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Yucel-Polat A, Campos-Melo D, Alikhah A, Strong MJ. Dynamic Localization of Paraspeckle Components under Osmotic Stress. Noncoding RNA 2024; 10:23. [PMID: 38668381 PMCID: PMC11053584 DOI: 10.3390/ncrna10020023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024] Open
Abstract
Paraspeckles are nuclear condensates formed by NEAT1_2 lncRNA and different RNA-binding proteins. In general, these membraneless organelles function in the regulation of gene expression and translation and in miRNA processing, and in doing this, they regulate cellular homeostasis and mediate pro-survival in the cell. Despite evidence showing the importance of paraspeckles in the stress response, the dynamics of paraspeckles and their components under conditions of osmotic stress remain unknown. We exposed HEK293T cells to sorbitol and examined NEAT1_2 expression using real-time PCR. Localization and quantification of the main paraspeckle components, NEAT1_2, PSPC1, NONO, and SFPQ, in different cellular compartments was performed using smFISH and immunofluorescence. Our findings showed a significant decrease in total NEAT1_2 expression in cells after osmotic stress. Sorbitol shifted the subcellular localization of NEAT1_2, PSPC1, NONO, and SFPQ from the nucleus to the cytoplasm and decreased the number and size of NEAT1_2 foci in the nucleus. PSPC1 formed immunoreactive cytoplasmic fibrils under conditions of osmotic stress, which slowly disassembled under recovery. Our study deepens the paraspeckle dynamics in response to stress, suggesting a novel role for NEAT1_2 in the cytoplasm in osmotic stress and physiological conditions.
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Affiliation(s)
- Aysegul Yucel-Polat
- Molecular Medicine Group, Schulich School of Medicine & Dentistry, Robarts Research Institute, Western University, London, ON N6A 3K7, Canada; (A.Y.-P.); (A.A.)
| | - Danae Campos-Melo
- Molecular Medicine Group, Schulich School of Medicine & Dentistry, Robarts Research Institute, Western University, London, ON N6A 3K7, Canada; (A.Y.-P.); (A.A.)
| | - Asieh Alikhah
- Molecular Medicine Group, Schulich School of Medicine & Dentistry, Robarts Research Institute, Western University, London, ON N6A 3K7, Canada; (A.Y.-P.); (A.A.)
| | - Michael J. Strong
- Molecular Medicine Group, Schulich School of Medicine & Dentistry, Robarts Research Institute, Western University, London, ON N6A 3K7, Canada; (A.Y.-P.); (A.A.)
- Department of Clinical Neurological Sciences, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada
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Obuse C, Hirose T. Functional domains of nuclear long noncoding RNAs: Insights into gene regulation and intracellular architecture. Curr Opin Cell Biol 2023; 85:102250. [PMID: 37806294 DOI: 10.1016/j.ceb.2023.102250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/12/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023]
Abstract
Recent functional research on long noncoding RNAs (lncRNAs) has revealed their significant regulatory roles in gene expression and intracellular architecture. Well-characterized examples of such lncRNAs include Xist and NEAT1_2, which play critical roles in heterochromatin formation of inactive X-chromosomes and paraspeckle assembly, in mammalian cells. Both lncRNAs possess modular domain structures with multiple functionally distinct domains that serve as platforms for specific RNA-binding proteins (RBPs), which dictate the function of each lncRNA. Some of these RBPs bind characteristic RNA structures, which can be targeted by small chemical compounds that modulate lncRNA function by perturbing the interaction of RBPs with the RNA structures. Therefore, RNA structures hidden in lncRNAs represent a novel and potent type of therapeutic target.
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Affiliation(s)
- Chikashi Obuse
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan; Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita 565-0871, Japan
| | - Tetsuro Hirose
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita 565-0871, Japan.
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Yamamoto T, Yamazaki T, Ninomiya K, Hirose T. Nascent ribosomal RNA act as surfactant that suppresses growth of fibrillar centers in nucleolus. Commun Biol 2023; 6:1129. [PMID: 37935838 PMCID: PMC10630424 DOI: 10.1038/s42003-023-05519-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) has been thought to be the biophysical principle governing the assembly of the multiphase structures of nucleoli, the site of ribosomal biogenesis. Condensates assembled through LLPS increase their sizes to minimize the surface energy as far as their components are available. However, multiple microphases, fibrillar centers (FCs), dispersed in a nucleolus are stable and their sizes do not grow unless the transcription of pre-ribosomal RNA (pre-rRNA) is inhibited. To understand the mechanism of the suppression of the FC growth, we here construct a minimal theoretical model by taking into account nascent pre-rRNAs tethered to FC surfaces by RNA polymerase I. The prediction of this theory was supported by our experiments that quantitatively measure the dependence of the size of FCs on the transcription level. This work sheds light on the role of nascent RNAs in controlling the size of nuclear bodies.
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Affiliation(s)
- Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, 001-0021, Japan.
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8, Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Tomohiro Yamazaki
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, 565-0871, Japan.
| | - Kensuke Ninomiya
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, 565-0871, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 1-3 Yamadaoka, Suita, 565-0871, Japan
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Yamamoto T, Kinoshita K, Hirano T. Elasticity control of entangled chromosomes: Crosstalk between condensin complexes and nucleosomes. Biophys J 2023; 122:3869-3881. [PMID: 37571823 PMCID: PMC10560673 DOI: 10.1016/j.bpj.2023.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/18/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023] Open
Abstract
Condensin-mediated loop extrusion is now considered as the main driving force of mitotic chromosome assembly. Recent experiments have shown, however, that a class of mutant condensin complexes deficient in loop extrusion can assemble chromosome-like structures in Xenopus egg extracts, although these structures are somewhat different from those assembled by wild-type condensin complexes. In the absence of topoisomerase II (topo II), the mutant condensin complexes produce an unusual round-shaped structure termed a bean, which consists of a DNA-dense central core surrounded by a DNA-sparse halo. The mutant condensin complexes accumulate in the core, whereas histones are more concentrated in the halo than in the core. We consider that this peculiar structure serves as a model system to study how DNA entanglements, nucleosomes, and condensin functionally crosstalk with each other. To gain insight into how the bean structure is formed, here we construct a theoretical model. Our theory predicts that the core is formed by attractive interactions between mutant condensin complexes, whereas the halo is stabilized by the energy reduction through the selective accumulation of nucleosomes. The formation of the halo increases the elastic free energy due to the DNA entanglement in the core, but the latter free energy is compensated by condensin complexes that suppress the assembly of nucleosomes.
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Affiliation(s)
- Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery (ICReDD), Hokkaido University, Sapporo, Hokkaido, Japan.
| | | | - Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama, Japan
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Yamamoto T, Li W. Polymer brush inspired by ribosomal RNA transcription. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:61. [PMID: 37493801 DOI: 10.1140/epje/s10189-023-00323-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023]
Abstract
Pre-ribosomal RNAs are synthesized during the transcription by RNA polymerase I molecules localized at the surfaces of a nucleolus subcompartment. Inspired by the ribosomal RNA transcription, we here develop a scaling theory of a brush of polymers, where monomers are added to their grafted ends in the steady state. Our theory predicts that monomers newly added to the polymers stay at the vicinity of the surface due to the slow dynamics of the polymers and thus the polymer volume fraction increases with increasing the polymerization rate. The excluded volume interaction between polymers and reactant monomers suppresses the diffusion of reactant monomers and thus decreases the polymerization rate. The extent of the suppression of monomer diffusion increases with increasing the polymerization rate because the diffusion length decreases, rather than the condensation of polymers due to their slow dynamics.
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Affiliation(s)
- Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, 001-0021, Hokkaido, Japan.
| | - Wei Li
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, 001-0021, Hokkaido, Japan
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Yamazaki T, Yamamoto T, Hirose T. Micellization: A new principle in the formation of biomolecular condensates. Front Mol Biosci 2022; 9:974772. [PMID: 36106018 PMCID: PMC9465675 DOI: 10.3389/fmolb.2022.974772] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/20/2022] [Indexed: 11/18/2022] Open
Abstract
Phase separation is a fundamental mechanism for compartmentalization in cells and leads to the formation of biomolecular condensates, generally containing various RNA molecules. RNAs are biomolecules that can serve as suitable scaffolds for biomolecular condensates and determine their forms and functions. Many studies have focused on biomolecular condensates formed by liquid-liquid phase separation (LLPS), one type of intracellular phase separation mechanism. We recently identified that paraspeckle nuclear bodies use an intracellular phase separation mechanism called micellization of block copolymers in their formation. The paraspeckles are scaffolded by NEAT1_2 long non-coding RNAs (lncRNAs) and their partner RNA-binding proteins (NEAT1_2 RNA-protein complexes [RNPs]). The NEAT1_2 RNPs act as block copolymers and the paraspeckles assemble through micellization. In LLPS, condensates grow without bound as long as components are available and typically have spherical shapes to minimize surface tension. In contrast, the size, shape, and internal morphology of the condensates are more strictly controlled in micellization. Here, we discuss the potential importance and future perspectives of micellization of block copolymers of RNPs in cells, including the construction of designer condensates with optimal internal organization, shape, and size according to design guidelines of block copolymers.
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Affiliation(s)
- Tomohiro Yamazaki
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- *Correspondence: Tomohiro Yamazaki, ; Tetsuro Hirose,
| | - Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Japan
- *Correspondence: Tomohiro Yamazaki, ; Tetsuro Hirose,
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