1
|
Yazaki J, Yamanashi T, Nemoto S, Kobayashi A, Han YW, Hasegawa T, Iwase A, Ishikawa M, Konno R, Imami K, Kawashima Y, Seita J. Mapping adipocyte interactome networks by HaloTag-enrichment-mass spectrometry. Biol Methods Protoc 2024; 9:bpae039. [PMID: 38884001 PMCID: PMC11180226 DOI: 10.1093/biomethods/bpae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/19/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024] Open
Abstract
Mapping protein interaction complexes in their natural state in vivo is arguably the Holy Grail of protein network analysis. Detection of protein interaction stoichiometry has been an important technical challenge, as few studies have focused on this. This may, however, be solved by artificial intelligence (AI) and proteomics. Here, we describe the development of HaloTag-based affinity purification mass spectrometry (HaloMS), a high-throughput HaloMS assay for protein interaction discovery. The approach enables the rapid capture of newly expressed proteins, eliminating tedious conventional one-by-one assays. As a proof-of-principle, we used HaloMS to evaluate the protein complex interactions of 17 regulatory proteins in human adipocytes. The adipocyte interactome network was validated using an in vitro pull-down assay and AI-based prediction tools. Applying HaloMS to probe adipocyte differentiation facilitated the identification of previously unknown transcription factor (TF)-protein complexes, revealing proteome-wide human adipocyte TF networks and shedding light on how different pathways are integrated.
Collapse
Affiliation(s)
- Junshi Yazaki
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Faculty of Agriculture, Laboratory for Genome Biology, Setsunan University, Osaka, 573-0101, Japan
| | - Takashi Yamanashi
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Medical Data Deep Learning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Tokyo, 103-0027, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, 305-8577, Japan
| | - Shino Nemoto
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Atsuo Kobayashi
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Yong-Woon Han
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Tomoko Hasegawa
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Akira Iwase
- Cell Function Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Masaki Ishikawa
- Department of Applied Genomics, Technology Development Team, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Ryo Konno
- Department of Applied Genomics, Technology Development Team, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Koshi Imami
- Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Technology Development Team, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Jun Seita
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Medical Data Deep Learning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Tokyo, 103-0027, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, 305-8577, Japan
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Takakuwa H, Yamazaki T, Souquere S, Adachi S, Yoshino H, Fujiwara N, Yamamoto T, Natsume T, Nakagawa S, Pierron G, Hirose T. Shell protein composition specified by the lncRNA NEAT1 domains dictates the formation of paraspeckles as distinct membraneless organelles. Nat Cell Biol 2023; 25:1664-1675. [PMID: 37932453 DOI: 10.1038/s41556-023-01254-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 09/12/2023] [Indexed: 11/08/2023]
Abstract
Many membraneless organelles (MLOs) formed through phase separation play crucial roles in various cellular processes. Although these MLOs co-exist in cells, how they maintain their independence without coalescence or engulfment remains largely unknown. Here, we investigated the molecular mechanism by which paraspeckles with core-shell architecture scaffolded by NEAT1_2 long noncoding RNAs exist as distinct MLOs. We identified NEAT1 deletion mutants that assemble paraspeckles that are incorporated into nuclear speckles. Several paraspeckle proteins, including SFPQ, HNRNPF and BRG1, prevent this incorporation and thus contribute to the segregation of paraspeckles from nuclear speckles. Shell localization of these proteins in the paraspeckles, which is determined by NEAT1_2 long noncoding RNA domains, is required for this segregation process. Conversely, U2-related spliceosomal proteins are involved in internalizing the paraspeckles into nuclear speckles. This study shows that the paraspeckle shell composition dictates the independence of MLOs in the nucleus, providing insights into the importance of the shell in defining features and functions of MLOs.
Collapse
Affiliation(s)
- Hiro Takakuwa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Tomohiro Yamazaki
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.
| | | | - Shungo Adachi
- Department of Proteomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hyura Yoshino
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Naoko Fujiwara
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, Japan
| | - Tohru Natsume
- Cellular and Molecular Biotechnology Research Institute, National Institute for Advanced Industrial Science and Technology, Tokyo, Japan
| | - Shinichi Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Gerard Pierron
- Centre National de la Recherche Scientifique, UMR-9196, Gustave Roussy, Villejuif, France
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
| |
Collapse
|
5
|
Ninomiya K, Yamazaki T, Hirose T. Satellite RNAs: emerging players in subnuclear architecture and gene regulation. EMBO J 2023; 42:e114331. [PMID: 37526230 PMCID: PMC10505914 DOI: 10.15252/embj.2023114331] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/13/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023] Open
Abstract
Satellite DNA is characterized by long, tandemly repeated sequences mainly found in centromeres and pericentromeric chromosomal regions. The recent advent of telomere-to-telomere sequencing data revealed the complete sequences of satellite regions, including centromeric α-satellites and pericentromeric HSat1-3, which together comprise ~ 5.7% of the human genome. Despite possessing constitutive heterochromatin features, these regions are transcribed to produce long noncoding RNAs with highly repetitive sequences that associate with specific sets of proteins to play various regulatory roles. In certain stress or pathological conditions, satellite RNAs are induced to assemble mesoscopic membraneless organelles. Specifically, under heat stress, nuclear stress bodies (nSBs) are scaffolded by HSat3 lncRNAs, which sequester hundreds of RNA-binding proteins. Upon removal of the stressor, nSBs recruit additional regulatory proteins, including protein kinases and RNA methylases, which modify the previously sequestered nSB components. The sequential recruitment of substrates and enzymes enables nSBs to efficiently regulate the splicing of hundreds of pre-mRNAs under limited temperature conditions. This review discusses the structural features and regulatory roles of satellite RNAs in intracellular architecture and gene regulation.
Collapse
Affiliation(s)
- Kensuke Ninomiya
- Graduate School of Frontier BiosciencesOsaka UniversitySuitaJapan
| | | | - Tetsuro Hirose
- Graduate School of Frontier BiosciencesOsaka UniversitySuitaJapan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI)Osaka UniversitySuitaJapan
| |
Collapse
|
6
|
Hirose T, Ninomiya K, Nakagawa S, Yamazaki T. A guide to membraneless organelles and their various roles in gene regulation. Nat Rev Mol Cell Biol 2023; 24:288-304. [PMID: 36424481 DOI: 10.1038/s41580-022-00558-8] [Citation(s) in RCA: 90] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2022] [Indexed: 11/25/2022]
Abstract
Membraneless organelles (MLOs) are detected in cells as dots of mesoscopic size. By undergoing phase separation into a liquid-like or gel-like phase, MLOs contribute to intracellular compartmentalization of specific biological functions. In eukaryotes, dozens of MLOs have been identified, including the nucleolus, Cajal bodies, nuclear speckles, paraspeckles, promyelocytic leukaemia protein (PML) nuclear bodies, nuclear stress bodies, processing bodies (P bodies) and stress granules. MLOs contain specific proteins, of which many possess intrinsically disordered regions (IDRs), and nucleic acids, mainly RNA. Many MLOs contribute to gene regulation by different mechanisms. Through sequestration of specific factors, MLOs promote biochemical reactions by simultaneously concentrating substrates and enzymes, and/or suppressing the activity of the sequestered factors elsewhere in the cell. Other MLOs construct inter-chromosomal hubs by associating with multiple loci, thereby contributing to the biogenesis of macromolecular machineries essential for gene expression, such as ribosomes and spliceosomes. The organization of many MLOs includes layers, which might have different biophysical properties and functions. MLOs are functionally interconnected and are involved in various diseases, prompting the emergence of therapeutics targeting them. In this Review, we introduce MLOs that are relevant to gene regulation and discuss their assembly, internal structure, gene-regulatory roles in transcription, RNA processing and translation, particularly in stress conditions, and their disease relevance.
Collapse
Affiliation(s)
- Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
| | - Kensuke Ninomiya
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Shinichi Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Tomohiro Yamazaki
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| |
Collapse
|
7
|
Mukherjee A, Islam S, Kieser RE, Kiss DL, Mukherjee C. Long noncoding RNAs are substrates for cytoplasmic capping enzyme. FEBS Lett 2023; 597:947-961. [PMID: 36856012 PMCID: PMC11119571 DOI: 10.1002/1873-3468.14603] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 03/02/2023]
Abstract
Cytoplasmic capping returns a cap to specific mRNAs, thus protecting uncapped RNAs from decay. Prior to the identification of cytoplasmic capping, uncapped mRNAs were thought to be degraded. Here, we test whether long noncoding RNAs (lncRNAs) are substrates of the cytoplasmic capping enzyme (cCE). The subcellular localisation of 14 lncRNAs associated with sarcomas were examined in U2OS osteosarcoma cells. We used 5' rapid amplification of cDNA ends (RACE) to assay uncapped forms of these lncRNAs. Inhibiting cytoplasmic capping elevated uncapped forms of selected lncRNAs indicating a plausible role of cCE in targeting them. Analysis of published cap analysis of gene expression (CAGE) data shows increased prevalence of certain 5'-RACE cloned sequences, suggesting that these uncapped lncRNAs are targets of cytoplasmic capping.
Collapse
Affiliation(s)
- Avik Mukherjee
- Institute of Health Sciences, Presidency University, Kolkata, India
| | - Safirul Islam
- Institute of Health Sciences, Presidency University, Kolkata, India
| | - Rachel E Kieser
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Daniel L Kiss
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Weill Cornell Medical College, New York, NY, USA
- Houston Methodist Cancer Center, Houston, TX, USA
- Houston Methodist Academic Institute, Houston, TX, USA
| | | |
Collapse
|
8
|
Iwakiri J, Tanaka K, Chujo T, Takakuwa H, Yamazaki T, Terai G, Asai K, Hirose T. Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing. RNA (NEW YORK, N.Y.) 2023; 29:170-177. [PMID: 36384963 PMCID: PMC9891252 DOI: 10.1261/rna.079469.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
The mammalian cell nucleus contains dozens of membrane-less nuclear bodies that play significant roles in various aspects of gene expression. Several nuclear bodies are nucleated by specific architectural noncoding RNAs (arcRNAs) acting as structural scaffolds. We have reported that a minor population of cellular RNAs exhibits an unusual semi-extractable feature upon using the conventional procedure of RNA preparation and that needle shearing or heating of cell lysates remarkably improves extraction of dozens of RNAs. Because semi-extractable RNAs, including known arcRNAs, commonly localize in nuclear bodies, this feature may be a hallmark of arcRNAs. Using the semi-extractability of RNA, we performed genome-wide screening of semi-extractable long noncoding RNAs to identify new candidate arcRNAs for arcRNA under hyperosmotic and heat stress conditions. After screening stress-inducible and semi-extractable RNAs, hundreds of readthrough downstream-of-gene (DoG) transcripts over several hundreds of kilobases, many of which were not detected among RNAs prepared by the conventional extraction procedure, were found to be stress-inducible and semi-extractable. We further characterized some of the abundant DoGs and found that stress-inducible transient extension of the 3'-UTR made DoGs semi-extractable. Furthermore, they were localized in distinct nuclear foci that were sensitive to 1,6-hexanediol. These data suggest that semi-extractable DoGs exhibit arcRNA-like features and our semi-extractable RNA-seq is a powerful tool to extensively monitor DoGs that are induced under specific physiological conditions.
Collapse
Affiliation(s)
- Junichi Iwakiri
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Kumiko Tanaka
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Takeshi Chujo
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Hiro Takakuwa
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Tomohiro Yamazaki
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Goro Terai
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Kiyoshi Asai
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Tetsuro Hirose
- 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
| |
Collapse
|
9
|
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.
Collapse
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,
| |
Collapse
|
10
|
Yamamoto T, Yamazaki T, Hirose T. Triblock copolymer micelle model of spherical paraspeckles. Front Mol Biosci 2022; 9:925058. [PMID: 36072433 PMCID: PMC9441768 DOI: 10.3389/fmolb.2022.925058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Paraspeckles are nuclear bodies scaffolded by RNP complexes of NEAT1_2 RNA transcripts and multiple RNA-binding proteins. The assembly of paraspeckles is coupled with the transcription of NEAT1_2. Paraspeckles form the core-shell structure, where the two terminal regions of NEAT1_2 RNP complexes compose the shell of the paraspeckle and the middle regions of these complexes compose the core. We here construct a theoretical model of paraspeckles by taking into account the transcription of NEAT1_2 in an extension of the theory of block copolymer micelles. This theory predicts that the core-shell structure of a paraspeckle is assembled by the association of the middle region of NEAT1_2 RNP complexes due to the multivalent interactions between RBPs bound to these regions and by the relative affinity of the terminal regions of the complexes to the nucleoplasm. The latter affinity results in the effective repulsive interactions between terminal regions of the RNA complexes and limits the number of complexes composing the paraspeckle. In the wild type, the repulsive interaction between the middle and terminal block dominates the thermal fluctuation. However, the thermal fluctuation can be significant in a mutant, where a part of the terminal regions of NEAT1_2 is deleted, and distributes the shortened terminal regions randomly between the shell and the core, consistent with our recent experiments. With the upregulated transcription, the shortened terminal regions of NEAT1_2 in a deletion mutant is localized to the core to decrease the repulsive interaction between the terminal regions, while the structure does not change with the upregulation in the wild type. The robustness of the structure of paraspeckles in the wild type results from the polymeric nature of NEAT1_2 complexes.
Collapse
Affiliation(s)
- Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Japan
- *Correspondence: Tetsuya Yamamoto,
| | - Tomohiro Yamazaki
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| |
Collapse
|
11
|
Box-shaped ribozyme octamer formed by face-to-face dimerization of a pair of square-shaped ribozyme tetramers. J Biosci Bioeng 2022; 134:195-202. [PMID: 35810135 DOI: 10.1016/j.jbiosc.2022.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 11/21/2022]
Abstract
Naturally occurring ribozymes with defined three-dimensional (3D) structures serve as promising platforms for the design and construction of artificial RNA nanostructures. We constructed a hexameric ribozyme nanostructure by face-to-face dimerization of a pair of triangular ribozyme trimers, unit RNAs of which were derived from the Tetrahymena group I ribozyme. In this study, we have expanded the dimerization strategy to a square-shaped ribozyme tetramer by introducing four pillar units. The resulting box-shaped nanostructures, which contained eight ribozyme units, can be assembled from either four or two components of their unit RNAs.
Collapse
|
12
|
Bose M, Lampe M, Mahamid J, Ephrussi A. Liquid-to-solid phase transition of oskar ribonucleoprotein granules is essential for their function in Drosophila embryonic development. Cell 2022; 185:1308-1324.e23. [PMID: 35325593 PMCID: PMC9042795 DOI: 10.1016/j.cell.2022.02.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 11/24/2021] [Accepted: 02/18/2022] [Indexed: 01/05/2023]
Abstract
Asymmetric localization of oskar ribonucleoprotein (RNP) granules to the oocyte posterior is crucial for abdominal patterning and germline formation in the Drosophila embryo. We show that oskar RNP granules in the oocyte are condensates with solid-like physical properties. Using purified oskar RNA and scaffold proteins Bruno and Hrp48, we confirm in vitro that oskar granules undergo a liquid-to-solid phase transition. Whereas the liquid phase allows RNA incorporation, the solid phase precludes incorporation of additional RNA while allowing RNA-dependent partitioning of client proteins. Genetic modification of scaffold granule proteins or tethering the intrinsically disordered region of human fused in sarcoma (FUS) to oskar mRNA allowed modulation of granule material properties in vivo. The resulting liquid-like properties impaired oskar localization and translation with severe consequences on embryonic development. Our study reflects how physiological phase transitions shape RNA-protein condensates to regulate the localization and expression of a maternal RNA that instructs germline formation. oskar RNP granules in the developing oocyte are solid-like condensates oskar RNP granules undergo liquid-to-solid phase transition in vitro The liquid phase incorporates mRNA, while the solid phase enriches specific proteins Perturbing the solid state impairs oskar localization, translation, and development
Collapse
Affiliation(s)
- Mainak Bose
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Marko Lampe
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
| |
Collapse
|
13
|
Yamazaki T, Yamamoto T. Statistical Thermodynamics Approach for Intracellular Phase Separation. Methods Mol Biol 2022; 2509:361-393. [PMID: 35796975 DOI: 10.1007/978-1-0716-2380-0_22] [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] [Indexed: 06/15/2023]
Abstract
Phase separation is one of the fundamental processes to compartmentalize biomolecules in living cells. RNA-protein complexes (RNPs) often scaffold biomolecular condensates formed through phase separation. We here present a statistical thermodynamics approach to investigate intracellular phase separation. We first present the statistical thermodynamic theory of the liquid-liquid phase separation (LLPS) of two molecules (such as proteins and solvent molecules) and of a polymer solution (such as RNPs and solvent molecules). Condensates produced by LLPS show coarsening and/or coalescence to minimize their total surface area. In addition to the LLPS, there are other types of self-assembly, such as microphase separation, micellization, emulsification, and vesiculation, with which the growth of the assembly stops with optimal size and shape. We also describe a scaling theory of micelles of block copolymers, where their structures are analogous to the core-shell structure of paraspeckle nuclear bodies scaffolded by RNPs of NEAT1_2 long noncoding RNAs (lncRNAs) and RNA-binding proteins (RBPs). These theories treat the self-assembly of polymers in the thermodynamic equilibrium, where their concentrations and compositions do not change with time. In contrast, RNPs are produced according to the transcription of RNAs and are degraded with time. We therefore take into account the dynamical aspect of the production of RNPs in an extension of the theory of the self-assembly of soft matter. Finally, we discuss the structure of paraspeckles as an example to demonstrate that an approach combining experiment and theory is powerful to investigate the mechanism of intracellular phase separation.
Collapse
Affiliation(s)
- Tomohiro Yamazaki
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.
| | - Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, Japan
- PRESTO, Japan Science and Technology Agency (JST), Saitama, Japan
| |
Collapse
|
14
|
Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen CK, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Noncoding RNAs: biology and applications-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:118-141. [PMID: 34791665 PMCID: PMC9808899 DOI: 10.1111/nyas.14713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 01/07/2023]
Abstract
The human transcriptome contains many types of noncoding RNAs, which rival the number of protein-coding species. From long noncoding RNAs (lncRNAs) that are over 200 nucleotides long to piwi-interacting RNAs (piRNAs) of only 20 nucleotides, noncoding RNAs play important roles in regulating transcription, epigenetic modifications, translation, and cell signaling. Roles for noncoding RNAs in disease mechanisms are also being uncovered, and several species have been identified as potential drug targets. On May 11-14, 2021, the Keystone eSymposium "Noncoding RNAs: Biology and Applications" brought together researchers working in RNA biology, structure, and technologies to accelerate both the understanding of RNA basic biology and the translation of those findings into clinical applications.
Collapse
Affiliation(s)
| | - Edith Heard
- European Molecular Biology Laboratory (EMBL), Heidelberg, Heidelberg, Germany
- Collège de France, Paris, France
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of the Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- School of Life Sciences, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou, China
| | | | - Sofia A Quinodoz
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor and Genetics Program, Stony Brook University, Stony Brook, New York
| | - Sarah D Diermeier
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Allison M Porman
- Biochemistry and Molecular Genetics Department, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Dhiraj Kumar
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark W Feinberg
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Xiaohua Shen
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - Juan Pablo Unfried
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, Universidad de Navarra (UNAV), Pamplona, Spain
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital; and Department for BioMedical Research University of Bern, Bern, Switzerland
- School of Biology and Environmental Science and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chun-Kan Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Adelheid Lempradl
- Department of Metabolism and Nutritional Programming, Van Andel Research Institute, Grand Rapids, Michigan
| | - Sean E McGeary
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
- Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Lamia Wahba
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Anna Marie Pyle
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
- Connecticut and Howard Hughes Medical Institute, Chevy Chase, Maryland
| | | | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | - Róża K Przanowska
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California
- Howard Hughes Medical Institute, Stanford University, Stanford, California
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College of Cornell University, New York, New York
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, California
| | - Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, California
| | - Joshua T Mendell
- Department of Molecular Biology, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine; and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Lin He
- Division of Cellular and Developmental Biology, Molecular and Cell Biology Department, University of California at Berkeley, Berkeley, California
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center and Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Bioland Laboratory; Program of Molecular Medicine, Zhongshan School of Medicine, Sun Yat-sen University; and Fountain-Valley Institute for Life Sciences, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences Guangzhou, Guangzhou, China
| | - John L Rinn
- Department of Biochemistry, BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado
| | - Mukesh Kumar Lalwani
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, Scotland, United Kingdom
| | - Murat Can Kalem
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, New York
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry and Center for RNA Biology, University of Rochester, Rochester, New York
| | - Xuhang Liu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, New York
| |
Collapse
|
15
|
Mannen T, Goto M, Yoshizawa T, Yamashita A, Hirose T, Hayano T. Distinct RNA polymerase transcripts direct the assembly of phase-separated DBC1 nuclear bodies in different cell lines. Mol Biol Cell 2021; 32:ar33. [PMID: 34495685 PMCID: PMC8693952 DOI: 10.1091/mbc.e21-02-0081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The mammalian cell nucleus is a highly organized organelle that contains membrane-less structures referred to as nuclear bodies (NBs). Some NBs carry specific RNA types that play architectural roles in their formation. Here, we show two types of RNase-sensitive DBC1-containing NBs, DBC1 nuclear body (DNB) in HCT116 cells and Sam68 nuclear body (SNB) in HeLa cells, that exhibit phase-separated features and are constructed using RNA polymerase I or II transcripts in a cell type–specific manner. We identified additional protein components present in DNB by immunoprecipitation–mass spectrometry, some of which (DBC1 and heterogeneous nuclear ribonucleoprotein L [HNRNPL]) are required for DNB formation. The rescue experiment using the truncated HNRNPL mutants revealed that two RNA-binding domains and intrinsically disordered regions of HNRNPL play significant roles in DNB formation. All these domains of HNRNPL promote in vitro droplet formation, suggesting the need for multivalent interactions between HNRNPL and RNA as well as proteins in DNB formation.
Collapse
Affiliation(s)
- Taro Mannen
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Masato Goto
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Takuya Yoshizawa
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Akio Yamashita
- Graduate School of Medicine, University of the Ryukyus, Nishihara-cho 903-0215, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Toshiya Hayano
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| |
Collapse
|
16
|
Herbert A. The Simple Biology of Flipons and Condensates Enhances the Evolution of Complexity. Molecules 2021; 26:molecules26164881. [PMID: 34443469 PMCID: PMC8400190 DOI: 10.3390/molecules26164881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 01/09/2023] Open
Abstract
The classical genetic code maps nucleotide triplets to amino acids. The associated sequence composition is complex, representing many elaborations during evolution of form and function. Other genomic elements code for the expression and processing of RNA transcripts. However, over 50% of the human genome consists of widely dispersed repetitive sequences. Among these are simple sequence repeats (SSRs), representing a class of flipons, that under physiological conditions, form alternative nucleic acid conformations such as Z-DNA, G4 quartets, I-motifs, and triplexes. Proteins that bind in a structure-specific manner enable the seeding of condensates with the potential to regulate a wide range of biological processes. SSRs also encode the low complexity peptide repeats to patch condensates together, increasing the number of combinations possible. In situations where SSRs are transcribed, SSR-specific, single-stranded binding proteins may further impact condensate formation. Jointly, flipons and patches speed evolution by enhancing the functionality of condensates. Here, the focus is on the selection of SSR flipons and peptide patches that solve for survival under a wide range of environmental contexts, generating complexity with simple parts.
Collapse
Affiliation(s)
- Alan Herbert
- Unit 3412, Discovery, InsideOutBio 42 8th Street, Charlestown, MA 02129, USA
| |
Collapse
|
17
|
Phase Separation in RNA Biology. J Genet Genomics 2021; 48:872-880. [PMID: 34371110 DOI: 10.1016/j.jgg.2021.07.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/23/2022]
Abstract
Formation of biomolecular condensates via liquid-liquid phase separation (LLPS) is an advantageous strategy for cells to organize subcellular compartments for diverse functions. The involvement of LLPS is more widespread and overrepresented in RNA-related biological processes. This is in part because that RNAs are intrinsically multivalent macromolecules and the presence of RNAs affects the formation, dissolution and biophysical properties of biomolecular condensates formed by LLPS. Emerging studies have illustrated how LLPS participates in RNA transcription, splicing, processing, quality control, translation and function. The interconnected regulation between LLPS and RNAs ensures tight control of RNA-related cellular functions.
Collapse
|
18
|
Affiliation(s)
- Tomohiro Yamazaki
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan.
| |
Collapse
|
19
|
Ninomiya K, Iwakiri J, Aly MK, Sakaguchi Y, Adachi S, Natsume T, Terai G, Asai K, Suzuki T, Hirose T. m 6 A modification of HSATIII lncRNAs regulates temperature-dependent splicing. EMBO J 2021; 40:e107976. [PMID: 34184765 DOI: 10.15252/embj.2021107976] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/24/2021] [Accepted: 05/28/2021] [Indexed: 12/21/2022] Open
Abstract
Nuclear stress bodies (nSBs) are nuclear membraneless organelles formed around stress-inducible HSATIII architectural long noncoding RNAs (lncRNAs). nSBs repress splicing of hundreds of introns during thermal stress recovery, which are partly regulated by CLK1 kinase phosphorylation of temperature-dependent Ser/Arg-rich splicing factors (SRSFs). Here, we report a distinct mechanism for this splicing repression through protein sequestration by nSBs. Comprehensive identification of RNA-binding proteins revealed HSATIII association with proteins related to N6 -methyladenosine (m6 A) RNA modification. 11% of the first adenosine in the repetitive HSATIII sequence were m6 A-modified. nSBs sequester the m6 A writer complex to methylate HSATIII, leading to subsequent sequestration of the nuclear m6 A reader, YTHDC1. Sequestration of these factors from the nucleoplasm represses m6 A modification of pre-mRNAs, leading to repression of m6 A-dependent splicing during stress recovery phase. Thus, nSBs serve as a common platform for regulation of temperature-dependent splicing through dual mechanisms employing two distinct ribonucleoprotein modules with partially m6 A-modified architectural lncRNAs.
Collapse
Affiliation(s)
- Kensuke Ninomiya
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Junichi Iwakiri
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Mahmoud Khamis Aly
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.,Faculty of Biotechnology, Modern Sciences and Arts University, Giza, Egypt
| | - Yuriko Sakaguchi
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Shungo Adachi
- Cellular and Molecular Biotechnology Research Institute, National Institute for Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Tohru Natsume
- Cellular and Molecular Biotechnology Research Institute, National Institute for Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Goro Terai
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Kiyoshi Asai
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Tsutomu Suzuki
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| |
Collapse
|
20
|
Yamazaki T, Yamamoto T, Yoshino H, Souquere S, Nakagawa S, Pierron G, Hirose T. Paraspeckles are constructed as block copolymer micelles. EMBO J 2021; 40:e107270. [PMID: 33885174 PMCID: PMC8204865 DOI: 10.15252/embj.2020107270] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/14/2021] [Accepted: 03/18/2021] [Indexed: 01/20/2023] Open
Abstract
Paraspeckles are constructed by NEAT1_2 architectural long noncoding RNAs. Their characteristic cylindrical shapes, with highly ordered internal organization, distinguish them from typical liquid-liquid phase-separated condensates. We experimentally and theoretically investigated how the shape and organization of paraspeckles are determined. We identified the NEAT1_2 RNA domains responsible for shell localization of the NEAT1_2 ends, which determine the characteristic internal organization. Using the soft matter physics, we then applied a theoretical framework to understand the principles that determine NEAT1_2 organization as well as shape, number, and size of paraspeckles. By treating paraspeckles as amphipathic block copolymer micelles, we could explain and predict the experimentally observed behaviors of paraspeckles upon NEAT1_2 domain deletions or transcriptional modulation. Thus, we propose that paraspeckles are block copolymer micelles assembled through a type of microphase separation, micellization. This work provides an experiment-based theoretical framework for the concept that ribonucleoprotein complexes (RNPs) can act as block copolymers to form RNA-scaffolding biomolecular condensates with optimal sizes and structures in cells.
Collapse
Affiliation(s)
| | - Tetsuya Yamamoto
- Institute for Chemical Reaction Design and DiscoveryHokkaido UniversitySapporoJapan
| | - Hyura Yoshino
- Institute for Genetic MedicineHokkaido UniversitySapporoJapan
| | | | | | - Gerard Pierron
- Centre National de la Recherche ScientifiqueUMR‐9196Gustave RoussyVillejuifFrance
| | - Tetsuro Hirose
- Graduate School of Frontier BiosciencesOsaka UniversitySuitaJapan
- Institute for Genetic MedicineHokkaido UniversitySapporoJapan
| |
Collapse
|
21
|
Connecting the "dots": RNP granule network in health and disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119058. [PMID: 33989700 DOI: 10.1016/j.bbamcr.2021.119058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 12/26/2022]
Abstract
All cells contain ribonucleoprotein (RNP) granules - large membraneless structures composed of RNA and proteins. Recent breakthroughs in RNP granule research have brought a new appreciation of their crucial role in organising virtually all cellular processes. Cells widely exploit the flexible, dynamic nature of RNP granules to adapt to a variety of functional states and the ever-changing environment. Constant exchange of molecules between the different RNP granules connects them into a network. This network controls basal cellular activities and is remodelled to enable efficient stress response. Alterations in RNP granule structure and regulation have been found to lead to fatal human diseases. The interconnectedness of RNP granules suggests that the RNP granule network as a whole becomes affected in disease states such as a representative neurodegenerative disease amyotrophic lateral sclerosis (ALS). In this review, we summarize available evidence on the communication between different RNP granules and on the RNP granule network disruption as a primary ALS pathomechanism.
Collapse
|
22
|
Gerovac M, Vogel J, Smirnov A. The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches. Front Mol Biosci 2021; 8:661448. [PMID: 33898526 PMCID: PMC8058203 DOI: 10.3389/fmolb.2021.661448] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022] Open
Abstract
Macromolecular complexes of proteins and RNAs are essential building blocks of cells. These stable supramolecular particles can be viewed as minimal biochemical units whose structural organization, i.e., the way the RNA and the protein interact with each other, is directly linked to their biological function. Whether those are dynamic regulatory ribonucleoproteins (RNPs) or integrated molecular machines involved in gene expression, the comprehensive knowledge of these units is critical to our understanding of key molecular mechanisms and cell physiology phenomena. Such is the goal of diverse complexomic approaches and in particular of the recently developed gradient profiling by sequencing (Grad-seq). By separating cellular protein and RNA complexes on a density gradient and quantifying their distributions genome-wide by mass spectrometry and deep sequencing, Grad-seq charts global landscapes of native macromolecular assemblies. In this review, we propose a function-based ontology of stable RNPs and discuss how Grad-seq and related approaches transformed our perspective of bacterial and eukaryotic ribonucleoproteins by guiding the discovery of new RNA-binding proteins and unusual classes of noncoding RNAs. We highlight some methodological aspects and developments that permit to further boost the power of this technique and to look for exciting new biology in understudied and challenging biological models.
Collapse
Affiliation(s)
- Milan Gerovac
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Alexandre Smirnov
- UMR 7156—Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, CNRS, Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
| |
Collapse
|
23
|
Sas-Nowosielska H, Magalska A. Long Noncoding RNAs-Crucial Players Organizing the Landscape of the Neuronal Nucleus. Int J Mol Sci 2021; 22:ijms22073478. [PMID: 33801737 PMCID: PMC8037058 DOI: 10.3390/ijms22073478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/25/2022] Open
Abstract
The ability to regulate chromatin organization is particularly important in neurons, which dynamically respond to external stimuli. Accumulating evidence shows that lncRNAs play important architectural roles in organizing different nuclear domains like inactive chromosome X, splicing speckles, paraspeckles, and Gomafu nuclear bodies. LncRNAs are abundantly expressed in the nervous system where they may play important roles in compartmentalization of the cell nucleus. In this review we will describe the architectural role of lncRNAs in the nuclei of neuronal cells.
Collapse
|
24
|
Kim W, Kim DY, Lee KH. RNA-Binding Proteins and the Complex Pathophysiology of ALS. Int J Mol Sci 2021; 22:ijms22052598. [PMID: 33807542 PMCID: PMC7961459 DOI: 10.3390/ijms22052598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/21/2022] Open
Abstract
Genetic analyses of patients with amyotrophic lateral sclerosis (ALS) have identified disease-causing mutations and accelerated the unveiling of complex molecular pathogenic mechanisms, which may be important for understanding the disease and developing therapeutic strategies. Many disease-related genes encode RNA-binding proteins, and most of the disease-causing RNA or proteins encoded by these genes form aggregates and disrupt cellular function related to RNA metabolism. Disease-related RNA or proteins interact or sequester other RNA-binding proteins. Eventually, many disease-causing mutations lead to the dysregulation of nucleocytoplasmic shuttling, the dysfunction of stress granules, and the altered dynamic function of the nucleolus as well as other membrane-less organelles. As RNA-binding proteins are usually components of several RNA-binding protein complexes that have other roles, the dysregulation of RNA-binding proteins tends to cause diverse forms of cellular dysfunction. Therefore, understanding the role of RNA-binding proteins will help elucidate the complex pathophysiology of ALS. Here, we summarize the current knowledge regarding the function of disease-associated RNA-binding proteins and their role in the dysfunction of membrane-less organelles.
Collapse
Affiliation(s)
- Wanil Kim
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
| | - Do-Yeon Kim
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu 41940, Korea
- Correspondence: (D.-Y.K.); (K.-H.L.); Tel.: +82-53-660-6880 (D.-Y.K.); +82-53-819-7743 (K.-H.L.)
| | - Kyung-Ha Lee
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
- Correspondence: (D.-Y.K.); (K.-H.L.); Tel.: +82-53-660-6880 (D.-Y.K.); +82-53-819-7743 (K.-H.L.)
| |
Collapse
|
25
|
Good KV, Vincent JB, Ausió J. MeCP2: The Genetic Driver of Rett Syndrome Epigenetics. Front Genet 2021; 12:620859. [PMID: 33552148 PMCID: PMC7859524 DOI: 10.3389/fgene.2021.620859] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Mutations in methyl CpG binding protein 2 (MeCP2) are the major cause of Rett syndrome (RTT), a rare neurodevelopmental disorder with a notable period of developmental regression following apparently normal initial development. Such MeCP2 alterations often result in changes to DNA binding and chromatin clustering ability, and in the stability of this protein. Among other functions, MeCP2 binds to methylated genomic DNA, which represents an important epigenetic mark with broad physiological implications, including neuronal development. In this review, we will summarize the genetic foundations behind RTT, and the variable degrees of protein stability exhibited by MeCP2 and its mutated versions. Also, past and emerging relationships that MeCP2 has with mRNA splicing, miRNA processing, and other non-coding RNAs (ncRNA) will be explored, and we suggest that these molecules could be missing links in understanding the epigenetic consequences incurred from genetic ablation of this important chromatin modifier. Importantly, although MeCP2 is highly expressed in the brain, where it has been most extensively studied, the role of this protein and its alterations in other tissues cannot be ignored and will also be discussed. Finally, the additional complexity to RTT pathology introduced by structural and functional implications of the two MeCP2 isoforms (MeCP2-E1 and MeCP2-E2) will be described. Epigenetic therapeutics are gaining clinical popularity, yet treatment for Rett syndrome is more complicated than would be anticipated for a purely epigenetic disorder, which should be taken into account in future clinical contexts.
Collapse
Affiliation(s)
- Katrina V. Good
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - John B. Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| |
Collapse
|
26
|
Johnson SJ, Cooper TA. Overlapping mechanisms of lncRNA and expanded microsatellite RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1634. [PMID: 33191580 PMCID: PMC7880542 DOI: 10.1002/wrna.1634] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/14/2020] [Accepted: 10/20/2020] [Indexed: 12/15/2022]
Abstract
RNA has major regulatory roles in a wide range of biological processes and a surge of RNA research has led to the classification of numerous functional RNA species. One example is long noncoding RNAs (lncRNAs) that are structurally complex transcripts >200 nucleotides (nt) in length and lacking a canonical open reading frame (ORF). Despite a general lack of sequence conservation and low expression levels, many lncRNAs have been shown to have functionality in diverse biological processes as well as in mechanisms of disease. In parallel with the growing understanding of lncRNA functions, there is a growing subset of microsatellite expansion disorders in which the primary mechanism of pathogenesis is an RNA gain of function arising from RNA transcripts from the mutant allele. Microsatellite expansion disorders are caused by an expansion of short (3-10 nt) repeats located within coding genes. Expanded repeat-containing RNA mediates toxicity through multiple mechanisms, the details of which remain only partially understood. The purpose of this review is to highlight the links between functional mechanisms of lncRNAs and the potential pathogenic mechanisms of expanded microsatellite RNA. These shared mechanisms include protein sequestration, peptide translation, micro-RNA (miRNA) processing, and miRNA sequestration. Recognizing the parallels between the normal functions of lncRNAs and the negative impact of expanded microsatellite RNA on biological processes can provide reciprocal understanding to the roles of both RNA species. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- Sara J Johnson
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Thomas A Cooper
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
27
|
Razin SV, Ulianov SV. Divide and Rule: Phase Separation in Eukaryotic Genome Functioning. Cells 2020; 9:cells9112480. [PMID: 33203115 PMCID: PMC7696541 DOI: 10.3390/cells9112480] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
The functioning of a cell at various organizational levels is determined by the interactions between macromolecules that promote cellular organelle formation and orchestrate metabolic pathways via the control of enzymatic activities. Although highly specific and relatively stable protein-protein, protein-DNA, and protein-RNA interactions are traditionally suggested as the drivers for cellular function realization, recent advances in the discovery of weak multivalent interactions have uncovered the role of so-called macromolecule condensates. These structures, which are highly divergent in size, composition, function, and cellular localization are predominantly formed by liquid-liquid phase separation (LLPS): a physical-chemical process where an initially homogenous solution turns into two distinct phases, one of which contains the major portion of the dissolved macromolecules and the other one containing the solvent. In a living cell, LLPS drives the formation of membrane-less organelles such as the nucleolus, nuclear bodies, and viral replication factories and facilitates the assembly of complex macromolecule aggregates possessing regulatory, structural, and enzymatic functions. Here, we discuss the role of LLPS in the spatial organization of eukaryotic chromatin and regulation of gene expression in normal and pathological conditions.
Collapse
Affiliation(s)
- Sergey V. Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119017 Moscow, Russia;
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119017 Moscow, Russia
| | - Sergey V. Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119017 Moscow, Russia;
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119017 Moscow, Russia
- Correspondence: ; Tel.: +7-499-135-9787
| |
Collapse
|
28
|
The Emerging Role of the RNA-Binding Protein SFPQ in Neuronal Function and Neurodegeneration. Int J Mol Sci 2020; 21:ijms21197151. [PMID: 32998269 PMCID: PMC7582472 DOI: 10.3390/ijms21197151] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) are a class of proteins known for their diverse roles in RNA biogenesis, from regulating transcriptional processes in the nucleus to facilitating translation in the cytoplasm. With higher demand for RNA metabolism in the nervous system, RBP misregulation has been linked to a wide range of neurological and neurodegenerative diseases. One of the emerging RBPs implicated in neuronal function and neurodegeneration is splicing factor proline- and glutamine-rich (SFPQ). SFPQ is a ubiquitous and abundant RBP that plays multiple regulatory roles in the nucleus such as paraspeckle formation, DNA damage repair, and various transcriptional regulation processes. An increasing number of studies have demonstrated the nuclear and also cytoplasmic roles of SFPQ in neurons, particularly in post-transcriptional regulation and RNA granule formation. Not surprisingly, the misregulation of SFPQ has been linked to pathological features shown by other neurodegenerative disease-associated RBPs such as aberrant RNA splicing, cytoplasmic mislocalization, and aggregation. In this review, we discuss recent findings on the roles of SFPQ with a particular focus on those in neuronal development and homeostasis as well as its implications in neurodegenerative diseases.
Collapse
|
29
|
Tauber D, Tauber G, Parker R. Mechanisms and Regulation of RNA Condensation in RNP Granule Formation. Trends Biochem Sci 2020; 45:764-778. [PMID: 32475683 PMCID: PMC7211619 DOI: 10.1016/j.tibs.2020.05.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/20/2020] [Accepted: 05/05/2020] [Indexed: 01/01/2023]
Abstract
Ribonucleoprotein (RNP) granules are RNA-protein assemblies that are involved in multiple aspects of RNA metabolism and are linked to memory, development, and disease. Some RNP granules form, in part, through the formation of intermolecular RNA-RNA interactions. In vitro, such trans RNA condensation occurs readily, suggesting that cells require mechanisms to modulate RNA-based condensation. We assess the mechanisms of RNA condensation and how cells modulate this phenomenon. We propose that cells control RNA condensation through ATP-dependent processes, static RNA buffering, and dynamic post-translational mechanisms. Moreover, perturbations in these mechanisms can be involved in disease. This reveals multiple cellular mechanisms of kinetic and thermodynamic control that maintain the proper distribution of RNA molecules between dispersed and condensed forms.
Collapse
Affiliation(s)
- Devin Tauber
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80308, USA
| | - Gabriel Tauber
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80308, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80308, USA.
| |
Collapse
|
30
|
Emerging Insights on the Biological Impact of Extracellular Vesicle-Associated ncRNAs in Multiple Myeloma. Noncoding RNA 2020; 6:ncrna6030030. [PMID: 32764460 PMCID: PMC7549345 DOI: 10.3390/ncrna6030030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/30/2020] [Accepted: 08/04/2020] [Indexed: 12/11/2022] Open
Abstract
Increasing evidence indicates that extracellular vesicles (EVs) released from both tumor cells and the cells of the bone marrow microenvironment contribute to the pathobiology of multiple myeloma (MM). Recent studies on the mechanisms by which EVs exert their biological activity have indicated that the non-coding RNA (ncRNA) cargo is key in mediating their effect on MM development and progression. In this review, we will first discuss the role of EV-associated ncRNAs in different aspects of MM pathobiology, including proliferation, angiogenesis, bone disease development, and drug resistance. Finally, since ncRNAs carried by MM vesicles have also emerged as a promising tool for early diagnosis and therapy response prediction, we will report evidence of their potential use as clinical biomarkers.
Collapse
|
31
|
Razin SV, Gavrilov AA. The Role of Liquid–Liquid Phase Separation in the Compartmentalization of Cell Nucleus and Spatial Genome Organization. BIOCHEMISTRY (MOSCOW) 2020; 85:643-650. [DOI: 10.1134/s0006297920060012] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
32
|
RNA-mediated regulation of chromatin structures. Genes Genomics 2020; 42:609-617. [PMID: 32297146 DOI: 10.1007/s13258-020-00929-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 03/27/2020] [Indexed: 12/26/2022]
Abstract
It is now evident that transcriptional gene regulation usually requires the re-organization of chromatin architecture. Increasing evidence suggested various kinds of RNAs are involved in this process. Especially the nascent RNAs retained at their site of transcription can serve as a scaffold for organizing transcriptionally either favorable or unfavorable chromatin structures. An emerging concept of phase separation explains how these chromatin structures can be maintained as physically discrete subcompartments within membrane-less nucleoplasm. Evidences that support the crucial role of nascent RNAs in the formation of phase-separated condensates are now rapidly growing.
Collapse
|