2007; 3: 118-130Crossref (212) 141.Doetsch M. al.Transient folding.FEBS 278: 1634-1642Crossref 142.Woodson S.A. al.Proteins regulation.Microbiol. Spect. 6RWR-0026-2018Google reduce barriers conformations traps IA) act stabilize particular binding IB). To direct traps, various degrees partial unfolding, catalytic cycles unbinding [141.Doetsch 143.Russell al.Toward understanding remodeling proteins.RNA 2013; 10: 44-55Crossref (44) thus allowing fold convert conformation unfolded transition state strand-displacement mechanism IA B). Thermodynamic stabilizing destabilizing structures, blocking affinity IB).Because cis influence problem, particularly context granules, elevated compartmentalized redistribution one predict similarly kinetics thermodynamics self-assembly. Because ability possibility was suggested requirement formation. several histone locus paraspeckles, [29.Yamazaki T. al.Architectural formation.Cold Spring Harb. Symp. Quant. 2020039404Crossref Similarly, PBs depends cytosolic [30.Kedersha al.Dynamic shuttling Tia-1 accompanies recruitment mRNA granules.J. 2000; 151: 1257-1268Crossref (487) Scholar,31.Teixeira Processing nontranslating mRNAs.RNA. 371-382Crossref (447) Increasing pool decreasing initiation inhibiting degradation, increases SG PB respectively [32.Kedersha al.RNA-Binding Tiar link phosphorylation eIF-2α mammalian 1999; 147: 1431-1442Crossref (731) 33.Mazroui al.Inhibition ribosome induces independently eukaryotic factor 2α phosphorylation.Mol. 2006; 17: 4212-4219Crossref 34.Sheth Decapping decay messenger bodies.Science. 2003; 300: 805-808Crossref (857) creating injection transfection [35.Bounedjah O. al.Free excess upon polysome dissociation scaffold multimerization granules.Nucleic 42: 8678-8691Crossref (57) Scholar,36.Mahadevan K. al.RanBP2/Nup358 potentiates subset encoding secretory proteins.PLoS 11e1001545Crossref (33) Conversely, trapping them polysomes, widespread inhibits Scholar,37.Khong architecture translating ordered pathway compaction.J. 217: 4124-4140Crossref (32) 38.Burke J.M. al.RNase L reprograms turnover escaped antiviral mRNAs.Mol. 75: 1203-1217Abstract (8) 39.Yang al.G3BP1 tunable switch triggers separation assemble granules.Cell. 181: 325-345Abstract 40.Guillén-Boixet al.RNA-induced switching G3BP condensation.Cell. 346-361Abstract Additional comes correlations First, protein-free largely recapitulates transcriptome Second, prone G-quadruplexes seed SG-like foci lysates [26.Fay Third, promoted ionic whereas sensitive osmolarity influences both. G-rich repeats found repeat-expansion NH4OAc [25.Jain Finally, monomeric compete limit

Language: Английский

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Formation, function, and pathology of RNP granules

Cell, Journal Year: 2023, Volume and Issue: 186(22), P. 4737 - 4756

Published: Oct. 1, 2023

Language: Английский

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Cellular functions of eukaryotic RNA helicases and their links to human diseases

Nature Reviews Molecular Cell Biology, Journal Year: 2023, Volume and Issue: 24(10), P. 749 - 769

Published: July 20, 2023

Language: Английский

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Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle

Molecular Cell, Journal Year: 2024, Volume and Issue: 84(14), P. 2765 - 2784.e16

Published: July 1, 2024

Language: Английский

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Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms

Science, Journal Year: 2024, Volume and Issue: 384(6698)

Published: May 23, 2024

RNA splicing is highly prevalent in the brain and has strong links to neuropsychiatric disorders; yet, role of cell type-specific transcript-isoform diversity during human development not been systematically investigated. In this work, we leveraged single-molecule long-read sequencing deeply profile full-length transcriptome germinal zone cortical plate regions developing neocortex at tissue single-cell resolution. We identified 214,516 distinct isoforms, which 72.6% were novel (not previously annotated Gencode version 33), uncovered a substantial contribution diversity-regulated by binding proteins-in defining cellular identity neocortex. comprehensive isoform-centric gene annotation reprioritize thousands rare de novo risk variants elucidate genetic mechanisms for disorders.

Language: Английский

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A subpopulation of cortical neurons altered by mutations in the autism risk gene DDX3X

Biology Open, Journal Year: 2025, Volume and Issue: 14(1)

Published: Jan. 15, 2025

ABSTRACT Cell fate decisions during cortical development sculpt the identity of long-range connections that subserve complex behaviors. These are largely dictated by mutually exclusive transcription factors, including CTIP2/Bcl11b for subcerebral projection neurons and BRN1/Pou3f3 intra-telencephalic neurons. We have recently reported balance CTIP2-expressing is altered in a mouse model DDX3X syndrome, female-biased neurodevelopmental disorder associated with intellectual disability, autism spectrum disorder, significant motor challenges. Here, we studied developmental dynamics subpopulation co-expressing CTIP2 BRN1. found CTIP2+BRN1+ born early phases neurogenesis like other CTIP2+ neurons, peak expression perinatal life, persist adult brains. also excessive number prenatal mature areas Ddx3x mutant mice, translating into laminar distribution extending axons to brainstem. findings underscore critical role molecular specification health disease.

Language: Английский

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DDX3 depletion represses translation of mRNAs with complex 5′ UTRs

Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 49(9), P. 5336 - 5350

Published: April 9, 2021

Abstract DDX3 is an RNA chaperone of the DEAD-box family that regulates translation. Ded1, yeast ortholog DDX3, a global regulator translation, whereas thought to preferentially affect subset mRNAs. However, set mRNAs are regulated by unknown, along with relationship between binding and activity. Here, we use ribosome profiling, RNA-seq, PAR-CLIP define in human cells. We find while binds highly expressed mRNAs, depletion particularly affects translation small transcriptome. further site on helix 16 ribosomal rRNA, placing it immediately adjacent mRNA entry channel. Translation changes caused depleting levels or expressing inactive point mutation different, consistent different association these genetic variant types disease. Taken together, this work defines transcriptome responsive inhibition, relevance for basic biology disease states where altered.

Language: Английский

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Sequential inverse dysregulation of the RNA helicases DDX3X and DDX3Y facilitates MYC-driven lymphomagenesis

Molecular Cell, Journal Year: 2021, Volume and Issue: 81(19), P. 4059 - 4075.e11

Published: Aug. 25, 2021

DDX3X is a ubiquitously expressed RNA helicase involved in multiple stages of biogenesis. frequently mutated Burkitt lymphoma, but the functional basis for this unknown. Here, we show that loss-of-function mutations are also enriched MYC-translocated diffuse large B cell lymphoma and reveal cooperation between mutant MYC. promotes translation mRNA encoding components core translational machinery, thereby driving global protein synthesis. Loss-of-function moderate MYC-driven synthesis, buffering MYC-induced proteotoxic stress during early lymphomagenesis. Established cells restore full synthetic capacity by aberrant expression DDX3Y, Y chromosome homolog, which normally restricted to testis. These findings loss function can buffer highlight male lymphomas then compensate ectopic DDX3Y expression.

Language: Английский

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Sexually dimorphic RNA helicases DDX3X and DDX3Y differentially regulate RNA metabolism through phase separation

Molecular Cell, Journal Year: 2022, Volume and Issue: 82(14), P. 2588 - 2603.e9

Published: May 18, 2022

Language: Английский

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DDX3X and DDX3Y are redundant in protein synthesis

RNA, Journal Year: 2021, Volume and Issue: 27(12), P. 1577 - 1588

Published: Sept. 17, 2021

DDX3 is a DEAD-box RNA helicase that regulates translation and encoded by the X- Y-linked paralogs DDX3X DDX3Y . While ubiquitously expressed in human tissues essential for viability, male-specific shows lower more variable expression than somatic tissues. Heterozygous genetic lesions mediate class of developmental disorders called syndrome, while loss implicated male infertility. One possible explanation female-bias syndrome encodes polypeptide with different biochemical activity. In this study, we use ribosome profiling vitro to demonstrate play functionally redundant roles translation. We find transcripts are sensitive depletion or mutation rescued complementation DDX3Y. Our data indicate proteins can complement each other context mRNA cells. not large fraction central nervous system. These findings suggest differences, differences paralog-dependent protein synthesis, underlie sex-bias DDX3X-associated diseases.

Language: Английский

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