1
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Montano C, Flores-Arenas C, Carpenter S. LncRNAs, nuclear architecture and the immune response. Nucleus 2024; 15:2350182. [PMID: 38738760 PMCID: PMC11093052 DOI: 10.1080/19491034.2024.2350182] [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: 02/05/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024] Open
Abstract
Long noncoding RNAs (LncRNAs) are key regulators of gene expression and can mediate their effects in both the nucleus and cytoplasm. Some of the best-characterized lncRNAs are localized within the nucleus, where they modulate the nuclear architecture and influence gene expression. In this review, we discuss the role of lncRNAs in nuclear architecture in the context of their gene regulatory functions in innate immunity. Here, we discuss various approaches to functionally characterize nuclear-localized lncRNAs and the challenges faced in the field.
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Affiliation(s)
- Christy Montano
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Cristina Flores-Arenas
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Susan Carpenter
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
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2
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Toya H, Okamatsu-Ogura Y, Yokoi S, Kurihara M, Mito M, Iwasaki S, Hirose T, Nakagawa S. The essential role of architectural noncoding RNA Neat1 in cold-induced beige adipocyte differentiation in mice. RNA (NEW YORK, N.Y.) 2024; 30:1011-1024. [PMID: 38692841 PMCID: PMC11251523 DOI: 10.1261/rna.079972.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/08/2024] [Indexed: 05/03/2024]
Abstract
Neat1 is an architectural RNA that provides the structural basis for nuclear bodies known as paraspeckles. Although the assembly processes by which Neat1 organizes paraspeckle components are well-documented, the physiological functions of Neat1 are not yet fully understood. This is partly because Neat1 knockout (KO) mice, lacking paraspeckles, do not exhibit overt phenotypes under normal laboratory conditions. During our search for conditions that elicit clear phenotypes in Neat1 KO mice, we discovered that the differentiation of beige adipocytes-inducible thermogenic cells that emerge upon cold exposure-is severely impaired in these mutant mice. Neat1_2, the architectural isoform of Neat1, is transiently upregulated during the early stages of beige adipocyte differentiation, coinciding with increased paraspeckle formation. Genes with altered expression during beige adipocyte differentiation typically cluster at specific chromosomal locations, some of which move closer to paraspeckles upon cold exposure. These observations suggest that paraspeckles might coordinate the regulation of these gene clusters by controlling the activity of certain transcriptional condensates that coregulate multiple genes. We propose that our findings highlight a potential role for Neat1 and paraspeckles in modulating chromosomal organization and gene expression, potentially crucial processes for the differentiation of beige adipocytes.
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Affiliation(s)
- Hikaru Toya
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Yuko Okamatsu-Ogura
- Laboratory of Biochemistry, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan
| | - Saori Yokoi
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Misuzu Kurihara
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
| | - Tetsuro Hirose
- RNA Biofunction Laboratory, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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3
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Murray-Nerger LA, Lozano C, Burton EM, Liao Y, Ungerleider NA, Guo R, Gewurz BE. The nucleic acid binding protein SFPQ represses EBV lytic reactivation by promoting histone H1 expression. Nat Commun 2024; 15:4156. [PMID: 38755141 PMCID: PMC11099029 DOI: 10.1038/s41467-024-48333-x] [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: 10/24/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
Epstein-Barr virus (EBV) uses a biphasic lifecycle of latency and lytic reactivation to infect >95% of adults worldwide. Despite its central role in EBV persistence and oncogenesis, much remains unknown about how EBV latency is maintained. We used a human genome-wide CRISPR/Cas9 screen to identify that the nuclear protein SFPQ was critical for latency. SFPQ supported expression of linker histone H1, which stabilizes nucleosomes and regulates nuclear architecture, but has not been previously implicated in EBV gene regulation. H1 occupied latent EBV genomes, including the immediate early gene BZLF1 promoter. Upon reactivation, SFPQ was sequestered into sub-nuclear puncta, and EBV genomic H1 occupancy diminished. Enforced H1 expression blocked EBV reactivation upon SFPQ knockout, confirming it as necessary downstream of SFPQ. SFPQ knockout triggered reactivation of EBV in B and epithelial cells, as well as of Kaposi's sarcoma-associated herpesvirus in B cells, suggesting a conserved gamma-herpesvirus role. These findings highlight SFPQ as a major regulator of H1 expression and EBV latency.
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Affiliation(s)
- Laura A Murray-Nerger
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Program in Virology, Boston, MA, 02115, USA
- Center for Integrated Solutions to Infectious Diseases, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Clarisel Lozano
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Eric M Burton
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Program in Virology, Boston, MA, 02115, USA
- Center for Integrated Solutions to Infectious Diseases, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Yifei Liao
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Program in Virology, Boston, MA, 02115, USA
- Center for Integrated Solutions to Infectious Diseases, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | | | - Rui Guo
- Department of Molecular Biology and Microbiology, Tufts University, Medford, MA, 02155, USA
| | - Benjamin E Gewurz
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard Program in Virology, Boston, MA, 02115, USA.
- Center for Integrated Solutions to Infectious Diseases, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
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4
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Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N, Tartaglia GG. RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding. Chem Rev 2024; 124:4734-4777. [PMID: 38579177 PMCID: PMC11046439 DOI: 10.1021/acs.chemrev.3c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 04/07/2024]
Abstract
This comprehensive Review delves into the chemical principles governing RNA-mediated crowding events, commonly referred to as granules or biological condensates. We explore the pivotal role played by RNA sequence, structure, and chemical modifications in these processes, uncovering their correlation with crowding phenomena under physiological conditions. Additionally, we investigate instances where crowding deviates from its intended function, leading to pathological consequences. By deepening our understanding of the delicate balance that governs molecular crowding driven by RNA and its implications for cellular homeostasis, we aim to shed light on this intriguing area of research. Our exploration extends to the methodologies employed to decipher the composition and structural intricacies of RNA granules, offering a comprehensive overview of the techniques used to characterize them, including relevant computational approaches. Through two detailed examples highlighting the significance of noncoding RNAs, NEAT1 and XIST, in the formation of phase-separated assemblies and their influence on the cellular landscape, we emphasize their crucial role in cellular organization and function. By elucidating the chemical underpinnings of RNA-mediated molecular crowding, investigating the role of modifications, structures, and composition of RNA granules, and exploring both physiological and aberrant phase separation phenomena, this Review provides a multifaceted understanding of the intriguing world of RNA-mediated biological condensates.
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Affiliation(s)
- Elsa Zacco
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Laura Broglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Misuzu Kurihara
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Michele Monti
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Stefano Gustincich
- Central
RNA Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Annalisa Pastore
- UK
Dementia Research Institute at the Maurice Wohl Institute of King’s
College London, London SE5 9RT, U.K.
| | - Kathrin Plath
- Department
of Biological Chemistry, David Geffen School
of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Shinichi Nagakawa
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Andrea Cerase
- Blizard
Institute,
Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, U.K.
- Unit
of Cell and developmental Biology, Department of Biology, Università di Pisa, 56123 Pisa, Italy
| | - Natalia Sanchez de Groot
- Unitat
de Bioquímica, Departament de Bioquímica i Biologia
Molecular, Universitat Autònoma de
Barcelona, 08193 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
- Catalan
Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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5
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Wang J, Zhang Y, Gao J, Feng G, Liu C, Li X, Li P, Liu Z, Lu F, Wang L, Li W, Zhou Q, Liu Y. Alternative splicing of CARM1 regulated by LincGET-guided paraspeckles biases the first cell fate in mammalian early embryos. Nat Struct Mol Biol 2024:10.1038/s41594-024-01292-9. [PMID: 38658621 DOI: 10.1038/s41594-024-01292-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
The heterogeneity of CARM1 controls first cell fate bias during early mouse development. However, how this heterogeneity is established is unknown. Here, we show that Carm1 mRNA is of a variety of specific exon-skipping splicing (ESS) isoforms in mouse two-cell to four-cell embryos that contribute to CARM1 heterogeneity. Disruption of paraspeckles promotes the ESS of Carm1 precursor mRNAs (pre-mRNAs). LincGET, but not Neat1, is required for paraspeckle assembly and inhibits the ESS of Carm1 pre-mRNAs in mouse two-cell to four-cell embryos. We further find that LincGET recruits paraspeckles to the Carm1 gene locus through HNRNPU. Interestingly, PCBP1 binds the Carm1 pre-mRNAs and promotes its ESS in the absence of LincGET. Finally, we find that the ESS seen in mouse two-cell to four-cell embryos decreases CARM1 protein levels and leads to trophectoderm fate bias. Our findings demonstrate that alternative splicing of CARM1 has an important role in first cell fate determination.
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Affiliation(s)
- Jiaqiang Wang
- College of Life Science, Northeast Agricultural University, Harbin, China.
| | - Yiwei Zhang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Jiaze Gao
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xueke Li
- College of Life Science, Northeast Agricultural University, Harbin, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Pengcheng Li
- College of Life Science, Northeast Agricultural University, Harbin, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhonghua Liu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Leyun Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | - Yusheng Liu
- College of Life Science, Northeast Forestry University, Harbin, China.
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6
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Godet AC, Roussel E, Laugero N, Morfoisse F, Lacazette E, Garmy-Susini B, Prats AC. Translational control by long non-coding RNAs. Biochimie 2024; 217:42-53. [PMID: 37640229 DOI: 10.1016/j.biochi.2023.08.015] [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: 04/25/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Long non-coding (lnc) RNAs, once considered as junk and useless, are now broadly recognized to have major functions in the cell. LncRNAs are defined as non-coding RNAs of more than 200 nucleotides, regulate all steps of gene expression. Their origin is diverse, they can arise from intronic, intergenic or overlapping region, in sense or antisense direction. LncRNAs are mainly described for their action on transcription, while their action at the translational level is more rarely cited. However, the bibliography in the field is more and more abundant. The present synopsis of lncRNAs involved in the control of translation reveals a wide field of regulation of gene expression, with at least nine distinct molecular mechanisms. Furthermore, it appears that all these lncRNAs are involved in various pathologies including cancer, cardiovascular and neurodegenerative diseases.
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Affiliation(s)
- Anne-Claire Godet
- UMR 1297-I2MC, Inserm, Université de Toulouse, UT3, Toulouse, France; Threonin Design, 220 Chemin de Montabon, Le Touvet, France
| | - Emilie Roussel
- UMR 1297-I2MC, Inserm, Université de Toulouse, UT3, Toulouse, France
| | - Nathalie Laugero
- UMR 1297-I2MC, Inserm, Université de Toulouse, UT3, Toulouse, France
| | - Florent Morfoisse
- UMR 1297-I2MC, Inserm, Université de Toulouse, UT3, Toulouse, France
| | - Eric Lacazette
- UMR 1297-I2MC, Inserm, Université de Toulouse, UT3, Toulouse, France
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7
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Marshall AC, Cummins J, Kobelke S, Zhu T, Widagdo J, Anggono V, Hyman A, Fox AH, Bond CS, Lee M. Different Low-complexity Regions of SFPQ Play Distinct Roles in the Formation of Biomolecular Condensates. J Mol Biol 2023; 435:168364. [PMID: 37952770 DOI: 10.1016/j.jmb.2023.168364] [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: 08/30/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Demixing of proteins and nucleic acids into condensed liquid phases is rapidly emerging as a ubiquitous mechanism underlying the complex spatiotemporal organisation of molecules within the cell. Long disordered regions of low sequence complexity (LCRs) are a common feature of proteins that form liquid-like microscopic biomolecular condensates. In particular, RNA-binding proteins with prion-like regions have emerged as key drivers of liquid demixing to form condensates such as nucleoli, paraspeckles and stress granules. Splicing factor proline- and glutamine-rich (SFPQ) is an RNA- and DNA-binding protein essential for DNA repair and paraspeckle formation. SFPQ contains two LCRs of different length and composition. Here, we show that the shorter C-terminal LCR of SFPQ is the main region responsible for the condensation of SFPQ in vitro and in the cell nucleus. In contrast, we find that the longer N-terminal prion-like LCR of SFPQ attenuates condensation of the full-length protein, suggesting a more regulatory role in preventing aberrant condensate formation in the cell. The compositions of these respective LCRs are discussed with reference to current literature. Our data add nuance to the emerging understanding of biomolecular condensation, by providing the first example of a common multifunctional nucleic acid-binding protein with an extensive prion-like region that serves to regulate rather than drive condensate formation.
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Affiliation(s)
- Andrew C Marshall
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Jerry Cummins
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Simon Kobelke
- School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Tianyi Zhu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jocelyn Widagdo
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Victor Anggono
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Anthony Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Archa H Fox
- School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia.
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia.
| | - Mihwa Lee
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
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8
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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.
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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.
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9
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Kaddis Maldonado R, Lambert GS, Rice BL, Sudol M, Flanagan JM, Parent LJ. The Rous sarcoma virus Gag Polyprotein Forms Biomolecular Condensates Driven by Intrinsically-disordered Regions. J Mol Biol 2023; 435:168182. [PMID: 37328094 PMCID: PMC10527454 DOI: 10.1016/j.jmb.2023.168182] [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: 01/04/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/18/2023]
Abstract
Biomolecular condensates (BMCs) play important roles incellular structures includingtranscription factories, splicing speckles, and nucleoli. BMCs bring together proteins and other macromolecules, selectively concentrating them so that specific reactions can occur without interference from the surrounding environment. BMCs are often made up of proteins that contain intrinsically disordered regions (IDRs), form phase-separated spherical puncta, form liquid-like droplets that undergo fusion and fission, contain molecules that are mobile, and are disrupted with phase-dissolving drugs such as 1,6-hexanediol. In addition to cellular proteins, many viruses, including influenza A, SARS-CoV-2, and human immunodeficiency virus type 1 (HIV-1) encode proteins that undergo phase separation and rely on BMC formation for replication. In prior studies of the retrovirus Rous sarcoma virus (RSV), we observed that the Gag protein forms discrete spherical puncta in the nucleus, cytoplasm, and at the plasma membrane that co-localize with viral RNA and host factors, raising the possibility that RSV Gag forms BMCs that participate in the intracellular phase of the virion assembly pathway. In our current studies, we found that Gag contains IDRs in the N-terminal (MAp2p10) and C-terminal (NC) regions of the protein and fulfills many criteria of BMCs. Although the role of BMC formation in RSV assembly requires further study, our results suggest the biophysical properties of condensates are required for the formation of Gag complexes in the nucleus and the cohesion of these complexes as they traffic through the nuclear pore, into the cytoplasm, and to the plasma membrane, where the final assembly and release of virus particles occurs.
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Affiliation(s)
- Rebecca Kaddis Maldonado
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA; Department of Microbiology & Immunology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Gregory S Lambert
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Breanna L Rice
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Malgorzata Sudol
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - John M Flanagan
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Leslie J Parent
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA; Department of Microbiology & Immunology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
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10
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Fritchie KJ, Dermawan JK, Astbury C, Sharma A, Bakhshwin A, Fuller L, Agrawal S, Wieland CN, Greipp PT, Azzato EM, Folpe AL, Billings SD. Novel NONO::TFE3 fusion and ALK co-expression identified in a subset of cutaneous microcystic/reticular schwannoma. Virchows Arch 2023; 483:237-243. [PMID: 37468653 DOI: 10.1007/s00428-023-03605-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/09/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Microcystic/reticular schwannoma (MRS) is a benign variant of schwannoma with a predilection for the gastrointestinal tract and skin. To date, genetic characterization of this tumor is limited. Prompted by the identification of TFE3::NONO fusion and ALK overexpression in an index case of MRS, a cohort of tumors was collected from institutional and consultation archives of two institutions. Next-generation sequencing (NGS), TFE3 fluorescence in situ hybridization (FISH), and TFE3 and ALK immunohistochemistry were performed, while clinicopathologic variables were documented. Eighteen MRS cases were identified (35 to 85 years) arising in the skin (n=8), gastrointestinal tract (n=5), adrenal gland (n=3), abdominal wall (n=1), and unknown site (n=1). Tumors showed a circumscribed to multinodular to plexiform low-power architecture with variable amounts of microcystic/reticular and solid schwannian components. Mitotic figures were scarce (0-1/10 HPFs), and atypia was absent. S100 protein and/or SOX10 immunoreactivity was noted in the microcystic/reticular and schwannian areas of all cases. NGS performed on two cutaneous tumors yielded NONO exon 12 fusion with TFE3 exon 4, and these lesions also showed HMB45 and ALK expression. Two additional cases showed ALK expression (1 weak), while a third was positive for TFE3, but these cases failed to show ALK or TFE3 rearrangement by FISH/NGS. There were no morphologic variables that correlated with the presence of NONO::TFE3. We identified a subset of microcystic/reticular schwannomas with NONO::TFE3 fusions and ALK co-expression, adding to the cohort of mesenchymal neoplasms that show ALK overexpression without rearrangement of the ALK gene.
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Affiliation(s)
- Karen J Fritchie
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, 2119 E 93rd Street, L15, Cleveland, OH, 44195, USA.
| | - Josephine K Dermawan
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, 2119 E 93rd Street, L15, Cleveland, OH, 44195, USA
| | - Caroline Astbury
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, 2119 E 93rd Street, L15, Cleveland, OH, 44195, USA
| | - Anurag Sharma
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, 2119 E 93rd Street, L15, Cleveland, OH, 44195, USA
| | - Ahmed Bakhshwin
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, 2119 E 93rd Street, L15, Cleveland, OH, 44195, USA
| | - Lanisha Fuller
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, 2119 E 93rd Street, L15, Cleveland, OH, 44195, USA
| | - Shruti Agrawal
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Dermatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Carilyn N Wieland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Dermatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Elizabeth M Azzato
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, 2119 E 93rd Street, L15, Cleveland, OH, 44195, USA
| | - Andrew L Folpe
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Steven D Billings
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, 2119 E 93rd Street, L15, Cleveland, OH, 44195, USA
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11
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Kathman SG, Koo SJ, Lindsey GL, Her HL, Blue SM, Li H, Jaensch S, Remsberg JR, Ahn K, Yeo GW, Ghosh B, Cravatt BF. Remodeling oncogenic transcriptomes by small molecules targeting NONO. Nat Chem Biol 2023; 19:825-836. [PMID: 36864190 PMCID: PMC10337234 DOI: 10.1038/s41589-023-01270-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 01/20/2023] [Indexed: 03/04/2023]
Abstract
Much of the human proteome is involved in mRNA homeostasis, but most RNA-binding proteins lack chemical probes. Here we identify electrophilic small molecules that rapidly and stereoselectively decrease the expression of transcripts encoding the androgen receptor and its splice variants in prostate cancer cells. We show by chemical proteomics that the compounds engage C145 of the RNA-binding protein NONO. Broader profiling revealed that covalent NONO ligands suppress an array of cancer-relevant genes and impair cancer cell proliferation. Surprisingly, these effects were not observed in cells genetically disrupted for NONO, which were instead resistant to NONO ligands. Reintroduction of wild-type NONO, but not a C145S mutant, restored ligand sensitivity in NONO-disrupted cells. The ligands promoted NONO accumulation in nuclear foci and stabilized NONO-RNA interactions, supporting a trapping mechanism that may prevent compensatory action of paralog proteins PSPC1 and SFPQ. These findings show that NONO can be co-opted by covalent small molecules to suppress protumorigenic transcriptional networks.
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Affiliation(s)
- Stefan G Kathman
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
| | - Seong Joo Koo
- Molecular and Cellular Pharmacology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Beerse, Belgium
| | - Garrett L Lindsey
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Hsuan-Lin Her
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Haoxin Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Steffen Jaensch
- High Dimensional and Computational Biology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Beerse, Belgium
| | - Jarrett R Remsberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Kay Ahn
- Molecular and Cellular Pharmacology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Spring House, PA, USA.
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Brahma Ghosh
- Discovery Chemistry, Janssen Research and Development, Spring House, PA, USA.
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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12
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Maldonado RK, Rice BL, Lambert GS, Sudol M, Flanagan JM, Parent LJ. The Rous sarcoma virus Gag polyprotein forms biomolecular condensates driven by intrinsically-disordered regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536043. [PMID: 37066255 PMCID: PMC10104128 DOI: 10.1101/2023.04.07.536043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Biomolecular condensates (BMCs) play important roles in cellular structures including transcription factories, splicing speckles, and nucleoli. BMCs bring together proteins and other macromolecules, selectively concentrating them so that specific reactions can occur without interference from the surrounding environment. BMCs are often made up of proteins that contain intrinsically disordered regions (IDRs), form phase-separated spherical puncta, form liquid-like droplets that undergo fusion and fission, contain molecules that are mobile, and are disrupted with phase-dissolving drugs such as 1,6-hexanediol. In addition to cellular proteins, many viruses, including influenza A, SARS-CoV-2, and human immunodeficiency virus type 1 (HIV-1) encode proteins that undergo phase separation and rely on BMC formation for replication. In prior studies of the retrovirus Rous sarcoma virus (RSV), we observed that the Gag protein forms discrete spherical puncta in the nucleus, cytoplasm, and at the plasma membrane that co-localize with viral RNA and host factors, raising the possibility that RSV Gag forms BMCs that participate in the virion intracellular assembly pathway. In our current studies, we found that Gag contains IDRs in the N-terminal (MAp2p10) and C-terminal (NC) regions of the protein and fulfills many criteria of BMCs. Although the role of BMC formation in RSV assembly requires further study, our results suggest the biophysical properties of condensates are required for the formation of Gag complexes in the nucleus and the cohesion of these complexes as they traffic through the nuclear pore, into the cytoplasm, and to the plasma membrane, where the final assembly and release of virus particles occurs.
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13
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Zhang Y, Cui D, Huang M, Zheng Y, Zheng B, Chen L, Chen Q. NONO regulates B-cell development and B-cell receptor signaling. FASEB J 2023; 37:e22862. [PMID: 36906291 DOI: 10.1096/fj.202201909rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 03/13/2023]
Abstract
The paraspeckle protein NONO is a multifunctional nuclear protein participating in the regulation of transcriptional regulation, mRNA splicing and DNA repair. However, whether NONO plays a role in lymphopoiesis is not known. In this study, we generated mice with global deletion of NONO and bone marrow (BM) chimeric mice in which NONO is deleted in all of mature B cells. We found that the global deletion of NONO in mice did not affect T-cell development but impaired early B-cell development in BM at pro- to pre-B-cell transition stage and B-cell maturation in the spleen. Studies of BM chimeric mice demonstrated that the impaired B-cell development in NONO-deficient mice is B-cell-intrinsic. NONO-deficient B cells displayed normal BCR-induced cell proliferation but increased BCR-induced cell apoptosis. Moreover, we found that NONO deficiency impaired BCR-induced activation of ERK, AKT, and NF-κB pathways in B cells, and altered BCR-induced gene expression profile. Thus, NONO plays a critical role in B-cell development and BCR-induced B-cell activation.
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Affiliation(s)
- Yongguang Zhang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, China
| | - Dongya Cui
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, China
| | - Miaohui Huang
- Department of Reproductive Medicine, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, China
| | - Yongwei Zheng
- Guangzhou Bio-Gene Technology Co., Ltd, Guangzhou, China
| | - Baijiao Zheng
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, China
| | - Liling Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, China
| | - Qi Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, China
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14
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Zhang S, Cooper JAL, Chong YS, Naveed A, Mayoh C, Jayatilleke N, Liu T, Amos S, Kobelke S, Marshall AC, Meers O, Choi YS, Bond CS, Fox AH. NONO enhances mRNA processing of super-enhancer-associated GATA2 and HAND2 genes in neuroblastoma. EMBO Rep 2023; 24:e54977. [PMID: 36416237 PMCID: PMC9900351 DOI: 10.15252/embr.202254977] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
High-risk neuroblastoma patients have poor survival rates and require better therapeutic options. High expression of a multifunctional DNA and RNA-binding protein, NONO, in neuroblastoma is associated with poor patient outcome; however, there is little understanding of the mechanism of NONO-dependent oncogenic gene regulatory activity in neuroblastoma. Here, we used cell imaging, biochemical and genome-wide molecular analysis to reveal complex NONO-dependent regulation of gene expression. NONO forms RNA- and DNA-tethered condensates throughout the nucleus and undergoes phase separation in vitro, modulated by nucleic acid binding. CLIP analyses show that NONO mainly binds to the 5' end of pre-mRNAs and modulates pre-mRNA processing, dependent on its RNA-binding activity. NONO regulates super-enhancer-associated genes, including HAND2 and GATA2. Abrogating NONO RNA binding, or phase separation activity, results in decreased expression of HAND2 and GATA2. Thus, future development of agents that target RNA-binding activity of NONO may have therapeutic potential in this cancer context.
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Affiliation(s)
- Song Zhang
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Jack AL Cooper
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Yee Seng Chong
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Alina Naveed
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Chelsea Mayoh
- Children's Cancer Institute AustraliaRandwickNSWAustralia
- Centre for Childhood Cancer ResearchUNSW SydneyKensingtonNSWAustralia
- School of Women's and Children's HealthUNSW SydneyKensingtonNSWAustralia
| | - Nisitha Jayatilleke
- Children's Cancer Institute AustraliaRandwickNSWAustralia
- Centre for Childhood Cancer ResearchUNSW SydneyKensingtonNSWAustralia
| | - Tao Liu
- Children's Cancer Institute AustraliaRandwickNSWAustralia
- Centre for Childhood Cancer ResearchUNSW SydneyKensingtonNSWAustralia
| | - Sebastian Amos
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Simon Kobelke
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Andrew C Marshall
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Oliver Meers
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Yu Suk Choi
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Charles S Bond
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Archa H Fox
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
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15
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Reddy D, Bhattacharya S, Levy M, Zhang Y, Gogol M, Li H, Florens L, Workman JL. Paraspeckles interact with SWI/SNF subunit ARID1B to regulate transcription and splicing. EMBO Rep 2023; 24:e55345. [PMID: 36354291 PMCID: PMC9827562 DOI: 10.15252/embr.202255345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/12/2022] Open
Abstract
Paraspeckles are subnuclear RNA-protein structures that are implicated in important processes including cellular stress response, differentiation, and cancer progression. However, it is unclear how paraspeckles impart their physiological effect at the molecular level. Through biochemical analyses, we show that paraspeckles interact with the SWI/SNF chromatin-remodeling complex. This is specifically mediated by the direct interaction of the long-non-coding RNA NEAT1 of the paraspeckles with ARID1B of the cBAF-type SWI/SNF complex. Strikingly, ARID1B depletion, in addition to resulting in loss of interaction with the SWI/SNF complex, decreases the binding of paraspeckle proteins to chromatin modifiers, transcription factors, and histones. Functionally, the loss of ARID1B and NEAT1 influences the transcription and the alternative splicing of a common set of genes. Our findings reveal that dynamic granules such as the paraspeckles may leverage the specificity of epigenetic modifiers to impart their regulatory effect, thus providing a molecular basis for their function.
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Affiliation(s)
- Divya Reddy
- Stowers Institute for Medical ResearchKansas CityMOUSA
| | | | | | - Ying Zhang
- Stowers Institute for Medical ResearchKansas CityMOUSA
| | | | - Hua Li
- Stowers Institute for Medical ResearchKansas CityMOUSA
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16
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Lee PW, Marshall AC, Knott GJ, Kobelke S, Martelotto L, Cho E, McMillan PJ, Lee M, Bond CS, Fox AH. Paraspeckle subnuclear bodies depend on dynamic heterodimerisation of DBHS RNA-binding proteins via their structured domains. J Biol Chem 2022; 298:102563. [DOI: 10.1016/j.jbc.2022.102563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022] Open
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17
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Friedl MS, Djakovic L, Kluge M, Hennig T, Whisnant AW, Backes S, Dölken L, Friedel CC. HSV-1 and influenza infection induce linear and circular splicing of the long NEAT1 isoform. PLoS One 2022; 17:e0276467. [PMID: 36279270 PMCID: PMC9591066 DOI: 10.1371/journal.pone.0276467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/07/2022] [Indexed: 11/18/2022] Open
Abstract
The herpes simplex virus 1 (HSV-1) virion host shut-off (vhs) protein cleaves both cellular and viral mRNAs by a translation-initiation-dependent mechanism, which should spare circular RNAs (circRNAs). Here, we show that vhs-mediated degradation of linear mRNAs leads to an enrichment of circRNAs relative to linear mRNAs during HSV-1 infection. This was also observed in influenza A virus (IAV) infection, likely due to degradation of linear host mRNAs mediated by the IAV PA-X protein and cap-snatching RNA-dependent RNA polymerase. For most circRNAs, enrichment was not due to increased circRNA synthesis but due to a general loss of linear RNAs. In contrast, biogenesis of a circRNA originating from the long isoform (NEAT1_2) of the nuclear paraspeckle assembly transcript 1 (NEAT1) was induced both in HSV-1 infection-in a vhs-independent manner-and in IAV infection. This was associated with induction of novel linear splicing of NEAT1_2 both within and downstream of the circRNA. NEAT1_2 forms a scaffold for paraspeckles, nuclear bodies located in the interchromatin space, must likely remain unspliced for paraspeckle assembly and is up-regulated in HSV-1 and IAV infection. We show that NEAT1_2 splicing and up-regulation can be induced by ectopic co-expression of the HSV-1 immediate-early proteins ICP22 and ICP27, potentially linking increased expression and splicing of NEAT1_2. To identify other conditions with NEAT1_2 splicing, we performed a large-scale screen of published RNA-seq data. This uncovered both induction of NEAT1_2 splicing and poly(A) read-through similar to HSV-1 and IAV infection in cancer cells upon inhibition or knockdown of CDK7 or the MED1 subunit of the Mediator complex phosphorylated by CDK7. In summary, our study reveals induction of novel circular and linear NEAT1_2 splicing isoforms as a common characteristic of HSV-1 and IAV infection and highlights a potential role of CDK7 in HSV-1 or IAV infection.
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Affiliation(s)
- Marie-Sophie Friedl
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lara Djakovic
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Michael Kluge
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Adam W. Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Simone Backes
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Caroline C. Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
- * E-mail:
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18
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The role of long noncoding RNA (lncRNA) nuclear-enriched abundant transcript 1 (NEAT1) in immune diseases. Transpl Immunol 2022; 75:101716. [PMID: 36126903 DOI: 10.1016/j.trim.2022.101716] [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: 08/05/2022] [Revised: 08/30/2022] [Accepted: 09/13/2022] [Indexed: 11/22/2022]
Abstract
The long noncoding RNA (lncRNA) nuclear-enriched abundant transcript 1 (NEAT1) has been shown to be involved in the pathogenesis of several diseases. Herein, we discuss recent developments and insights into NEAT1 and its contribution to a variety of immune disorders. Our evaluations revealed that NEAT1's function in immune diseases seems to be focused on the modulation of paraspeckle expression and it is primarily associated with the nuclear retention of its mRNA. NEAT1 is also involved in the sequestration of paraspeckle proteins and in affecting the transcriptional expression of specific immune regulators. The expression of NEAT1 may be aberrantly upregulated in several immune pathologies, indicating that it could serve as a potential prognostic biomarker in these conditions. We summarized describing the expression changes and the role of NEAT1 in several immune diseases. We also described the mechanism of its regulation of the immune cell differentiation and function of NEAT1 in different disease.
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19
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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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20
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Wang J, Sachpatzidis A, Christian TD, Lomakin IB, Garen A, Konigsberg WH. Insight into the Tumor Suppression Mechanism from the Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) Complexed with a 30mer RNA from Murine Virus-like 30S Transcript-1. Biochemistry 2022; 61:1723-1734. [PMID: 35998361 DOI: 10.1021/acs.biochem.2c00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human polypyrimidine-binding splicing factor (PSF/SFPQ) is a tumor suppressor protein that regulates the gene expression of several proto-oncogenes and binds to the 5'-polyuridine negative-sense template (5'-PUN) of some RNA viruses. The activity of PSF is negatively regulated by long-noncoding RNAs, human metastasis associated in lung adenocarcinoma transcript-1 and murine virus-like 30S transcript-1 (VL30-1). PSF is a 707-amino acid protein that has a DNA-binding domain and two RNA recognition motifs (RRMs). Although the structure of the apo-truncated PSF is known, how PSF recognizes RNA remains elusive. Here, we report the 2.8 Å and 3.5 Å resolution crystal structures of a biologically active truncated construct of PSF (sPSF, consisting of residues 214-598) alone and in a complex with a 30mer fragment of VL30-1 RNA, respectively. The structure of the complex reveals how the 30mer RNA is recognized at two U-specific induced-fit binding pockets, located at the previously unrecognized domain-swapped, inter-subunit RRM1 (of the first subunit)-RRM2 (of the second subunit) interfaces that do not exist in the apo structure. Thus, the sPSF dimer appears to have two conformations in solution: one in a low-affinity state for RNA binding, as seen in the apo-structure, and the other in a high-affinity state for RNA binding, as seen in the sPSF-RNA complex. PSF undergoes an all or nothing transition between having two or no RNA-binding pockets. We predict that the RNA binds with a high degree of positive cooperativity. These structures provide an insight into a new regulatory mechanism that is likely involved in promoting malignancies and other human diseases.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, 333 Cedar Street, New Haven, Connecticut 06520-8114, USA
| | - Aristidis Sachpatzidis
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, 333 Cedar Street, New Haven, Connecticut 06520-8114, USA
| | - Thomas D Christian
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, 333 Cedar Street, New Haven, Connecticut 06520-8114, USA
| | - Ivan B Lomakin
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, 333 Cedar Street, New Haven, Connecticut 06520-8114, USA
| | - Alan Garen
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, 333 Cedar Street, New Haven, Connecticut 06520-8114, USA
| | - William H Konigsberg
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, 333 Cedar Street, New Haven, Connecticut 06520-8114, USA
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21
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Belmont AS. Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture. Cold Spring Harb Perspect Biol 2022; 14:a041268. [PMID: 34400557 PMCID: PMC9248822 DOI: 10.1101/cshperspect.a041268] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This work reviews nuclear compartments, defined broadly to include distinct nuclear structures, bodies, and chromosome domains. It first summarizes original cytological observations before comparing concepts of nuclear compartments emerging from microscopy versus genomic approaches and then introducing new multiplexed imaging approaches that promise in the future to meld both approaches. I discuss how previous models of radial distribution of chromosomes or the binary division of the genome into A and B compartments are now being refined by the recognition of more complex nuclear compartmentalization. The poorly understood question of how these nuclear compartments are established and maintained is then discussed, including through the modern perspective of phase separation, before moving on to address possible functions of nuclear compartments, using the possible role of nuclear speckles in modulating gene expression as an example. Finally, the review concludes with a discussion of future questions for this field.
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Affiliation(s)
- Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
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22
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Zhao J, Xie W, Yang Z, Zhao M, Ke T, Xu C, Li H, Chen Q, Wang QK. Identification and characterization of a special type of subnuclear structure: AGGF1-coated paraspeckles. FASEB J 2022; 36:e22366. [PMID: 35608889 DOI: 10.1096/fj.202101690rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 11/11/2022]
Abstract
AGGF1 is an angiogenic factor with G-Patch and FHA domains 1 described by our group. Gain-of-function mutations in AGGF1 cause Klippel-Trenaunay syndrome, whereas somatic loss-of-function mutations cause cancer. Paraspeckles are small membraneless subnuclear structures with a diameter of 0.5-1 μm, and composed of lncRNA NEAT1 as the scaffold and three core RNA-binding proteins NONO, PSPC1, and PSF. Here, we show that AGGF1 is a key regulatory and structural component of paraspeckles that induces paraspeckle formation, forms an outside rim of paraspeckles, wraps around the NONO/PSF/PSPC1/NEAT1 core, and regulates the size and number of paraspeckles. AGGF1-paraspeckles are larger (>1 μm) than conventional paraspeckles. RNA-FISH in combination with immunostaining shows that AGGF1, NONO, and NEAT1_2 co-localize in 20.58% of NEAT1_2-positive paraspeckles. Mechanistically, AGGF1 interacts with NONO, PSF, and HNRNPK, and upregulates NEAT1_2, a longer, 23 kb NEAT1 transcript with a key role in regulation of paraspeckle size and number. RNA-immunoprecipitation shows that AGGF1 interacts with NEAT1, which may be another possible mechanism underlying the formation of AGGF1-paraspeckles. NEAT1_2 knockdown reduces the number and size of AGGF1-paraspeckles. Functionally, AGGF1 regulates alternative RNA splicing as it decreases the exon skipping/inclusion ratio in a CD44 model. AGGF1 is also localized in some nuclear foci without NEAT1 or NONO, suggesting that AGGF1 is an important liquid-liquid phase separation (LLPS) driver for other types of AGGF1-positive nuclear condensates (referred to as AGGF1-bodies). Our results identify a special type of AGGF1-coated paraspeckles and provide important insights into the formation, structure, and function of paraspeckles.
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Affiliation(s)
- Jinyan Zhao
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Wen Xie
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Zhongcheng Yang
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Miao Zhao
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Tie Ke
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Chengqi Xu
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Hui Li
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Qiuyun Chen
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Qing K Wang
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
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23
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Shadrina OA, Kikhay TF, Agapkina YY, Gottikh MB. SFPQ and NONO Proteins and Long Non-Coding NEAT1 RNA: Cellular Functions and Role in the HIV-1 Life Cycle. Mol Biol 2022. [DOI: 10.1134/s0026893322020133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Expression and functions of long non-coding RNA NEAT1 and isoforms in breast cancer. Br J Cancer 2022; 126:551-561. [PMID: 34671127 PMCID: PMC8854383 DOI: 10.1038/s41416-021-01588-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/08/2021] [Accepted: 10/05/2021] [Indexed: 02/07/2023] Open
Abstract
NEAT1 is a highly abundant nuclear architectural long non-coding RNA. There are two overlapping NEAT1 isoforms, NEAT1_1 and NEAT1_2, of which the latter is an essential scaffold for the assembly of a class of nuclear ribonucleoprotein bodies called paraspeckles. Paraspeckle formation is elevated by a wide variety of cellular stressors and in certain developmental processes, either through transcriptional upregulation of the NEAT1 gene or through a switch from NEAT1_1 to NEAT1_2 isoform production. In such conditions, paraspeckles modulate cellular processes by sequestering proteins or RNA molecules. NEAT1 is abnormally expressed in many cancers and a growing body of evidence suggests that, in many cases, high NEAT1 levels are associated with therapy resistance and poor clinical outcome. Here we review the current knowledge of NEAT1 expression and functions in breast cancer, highlighting its established role in postnatal mammary gland development. We will discuss possible isoform-specific roles of NEAT1_1 and NEAT1_2 in different breast cancer subtypes, which critically needs to be considered when studying NEAT1 and breast cancer.
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25
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Schell B, Legrand P, Fribourg S. Crystal structure of SFPQ-NONO heterodimer. Biochimie 2022; 198:1-7. [PMID: 35245601 DOI: 10.1016/j.biochi.2022.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/18/2022] [Accepted: 02/25/2022] [Indexed: 12/20/2022]
Abstract
The Drosophila behavior/human splicing (DBHS) protein family is composed of the three members SFPQ, NONO and PSPC1. These proteins share a strong sequence and structural homology within the core-structured domains forming obligate homo- and heterodimers. This feature may lead to the simultaneous existence of six different dimeric complexes that sustain their function in many cellular processes such as pre-mRNA splicing, innate immunity, transcriptional regulation. In order to perform a complete structural analysis of all possible DBHS dimers, we have solved the crystal structure of the missing DBHS heterodimer SFPQ-NONO at 3.0 Å resolution. We identify subtle changes in amino acid composition and local secondary structure of the NOPS region orientation that may modulate affinity between complexes. Interestingly this area is found mutated in aggressive skin cancers and adenocarcinomas.
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Affiliation(s)
- Bianca Schell
- INSERM U1212 - CNRS 5320 & Université de Bordeaux, 146 Rue Léo Saignat, 33000, Bordeaux, France; Universität Konstanz, 78457, Konstanz, Germany
| | - Pierre Legrand
- Synchrotron SOLEIL, L'Orme des Merisiers, Gif-sur-Yvette, 91192, France
| | - Sébastien Fribourg
- INSERM U1212 - CNRS 5320 & Université de Bordeaux, 146 Rue Léo Saignat, 33000, Bordeaux, France.
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26
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Godet AC, Roussel E, David F, Hantelys F, Morfoisse F, Alves J, Pujol F, Ader I, Bertrand E, Burlet-Schiltz O, Froment C, Henras AK, Vitali P, Lacazette E, Tatin F, Garmy-Susini B, Prats AC. Long non-coding RNA Neat1 and paraspeckle components are translational regulators in hypoxia. eLife 2022; 11:69162. [PMID: 36546462 PMCID: PMC9799981 DOI: 10.7554/elife.69162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
Internal ribosome entry sites (IRESs) drive translation initiation during stress. In response to hypoxia, (lymph)angiogenic factors responsible for tissue revascularization in ischemic diseases are induced by the IRES-dependent mechanism. Here, we searched for IRES trans-acting factors (ITAFs) active in early hypoxia in mouse cardiomyocytes. Using knock-down and proteomics approaches, we show a link between a stressed-induced nuclear body, the paraspeckle, and IRES-dependent translation. Furthermore, smiFISH experiments demonstrate the recruitment of IRES-containing mRNA into paraspeckle during hypoxia. Our data reveal that the long non-coding RNA Neat1, an essential paraspeckle component, is a key translational regulator, active on IRESs of (lymph)angiogenic and cardioprotective factor mRNAs. In addition, paraspeckle proteins p54nrb and PSPC1 as well as nucleolin and RPS2, two p54nrb-interacting proteins identified by mass spectrometry, are ITAFs for IRES subgroups. Paraspeckle thus appears as a platform to recruit IRES-containing mRNAs and possibly host IRESome assembly. Polysome PCR array shows that Neat1 isoforms regulate IRES-dependent translation and, more widely, translation of mRNAs involved in stress response.
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Affiliation(s)
| | - Emilie Roussel
- UMR 1297-I2MC, Inserm, Université de ToulouseToulouseFrance
| | - Florian David
- UMR 1297-I2MC, Inserm, Université de ToulouseToulouseFrance
| | | | | | - Joffrey Alves
- UMR 1297-I2MC, Inserm, Université de ToulouseToulouseFrance
| | | | - Isabelle Ader
- UMR 1301-RESTORE, Inserm, CNRS 5070, Etablissement Français du Sang-Occitanie (EFS), National Veterinary School of Toulouse (ENVT), Université de ToulouseToulouseFrance
| | | | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRSToulouseFrance
| | - Carine Froment
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRSToulouseFrance
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de ToulouseToulouseFrance
| | - Patrice Vitali
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de ToulouseToulouseFrance
| | - Eric Lacazette
- UMR 1297-I2MC, Inserm, Université de ToulouseToulouseFrance
| | - Florence Tatin
- UMR 1297-I2MC, Inserm, Université de ToulouseToulouseFrance
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27
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Knott GJ, Chong YS, Passon DM, Liang XH, Deplazes E, Conte MR, Marshall AC, Lee M, Fox AH, Bond CS. Structural basis of dimerization and nucleic acid binding of human DBHS proteins NONO and PSPC1. Nucleic Acids Res 2021; 50:522-535. [PMID: 34904671 PMCID: PMC8754649 DOI: 10.1093/nar/gkab1216] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 12/29/2022] Open
Abstract
The Drosophila behaviour/human splicing (DBHS) proteins are a family of RNA/DNA binding cofactors liable for a range of cellular processes. DBHS proteins include the non-POU domain-containing octamer-binding protein (NONO) and paraspeckle protein component 1 (PSPC1), proteins capable of forming combinatorial dimers. Here, we describe the crystal structures of the human NONO and PSPC1 homodimers, representing uncharacterized DBHS dimerization states. The structures reveal a set of conserved contacts and structural plasticity within the dimerization interface that provide a rationale for dimer selectivity between DBHS paralogues. In addition, solution X-ray scattering and accompanying biochemical experiments describe a mechanism of cooperative RNA recognition by the NONO homodimer. Nucleic acid binding is reliant on RRM1, and appears to be affected by the orientation of RRM1, influenced by a newly identified 'β-clasp' structure. Our structures shed light on the molecular determinants for DBHS homo- and heterodimerization and provide a basis for understanding how DBHS proteins cooperatively recognize a broad spectrum of RNA targets.
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Affiliation(s)
- Gavin J Knott
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Yee Seng Chong
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Daniel M Passon
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Xue-Hai Liang
- Department of Core Antisense Research, IONIS Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Evelyne Deplazes
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Qld 4072, Australia
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Andrew C Marshall
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Mihwa Lee
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Vic 3086, Australia
| | - Archa H Fox
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
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28
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Abstract
Although long noncoding RNAs (lncRNAs) are generally expressed at low levels, emerging evidence has revealed that many play important roles in gene regulation by a variety of mechanisms as they engage with proteins. Given that the abundance of proteins often greatly exceeds that of their interacting lncRNAs, quantification of the relative abundance, or even the exact stoichiometry in some cases, within lncRNA-protein complexes is helpful for understanding of the mechanism(s) of action of lncRNAs. We discuss methods used to examine lncRNA and protein expression at the single cell, subcellular, and suborganelle levels, the average and local lncRNA concentration in cells, as well as how lncRNAs can modulate the functions of their interacting proteins even at a low stoichiometric concentration.
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Affiliation(s)
- Man Wu
- 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 Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Liang-Zhong Yang
- 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 Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - 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 Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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29
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Yamamoto K, Goyama S, Asada S, Fujino T, Yonezawa T, Sato N, Takeda R, Tsuchiya A, Fukuyama T, Tanaka Y, Yokoyama A, Toya H, Kon A, Nannya Y, Onoguchi-Mizutani R, Nakagawa S, Hirose T, Ogawa S, Akimitsu N, Kitamura T. A histone modifier, ASXL1, interacts with NONO and is involved in paraspeckle formation in hematopoietic cells. Cell Rep 2021; 36:109576. [PMID: 34433054 DOI: 10.1016/j.celrep.2021.109576] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 05/03/2021] [Accepted: 07/29/2021] [Indexed: 12/13/2022] Open
Abstract
Paraspeckles are membraneless organelles formed through liquid-liquid phase separation and consist of multiple proteins and RNAs, including NONO, SFPQ, and NEAT1. The role of paraspeckles and the component NONO in hematopoiesis remains unknown. In this study, we show histone modifier ASXL1 is involved in paraspeckle formation. ASXL1 forms phase-separated droplets, upregulates NEAT1 expression, and increases NONO-NEAT1 interactions through the C-terminal intrinsically disordered region (IDR). In contrast, a pathogenic ASXL mutant (ASXL1-MT) lacking IDR does not support the interaction of paraspeckle components. Furthermore, paraspeckles are disrupted and Nono localization is abnormal in the cytoplasm of hematopoietic stem and progenitor cells (HSPCs) derived from ASXL1-MT knockin mice. Nono depletion and the forced expression of cytoplasmic NONO impair the repopulating potential of HSPCs, as does ASXL1-MT. Our study indicates a link between ASXL1 and paraspeckle components in the maintenance of normal hematopoiesis.
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Affiliation(s)
- Keita Yamamoto
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Susumu Goyama
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shuhei Asada
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan; The Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, Japan
| | - Takeshi Fujino
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Taishi Yonezawa
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Naru Sato
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Reina Takeda
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Akiho Tsuchiya
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomofusa Fukuyama
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yosuke Tanaka
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Akihiko Yokoyama
- National Cancer Center Tsuruoka Metabolomics Laboratory, Yamagata, Japan
| | - Hikaru Toya
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Hokkaido, Japan
| | - Ayana Kon
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | | | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Hokkaido, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | | | - Toshio Kitamura
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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30
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Razin SV, Gavrilov AA. Non-coding RNAs in chromatin folding and nuclear organization. Cell Mol Life Sci 2021; 78:5489-5504. [PMID: 34117518 PMCID: PMC11072467 DOI: 10.1007/s00018-021-03876-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/24/2021] [Accepted: 06/05/2021] [Indexed: 12/19/2022]
Abstract
One of the most intriguing questions facing modern biology concerns how the genome directs the construction of cells, tissues, and whole organisms. It is tempting to suggest that the part of the genome that does not encode proteins contains architectural plans. We are still far from understanding how these plans work at the level of building tissues and the body as a whole. However, the results of recent studies demonstrate that at the cellular level, special non-coding RNAs serve as scaffolds for the construction of various intracellular structures. The term "architectural RNAs" was proposed to designate this subset of non-coding RNAs. In this review, we discuss the role of architectural RNAs in the construction of the cell nucleus and maintenance of the three-dimensional organization of the genome.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia.
- Faculty of Biology, M. V. Lomonosov Moscow State University, 119234, Moscow, Russia.
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
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31
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Tan X, Liu Y, Liu Y, Zhang T, Cong S. Dysregulation of long non-coding RNAs and their mechanisms in Huntington's disease. J Neurosci Res 2021; 99:2074-2090. [PMID: 34031910 DOI: 10.1002/jnr.24825] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 01/19/2021] [Accepted: 02/26/2021] [Indexed: 12/31/2022]
Abstract
Extensive alterations in gene regulatory networks are a typical characteristic of Huntington's disease (HD); these include alterations in protein-coding genes and poorly understood non-coding RNAs (ncRNAs), which are associated with pathology caused by mutant huntingtin. Long non-coding RNAs (lncRNAs) are an important class of ncRNAs involved in a variety of biological functions, including transcriptional regulation and post-transcriptional modification of many targets, and likely contributed to the pathogenesis of HD. While a number of changes in lncRNAs expression have been observed in HD, little is currently known about their functions. Here, we discuss their possible mechanisms and molecular functions, with a particular focus on their roles in transcriptional regulation. These findings give us a better insight into HD pathogenesis and may provide new targets for the treatment of this neurodegenerative disease.
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Affiliation(s)
- Xiaoping Tan
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Yang Liu
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Yan Liu
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Taiming Zhang
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Shuyan Cong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
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32
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Zhang L, Vickers TA, Sun H, Liang XH, Crooke ST. Binding of phosphorothioate oligonucleotides with RNase H1 can cause conformational changes in the protein and alter the interactions of RNase H1 with other proteins. Nucleic Acids Res 2021; 49:2721-2739. [PMID: 33577678 PMCID: PMC7969025 DOI: 10.1093/nar/gkab078] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023] Open
Abstract
We recently found that toxic PS-ASOs can cause P54nrb and PSF nucleolar mislocalization in an RNase H1-dependent manner. To better understand the underlying mechanisms of these observations, here we utilize different biochemical approaches to demonstrate that PS-ASO binding can alter the conformations of the bound proteins, as illustrated using recombinant RNase H1, P54nrb, PSF proteins and various isolated domains. While, in general, binding of PS-ASOs or ASO/RNA duplexes stabilizes the conformations of these proteins, PS-ASO binding may also cause the unfolding of RNase H1, including both the hybrid binding domain and the catalytic domain. The extent of conformational change correlates with the binding affinity of PS-ASOs to the proteins. Consequently, PS-ASO binding to RNase H1 induces the interaction of RNase H1 with P54nrb or PSF in a 2′-modification and sequence dependent manner, and toxic PS-ASOs tend to induce more interactions than non-toxic PS-ASOs. PS-ASO binding also enhances the interaction between P54nrb and PSF. However, the interaction between RNase H1 and P32 protein can be disrupted upon binding of PS-ASOs. Together, these results suggest that stronger binding of PS-ASOs can cause greater conformational changes of the bound proteins, subsequently affecting protein–protein interactions. These observations thus provide deeper understanding of the molecular basis of PS-ASO-induced protein mislocalization or degradation observed in cells and advance our understanding of why some PS-ASOs are cytotoxic.
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Affiliation(s)
- Lingdi Zhang
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Timothy A Vickers
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Antisense Drug discovery, Ionis Pharmaceuticals, Inc. Carlsbad, CA 92010, USA
| | - Xue-Hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
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33
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McCluggage F, Fox AH. Paraspeckle nuclear condensates: Global sensors of cell stress? Bioessays 2021; 43:e2000245. [PMID: 33748979 DOI: 10.1002/bies.202000245] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 12/31/2022]
Abstract
Paraspeckles are nuclear condensates, or membranelees organelles, that are built on the long noncoding RNA, NEAT1, and have been linked to many diseases. Although originally described as constitutive structures, here, in reviewing this field, we develop the hypothesis that cells increase paraspeckle abundance as part of a general stress response, to aid pro-survival pathways. Paraspeckles increase in many scenarios: when cells transform from one state to another, become infected with viruses and bacteria, begin to degenerate, under inflammation, in aging, and in cancer. Cells increase paraspeckles by increasing transcription of NEAT1 and adjusting its RNA processing. These increases in NEAT1 are driven by numerous stress-sensing signaling pathways, including signaling to mitochondria and stress granules, revealing crosstalk between the cytoplasm and nucleoplasm in the stress response. Thus, paraspeckles are an important piece of the puzzle in cellular homeostasis, and could be considered RNA-scaffolded nuclear equivalents of dynamic stress-induced structures that form in the cytoplasm. We speculate that, in general, cells rely on phase-separated paraspeckles to transiently tweak gene regulation in times of cellular flux.
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Affiliation(s)
- Finn McCluggage
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia, Australia.,School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Archa H Fox
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia, Australia.,School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
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34
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Abstract
The subcellular localization of RNAs correlates with their function and how they are regulated. Most protein-coding mRNAs are exported into the cytoplasm for protein synthesis, while some mRNA species, long noncoding RNAs, and some regulatory element-associated unstable transcripts tend to be retained in the nucleus, where they function as a regulatory unit and/or are regulated by nuclear surveillance pathways. While the mechanisms regulating mRNA export and localization have been well summarized, the mechanisms governing nuclear retention of RNAs, especially of noncoding RNAs, are seldomly reviewed. In this review, we summarize recent advances in the mechanistic study of RNA nuclear retention, especially for noncoding RNAs, from the angle of cis-acting elements embedded in RNA transcripts and their interaction with trans-acting factors. We also try to illustrate the general principles of RNA nuclear retention and we discuss potential areas for future investigation.
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Affiliation(s)
- Chong Tong
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yafei Yin
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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35
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Thankachan S, Bhardwaj BK, Venkatesh T, Suresh PS. Long Non-coding RNA NEAT1 as an Emerging Biomarker in Breast and Gynecologic Cancers: a Systematic Overview. Reprod Sci 2021; 28:2436-2447. [PMID: 33569749 DOI: 10.1007/s43032-021-00481-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/31/2021] [Indexed: 02/06/2023]
Abstract
Long non-coding RNAs (lncRNAs) are emerging regulators of cellular pathways, especially in cancer development. Among the lncRNAs, nuclear paraspeckle assembly transcript 1 (NEAT1) forms a scaffold for a nuclear body; the paraspeckle and aberrant expression of NEAT1 have been reported in breast and gynecologic cancers (ovarian, cervical, endometrial, and vulvar). Abundantly expressed NEAT1 in breast and gynecologic cancers generally contribute to tumor development by sponging its corresponding tumor-suppressive microRNAs or interacting with various regulatory proteins. The distinct expression of NEAT1 and its contribution to tumorigenic pathways make it a promising therapeutic target in breast and gynecologic cancers. Herein, we summarize the functions and molecular mechanisms of NEAT1 in human breast, ovarian, cervical, endometrial, and vulvar cancers. Furthermore, we emphasize its critical role in the formation of paraspeckle development and its functions. Conclusively, NEAT1 is a considerable biomarker with a bright prospect and can be therapeutically targeted to manage breast and gynecologic cancers.
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Affiliation(s)
- Sanu Thankachan
- School of Biotechnology, National Institute of Technology, Calicut, Kerala, 673601, India
| | | | - Thejaswini Venkatesh
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Kasargod, Kerala, 671316, India
| | - Padmanaban S Suresh
- School of Biotechnology, National Institute of Technology, Calicut, Kerala, 673601, India.
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Liang XH, De Hoyos CL, Shen W, Zhang L, Fazio M, Crooke ST. Solid-Phase Separation of Toxic Phosphorothioate Antisense Oligonucleotide-Protein Nucleolar Aggregates Is Cytoprotective. Nucleic Acid Ther 2021; 31:126-144. [PMID: 33534636 DOI: 10.1089/nat.2020.0923] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Phosphorothioate antisense oligonucleotides (PS-ASOs) interact with proteins and can localize to or induce the formation of a variety of subcellular PS-ASO-protein or PS-ASO-ribonucleoprotein aggregates. In this study, we show that these different aggregates that form with varying compositions at various concentrations in the cytosol, nucleus, and nucleolus may undergo phase separations in cells. Some aggregates can form with both nontoxic and toxic PS-ASOs, such as PS bodies, paraspeckles, and nuclear filaments. However, toxic PS-ASOs have been shown to form unique nucleolar aggregates that result in nucleolar dysfunction and apoptosis. These include liquid-like aggregates that we labeled "cloudy nucleoli" and solid-like perinucleolar filaments. Toxic nucleolar aggregates may undergo solid-phase separation and in the solid phase, protein mobility in and out of the aggregates is limited. Other aggregates appear to undergo liquid-phase separation, including paraspeckles and perinucleolar caps, in which protein mobility is negatively correlated with the binding affinity of the proteins to PS-ASOs. However, PS bodies and nuclear filaments are solid-like aggregates. Importantly, in cells that survived treatment with toxic PS-ASOs, solid-like PS-ASO aggregates accumulated, especially Hsc70-containing nucleolus-like structures, in which modest pre-rRNA transcriptional activity was retained and appeared to mitigate the nucleolar toxicity. This is the first demonstration that exogenous drugs, PS-ASOs, can form aggregates that undergo phase separations and that solid-phase separation of toxic PS-ASO-induced nucleolar aggregates is cytoprotective.
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Affiliation(s)
- Xue-Hai Liang
- Core Antisense Research and Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Cheryl Li De Hoyos
- Core Antisense Research and Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Wen Shen
- Core Antisense Research and Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Lingdi Zhang
- Core Antisense Research and Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Michael Fazio
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Stanley T Crooke
- Core Antisense Research and Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
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Organization and function of paraspeckles. Essays Biochem 2020; 64:875-882. [DOI: 10.1042/ebc20200010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/11/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022]
Abstract
Abstract
Paraspeckles are a type of subnuclear bodies built on the long noncoding RNA NEAT1 (nuclear paraspeckle assembly transcript 1, also known as MEN-ε/β or VINC-1). Paraspeckles are involved in many physiological processes including cellular stress responses, cell differentiation, corpus luteum formation and cancer progression. Recently, ultra-resolution microscopy coupled with multicolor-labeling of paraspeckle components (the NEAT1 RNA and paraspeckle proteins) revealed the exquisite details of paraspeckle structure and function. NEAT1 transcripts are radially arranged to form a core–shell spheroidal structure, while paraspeckle proteins (PSPs) localize within different layers. Functional dissection of NEAT1 shows that the subdomains of NEAT1_2 are important for RNA stability, isoform switching and paraspeckle assembly via a liquid–liquid phase separation (LLPS) mechanism. We review recent progress on structure and organization of paraspeckles as well as how paraspeckles spatiotemporally control gene regulation through sequestration of diverse proteins and RNAs in cells.
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38
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Thakur J, Henikoff S. Architectural RNA in chromatin organization. Biochem Soc Trans 2020; 48:1967-1978. [PMID: 32897323 PMCID: PMC7609026 DOI: 10.1042/bst20191226] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/20/2022]
Abstract
RNA plays a well-established architectural role in the formation of membraneless interchromatin nuclear bodies. However, a less well-known role of RNA is in organizing chromatin, whereby specific RNAs have been found to recruit chromatin modifier proteins. Whether or not RNA can act as an architectural molecule for chromatin remains unclear, partly because dissecting the architectural role of RNA from its regulatory role remains challenging. Studies that have addressed RNA's architectural role in chromatin organization rely on in situ RNA depletion using Ribonuclease A (RNase A) and suggest that RNA plays a major direct architectural role in chromatin organization. In this review, we will discuss these findings, candidate chromatin architectural long non-coding RNAs and possible mechanisms by which RNA, along with RNA binding proteins might be mediating chromatin organization.
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Affiliation(s)
- Jitendra Thakur
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, U.S.A
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, U.S.A
- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, U.S.A
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Ghosh S, Guimaraes JC, Lanzafame M, Schmidt A, Syed AP, Dimitriades B, Börsch A, Ghosh S, Mittal N, Montavon T, Correia AL, Danner J, Meister G, Terracciano LM, Pfeffer S, Piscuoglio S, Zavolan M. Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation. EMBO J 2020; 39:e103922. [PMID: 32812257 PMCID: PMC7507497 DOI: 10.15252/embj.2019103922] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 06/27/2020] [Accepted: 07/07/2020] [Indexed: 01/05/2023] Open
Abstract
Translational readthrough, i.e., elongation of polypeptide chains beyond the stop codon, was initially reported for viral RNA, but later found also on eukaryotic transcripts, resulting in proteome diversification and protein‐level modulation. Here, we report that AGO1x, an evolutionarily conserved translational readthrough isoform of Argonaute 1, is generated in highly proliferative breast cancer cells, where it curbs accumulation of double‐stranded RNAs (dsRNAs) and consequent induction of interferon responses and apoptosis. In contrast to other mammalian Argonaute protein family members with primarily cytoplasmic functions, AGO1x exhibits nuclear localization in the vicinity of nucleoli. We identify AGO1x interaction with the polyribonucleotide nucleotidyltransferase 1 (PNPT1) and show that the depletion of this protein further augments dsRNA accumulation. Our study thus uncovers a novel function of an Argonaute protein in buffering the endogenous dsRNA‐induced interferon responses, different than the canonical function of AGO proteins in the miRNA effector pathway. As AGO1x expression is tightly linked to breast cancer cell proliferation, our study thus suggests a new direction for limiting tumor growth.
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Affiliation(s)
- Souvik Ghosh
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Joao C Guimaraes
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Manuela Lanzafame
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Afzal Pasha Syed
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Beatrice Dimitriades
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Anastasiya Börsch
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Shreemoyee Ghosh
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Nitish Mittal
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Thomas Montavon
- Architecture et Réactivité de l'ARN, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Ana Luisa Correia
- Department of Biomedicine, University of Basel/University Hospital Basel, Basel, Switzerland
| | - Johannes Danner
- Department of Biochemistry, Department of Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Gunter Meister
- Department of Biochemistry, Department of Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | | | - Sébastien Pfeffer
- Architecture et Réactivité de l'ARN, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Salvatore Piscuoglio
- Institute of Pathology, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel/University Hospital Basel, Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
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Girbes Minguez M, Wolters-Eisfeld G, Lutz D, Buck F, Schachner M, Kleene R. The cell adhesion molecule L1 interacts with nuclear proteins via its intracellular domain. FASEB J 2020; 34:9869-9883. [PMID: 32533745 DOI: 10.1096/fj.201902242r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 02/05/2023]
Abstract
Proteolytic cleavage of the cell adhesion molecule L1 (L1) in brain tissue and in cultured cerebellar neurons results in the generation and nuclear import of a 30 kDa fragment comprising most of L1's C-terminal, intracellular domain. In search of molecules that interact with this domain, we performed affinity chromatography with the recombinant intracellular L1 domain and a nuclear extract from mouse brains, and identified potential nuclear L1 binding partners involved in transcriptional regulation, RNA processing and transport, DNA repair, chromatin remodeling, and nucleocytoplasmic transport. By co-immunoprecipitation and enzyme-linked immunosorbent assay using recombinant proteins, we verified the direct interaction between L1 and the nuclear binding partners non-POU domain containing octamer-binding protein and splicing factor proline/glutamine-rich. The proximity ligation assay confirmed this close interaction in cultures of cerebellar granule cells. Our findings suggest that L1 fragments regulate multiple nuclear functions in the nervous system. We discuss possible physiological and pathological roles of these interactions in regulation of chromatin structure, gene expression, RNA processing, and DNA repair.
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Affiliation(s)
- Maria Girbes Minguez
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Gerrit Wolters-Eisfeld
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - David Lutz
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Buck
- Zentrum für Diagnostik, Institut für Klinische Chemie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Melitta Schachner
- Center for Neuroscience, Shantou University Medical College, Shantou, China
- Keck Center for Collaborative Neuroscience and Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Ralf Kleene
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
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41
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Todorovski V, Fox AH, Choi YS. Matrix stiffness-sensitive long noncoding RNA NEAT1 seeded paraspeckles in cancer cells. Mol Biol Cell 2020; 31:1654-1662. [PMID: 32293985 PMCID: PMC7521846 DOI: 10.1091/mbc.e20-02-0097] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/15/2022] Open
Abstract
Cancer progression is influenced by changes in the tumor microenvironment, such as the stiffening of the extracellular matrix. Yet our understanding of how cancer cells sense and convert mechanical stimuli into biochemical signals and physiological responses is still limited. The long noncoding RNA nuclear paraspeckle assembly transcript 1 (NEAT1), which forms the backbone of subnuclear "paraspeckle" bodies, has been identified as a key genetic regulator in numerous cancers. Here, we investigated whether paraspeckles, as defined by NEAT1 localization, are mechanosensitive. Using tunable polyacrylamide hydrogels of extreme stiffnesses, we measured paraspeckle parameters in several cancer cell lines and observed an increase in paraspeckles in cells cultured on soft (3 kPa) hydrogels compared with stiffer (40 kPa) hydrogels. This response to soft substrate is erased when cells are first conditioned on stiff substrate, and then transferred onto soft hydrogels, suggestive of mechanomemory upstream of paraspeckle regulation. We also examined some well-characterized mechanosensitive markers, but found that lamin A expression, as well as YAP and MRTF-A nuclear translocation did not show consistent trends between stiffnesses, despite all cell types having increased migration, nuclear, and cell area on stiffer hydrogels. We thus propose that paraspeckles may prove of use as mechanosensors in cancer mechanobiology.
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Affiliation(s)
- Vanja Todorovski
- School of Human Sciences, The University of Western Australia, Crawley 6009, Australia
| | - Archa H. Fox
- School of Human Sciences, The University of Western Australia, Crawley 6009, Australia
- School of Molecular Sciences, The University of Western Australia, Crawley 6009, Australia
| | - Yu Suk Choi
- School of Human Sciences, The University of Western Australia, Crawley 6009, Australia
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42
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Taiana E, Ronchetti D, Todoerti K, Nobili L, Tassone P, Amodio N, Neri A. LncRNA NEAT1 in Paraspeckles: A Structural Scaffold for Cellular DNA Damage Response Systems? Noncoding RNA 2020; 6:ncrna6030026. [PMID: 32630183 PMCID: PMC7549348 DOI: 10.3390/ncrna6030026] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/25/2020] [Accepted: 06/28/2020] [Indexed: 12/13/2022] Open
Abstract
Nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA (lncRNA) reported to be frequently deregulated in various types of cancers and neurodegenerative processes. NEAT1 is an indispensable structural component of paraspeckles (PSs), which are dynamic and membraneless nuclear bodies that affect different cellular functions, including stress response. Furthermore, increasing evidence supports the crucial role of NEAT1 and essential structural proteins of PSs (PSPs) in the regulation of the DNA damage repair (DDR) system. This review aims to provide an overview of the current knowledge on the involvement of NEAT1 and PSPs in DDR, which might strengthen the rationale underlying future NEAT1-based therapeutic options in tumor and neurodegenerative diseases.
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Affiliation(s)
- Elisa Taiana
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
- Correspondence: (E.T.); (A.N.); Tel.: +39-02-5032-0420 (E.T. & A.N.)
| | - Domenica Ronchetti
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
| | - Katia Todoerti
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
| | - Lucia Nobili
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (P.T.); (N.A.)
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (P.T.); (N.A.)
| | - Antonino Neri
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
- Correspondence: (E.T.); (A.N.); Tel.: +39-02-5032-0420 (E.T. & A.N.)
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Jen HW, Gu DL, Lang YD, Jou YS. PSPC1 Potentiates IGF1R Expression to Augment Cell Adhesion and Motility. Cells 2020; 9:cells9061490. [PMID: 32570949 PMCID: PMC7349238 DOI: 10.3390/cells9061490] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/06/2020] [Accepted: 06/16/2020] [Indexed: 02/05/2023] Open
Abstract
Paraspeckle protein 1 (PSPC1) overexpression in cancers is known to be the pro-metastatic switch of tumor progression associated with poor prognosis of cancer patients. However, the detail molecular mechanisms to facilitate cancer cell migration remain elusive. Here, we conducted integrated analysis of human phospho-kinase antibody array, transcriptome analysis with RNA-seq, and proteomic analysis of protein pulldown to study the molecular detail of PSPC1-potentiated phenotypical transformation, adhesion, and motility in human hepatocellular carcinoma (HCC) cells. We found that PSPC1 overexpression re-assembles and augments stress fiber formations to promote recruitment of focal adhesion contacts at the protruding edge to facilitate cell migration. PSPC1 activated focal adhesion-associated kinases especially FAK/Src signaling to enhance cell adhesion and motility toward extracellular matrix (ECM). Integrated transcriptome and gene set enrichment analysis indicated that PSPC1 modulated receptor tyrosine kinase IGF1R involved in the focal adhesion pathway and induction of diverse integrins expression. Knockdown IGF1R expression and treatment of IGF1R inhibitor suppressed PSPC1-induced cell motility. Interestingly, knockdown PSPC1-interacted paraspeckle components including NONO, FUS, and the lncRNA Neat1 abolished PSPC1-activated IGF1R expression. Together, PSPC1 overexpression induced focal adhesion formation and facilitated cell motility via activation of IGF1R signaling. PSPC1 overexpression in tumors could be a potential biomarker of target therapy with IGF1R inhibitor for improvement of HCC therapy.
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Affiliation(s)
- Hsin-Wei Jen
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 11490, Taiwan;
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan; (D.-L.G.); (Y.-D.L.)
| | - De-Leung Gu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan; (D.-L.G.); (Y.-D.L.)
| | - Yaw-Dong Lang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan; (D.-L.G.); (Y.-D.L.)
| | - Yuh-Shan Jou
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 11490, Taiwan;
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan; (D.-L.G.); (Y.-D.L.)
- Correspondence:
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Crooke ST, Vickers TA, Liang XH. Phosphorothioate modified oligonucleotide-protein interactions. Nucleic Acids Res 2020; 48:5235-5253. [PMID: 32356888 PMCID: PMC7261153 DOI: 10.1093/nar/gkaa299] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/08/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Antisense oligonucleotides (ASOs) interact with target RNAs via hybridization to modulate gene expression through different mechanisms. ASO therapeutics are chemically modified and include phosphorothioate (PS) backbone modifications and different ribose and base modifications to improve pharmacological properties. Modified PS ASOs display better binding affinity to the target RNAs and increased binding to proteins. Moreover, PS ASO protein interactions can affect many aspects of their performance, including distribution and tissue delivery, cellular uptake, intracellular trafficking, potency and toxicity. In this review, we summarize recent progress in understanding PS ASO protein interactions, highlighting the proteins with which PS ASOs interact, the influence of PS ASO protein interactions on ASO performance, and the structure activity relationships of PS ASO modification and protein interactions. A detailed understanding of these interactions can aid in the design of safer and more potent ASO drugs, as illustrated by recent findings that altering ASO chemical modifications dramatically improves therapeutic index.
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45
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Live cell imaging and proteomic profiling of endogenous NEAT1 lncRNA by CRISPR/Cas9-mediated knock-in. Protein Cell 2020; 11:641-660. [PMID: 32458346 PMCID: PMC7452982 DOI: 10.1007/s13238-020-00706-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
In mammalian cells, long noncoding RNAs (lncRNAs) form complexes with proteins to execute various biological functions such as gene transcription, RNA processing and other signaling activities. However, methods to track endogenous lncRNA dynamics in live cells and screen for lncRNA interacting proteins are limited. Here, we report the development of CERTIS (CRISPR-mediated Endogenous lncRNA Tracking and Immunoprecipitation System) to visualize and isolate endogenous lncRNA, by precisely inserting a 24-repeat MS2 tag into the distal end of lncRNA locus through the CRISPR/Cas9 technology. In this study, we show that CERTIS effectively labeled the paraspeckle lncRNA NEAT1 without disturbing its physiological properties and could monitor the endogenous expression variation of NEAT1. In addition, CERTIS displayed superior performance on both short- and long-term tracking of NEAT1 dynamics in live cells. We found that NEAT1 and paraspeckles were sensitive to topoisomerase I specific inhibitors. Moreover, RNA Immunoprecipitation (RIP) of the MS2-tagged NEAT1 lncRNA successfully revealed several new protein components of paraspeckle. Our results support CERTIS as a tool suitable to track both spatial and temporal lncRNA regulation in live cells as well as study the lncRNA-protein interactomes.
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46
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Vickers TA, Rahdar M, Prakash TP, Crooke ST. Kinetic and subcellular analysis of PS-ASO/protein interactions with P54nrb and RNase H1. Nucleic Acids Res 2020; 47:10865-10880. [PMID: 31495875 PMCID: PMC6846478 DOI: 10.1093/nar/gkz771] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 08/21/2019] [Accepted: 08/28/2019] [Indexed: 01/16/2023] Open
Abstract
The rapid RNase H1-dependent mislocalization of heterodimer proteins P54nrb and PSF to nucleoli is an early event in the pathway that explains the effects of most toxic phosphorothioate ASOs (PS-ASOs). Using a recently developed NanoLuciferace (NLuc)-based structural complementation reporter system which allows us to observe ASO/protein interactions in real time in live cells, we have determined that safe and toxic PS-ASOs associate with these proteins with kinetics and impact on subcellular localization that differ. Toxic PS-ASOs interact in a complex that includes RNase H1, P54nrb and PSF; but RNase H1/P54nrb complexes were observed in only the cells treated with toxic, but not safe PS-ASOs. In addition, experiments performed in vitro suggest that RNA is also a required component of the complex. The protein–protein interaction between P54nrb and RNase H1 requires the spacer region of RNAse H1, while the P54nrb core domains are required for association with RNase H1. In addition, we have determined that PS-ASOs bind P54nrb via RRM1 and RRM2, while they bind RNase H1 primarily via the hybrid binding domain, however catalytic domain interactions also contribute to overall affinity. These ASO–protein interactions are highly influenced by the chemistry of the PS-ASO binding environment, however little correlation between affinity for specific proteins and PS-ASO toxicity was observed.
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Affiliation(s)
- Timothy A Vickers
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Meghdad Rahdar
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Thazha P Prakash
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
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Grosch M, Ittermann S, Rusha E, Greisle T, Ori C, Truong DJJ, O'Neill AC, Pertek A, Westmeyer GG, Drukker M. Nucleus size and DNA accessibility are linked to the regulation of paraspeckle formation in cellular differentiation. BMC Biol 2020; 18:42. [PMID: 32321486 PMCID: PMC7178590 DOI: 10.1186/s12915-020-00770-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/16/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Many long noncoding RNAs (lncRNAs) have been implicated in general and cell type-specific molecular regulation. Here, we asked what underlies the fundamental basis for the seemingly random appearance of nuclear lncRNA condensates in cells, and we sought compounds that can promote the disintegration of lncRNA condensates in vivo. RESULTS As a basis for comparing lncRNAs and cellular properties among different cell types, we screened lncRNAs in human pluripotent stem cells (hPSCs) that were differentiated to an atlas of cell lineages. We found that paraspeckles, which form by aggregation of the lncRNA NEAT1, are scaled by the size of the nucleus, and that small DNA-binding molecules promote the disintegration of paraspeckles and other lncRNA condensates. Furthermore, we found that paraspeckles regulate the differentiation of hPSCs. CONCLUSIONS Positive correlation between the size of the nucleus and the number of paraspeckles exist in numerous types of human cells. The tethering and structure of paraspeckles, as well as other lncRNAs, to the genome can be disrupted by small molecules that intercalate in DNA. The structure-function relationship of lncRNAs that regulates stem cell differentiation is likely to be determined by the dynamics of nucleus size and binding site accessibility.
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Affiliation(s)
- Markus Grosch
- Institute of Stem Cell Research (ISF), Helmholtz Zentrum München, Neuherberg, Germany
| | - Sebastian Ittermann
- Institute of Stem Cell Research (ISF), Helmholtz Zentrum München, Neuherberg, Germany
| | - Ejona Rusha
- Institute of Stem Cell Research (ISF), iPSC Core Facility, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tobias Greisle
- Institute of Stem Cell Research (ISF), Helmholtz Zentrum München, Neuherberg, Germany
| | - Chaido Ori
- Institute of Stem Cell Research (ISF), Helmholtz Zentrum München, Neuherberg, Germany.,Comprehensive Pneumology Center (CPC), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | | | - Adam C O'Neill
- Institute of Stem Cell Research (ISF), Helmholtz Zentrum München, Neuherberg, Germany
| | - Anna Pertek
- Institute of Stem Cell Research (ISF), iPSC Core Facility, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gil Gregor Westmeyer
- Institute of Biological and Medical Imaging (IBMI), Helmholtz Zentrum München, Neuherberg, Germany
| | - Micha Drukker
- Institute of Stem Cell Research (ISF), Helmholtz Zentrum München, Neuherberg, Germany. .,Institute of Stem Cell Research (ISF), iPSC Core Facility, Helmholtz Zentrum München, Neuherberg, Germany.
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48
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Isobe M, Toya H, Mito M, Chiba T, Asahara H, Hirose T, Nakagawa S. Forced isoform switching of Neat1_1 to Neat1_2 leads to the loss of Neat1_1 and the hyperformation of paraspeckles but does not affect the development and growth of mice. RNA (NEW YORK, N.Y.) 2020; 26:251-264. [PMID: 31822595 PMCID: PMC7025509 DOI: 10.1261/rna.072587.119] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/04/2019] [Indexed: 05/27/2023]
Abstract
Neat1 is a long noncoding RNA (lncRNA) that serves as an architectural component of the nuclear bodies known as paraspeckles. Two isoforms of Neat1, the short isoform Neat1_1 and the long isoform Neat1_2, are generated from the same gene locus by alternative 3' processing. Neat1_1 is the most abundant and the best conserved isoform expressed in various cell types, whereas Neat1_2 is expressed in a small population of particular cell types, including the tip cells of the intestinal epithelium. To investigate the physiological significance of isoform switching, we created mutant mice that solely expressed Neat1_2 by deleting the upstream polyadenylation (poly-A) signal (PAS) required for the production of Neat1_1. We observed the loss of Neat1_1 and strong up-regulation of Neat1_2 in various tissues and cells and the subsequent hyperformation of paraspeckles, especially in cells that normally express Neat1_2. However, the mutant mice were born at the expected Mendelian ratios and did not exhibit obvious external and histological abnormalities. These observations suggested that the hyperformation of paraspeckles does not interfere with the development and growth of these animals under normal laboratory conditions.
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Affiliation(s)
- Momo Isobe
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Hikaru Toya
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
| | - Tomoki Chiba
- Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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49
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Isobe M, Toya H, Mito M, Chiba T, Asahara H, Hirose T, Nakagawa S. Forced isoform switching of Neat1_1 to Neat1_2 leads to the loss of Neat1_1 and the hyperformation of paraspeckles but does not affect the development and growth of mice. RNA (NEW YORK, N.Y.) 2020. [PMID: 31822595 DOI: 10.1101/698068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Neat1 is a long noncoding RNA (lncRNA) that serves as an architectural component of the nuclear bodies known as paraspeckles. Two isoforms of Neat1, the short isoform Neat1_1 and the long isoform Neat1_2, are generated from the same gene locus by alternative 3' processing. Neat1_1 is the most abundant and the best conserved isoform expressed in various cell types, whereas Neat1_2 is expressed in a small population of particular cell types, including the tip cells of the intestinal epithelium. To investigate the physiological significance of isoform switching, we created mutant mice that solely expressed Neat1_2 by deleting the upstream polyadenylation (poly-A) signal (PAS) required for the production of Neat1_1. We observed the loss of Neat1_1 and strong up-regulation of Neat1_2 in various tissues and cells and the subsequent hyperformation of paraspeckles, especially in cells that normally express Neat1_2. However, the mutant mice were born at the expected Mendelian ratios and did not exhibit obvious external and histological abnormalities. These observations suggested that the hyperformation of paraspeckles does not interfere with the development and growth of these animals under normal laboratory conditions.
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Affiliation(s)
- Momo Isobe
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Hikaru Toya
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
| | - Tomoki Chiba
- Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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50
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Abstract
Liquid-liquid phase separation is emerging as the universal mechanism by which membraneless cellular granules form. Despite many previous studies on condensation of intrinsically disordered proteins and low complexity domains, we lack understanding about the role of RNA, which is the essential component of all ribonucleoprotein (RNP) granules. RNA, as an anionic polymer, is inherently an excellent platform for achieving multivalency and can accommodate many RNA binding proteins. Recent findings have highlighted the diverse function of RNA in tuning phase-separation propensity up or down, altering viscoelastic properties and thereby driving immiscibility between different condensates. In addition to contributing to the biophysical properties of droplets, RNA is a functionally critical constituent that defines the identity of cellular condensates and controls the temporal and spatial distribution of specific RNP granules. In this review, we summarize what we have learned so far about such roles of RNA in the context of in vitro and in vivo studies.
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Affiliation(s)
- Kevin Rhine
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Velinda Vidaurre
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA; .,Physics Frontier Center (Center for the Physics of Living Cells), University of Illinois, Urbana, Illinois 61801, USA
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