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Liu YT, Cao LY, Sun ZJ. The emerging roles of liquid-liquid phase separation in tumor immunity. Int Immunopharmacol 2024; 143:113212. [PMID: 39353387 DOI: 10.1016/j.intimp.2024.113212] [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: 07/06/2024] [Revised: 09/02/2024] [Accepted: 09/17/2024] [Indexed: 10/04/2024]
Abstract
Recent advancements in tumor immunotherapy, particularly PD-1 targeted therapy, have shown significant promise, marking major progress in tumor treatment approaches. Despite this, the development of resistance to therapy and mechanisms of immune evasion by tumors pose considerable obstacles to the broad application of immunotherapy. This necessitates a deeper exploration of complex immune signaling pathways integral to tumor immunity. This review aims to critically analyze the role of liquid-liquid phase separation (LLPS) within tumor immunity, specifically its impact on immune signaling pathways and its potential to foster the development of novel cancer therapies. LLPS, a biophysical process newly recognized for its ability to spontaneously segregate and organize biomacromolecules into liquid-like condensates through weak multivalent interactions, offers a novel perspective on the formation of signaling clusters and the functionality of immune molecules. The review delves into the micromolecular mechanisms behind the creation of signaling condensates via LLPS and reviews recent progress in adjusting signaling pathways pertinent to tumor immunity, including the T cell receptor (TCR), B cell receptor (BCR), immune checkpoints, and innate immune pathways such as the cGAS-STING pathway, stress granules, and the ADP-heptose-ALPK1 signaling axis. Furthermore, it considers the prospects of utilizing LLPS to generate groundbreaking cancer therapies capable of navigating past current treatment barriers. Through an extensive examination of LLPS's impact on tumor immunity, the review seeks to highlight novel therapeutic strategies and address the challenges and future directions in this rapidly evolving field.
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Affiliation(s)
- Yuan-Tong Liu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China; Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Lin-Yu Cao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
| | - Zhi-Jun Sun
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
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2
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Noguchi K, Suzuki H, Abe R, Horiuchi K, Onoguchi-Mizutani R, Akimitsu N, Ogawa S, Akiyama T, Ike Y, Ino Y, Kimura Y, Ryo A, Doi H, Tanaka F, Suzuki Y, Toyoda A, Yamaguchi Y, Takahashi H. Multi-omics analysis using antibody-based in situ biotinylation technique suggests the mechanism of Cajal body formation. Cell Rep 2024; 43:114734. [PMID: 39283744 DOI: 10.1016/j.celrep.2024.114734] [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: 08/20/2023] [Revised: 04/30/2024] [Accepted: 08/23/2024] [Indexed: 09/28/2024] Open
Abstract
Membrane-less subcellular compartments play important roles in various cellular functions. Although techniques exist to identify components of cellular bodies, a comprehensive method for analyzing both static and dynamic states has not been established. Here, we apply an antibody-based in situ biotinylation proximity-labeling technique to identify components of static and dynamic nuclear bodies. Using this approach, we comprehensively identify DNA, RNA, and protein components of Cajal bodies (CBs) and then clarify their interactome. By inhibiting transcription, we capture dynamic changes in CBs. Our analysis reveals that nascent small nuclear RNAs (snRNAs) transcribed in CBs contribute to CB formation by assembling RNA-binding proteins, including frontotemporal dementia-related proteins, RNA-binding motif proteins, and heterogeneous nuclear ribonucleoproteins.
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Affiliation(s)
- Keisuke Noguchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Ryota Abe
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Keiko Horiuchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Rena Onoguchi-Mizutani
- R&D Department, Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Nobuyoshi Akimitsu
- R&D Department, Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Shintaro Ogawa
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Tomohiko Akiyama
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Yoko Ike
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Yoko Ino
- Advance Medical Research Center, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 216-0004, Japan
| | - Yayoi Kimura
- Advance Medical Research Center, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 216-0004, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 216-0004, Japan; Department of Virology III, National Institute of Infectious Diseases, 4-7-1, Gakuen Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yuki Yamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, Kanagawa 226-8501, Japan.
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan.
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3
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Chakraborty S, Mishra J, Roy A, Niharika, Manna S, Baral T, Nandi P, Patra S, Patra SK. Liquid-liquid phase separation in subcellular assemblages and signaling pathways: Chromatin modifications induced gene regulation for cellular physiology and functions including carcinogenesis. Biochimie 2024; 223:74-97. [PMID: 38723938 DOI: 10.1016/j.biochi.2024.05.007] [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: 12/06/2023] [Revised: 03/08/2024] [Accepted: 05/04/2024] [Indexed: 05/24/2024]
Abstract
Liquid-liquid phase separation (LLPS) describes many biochemical processes, including hydrogel formation, in the integrity of macromolecular assemblages and existence of membraneless organelles, including ribosome, nucleolus, nuclear speckles, paraspeckles, promyelocytic leukemia (PML) bodies, Cajal bodies (all exert crucial roles in cellular physiology), and evidence are emerging day by day. Also, phase separation is well documented in generation of plasma membrane subdomains and interplay between membranous and membraneless organelles. Intrinsically disordered regions (IDRs) of biopolymers/proteins are the most critical sticking regions that aggravate the formation of such condensates. Remarkably, phase separated condensates are also involved in epigenetic regulation of gene expression, chromatin remodeling, and heterochromatinization. Epigenetic marks on DNA and histones cooperate with RNA-binding proteins through their IDRs to trigger LLPS for facilitating transcription. How phase separation coalesces mutant oncoproteins, orchestrate tumor suppressor genes expression, and facilitated cancer-associated signaling pathways are unravelling. That autophagosome formation and DYRK3-mediated cancer stem cell modification also depend on phase separation is deciphered in part. In view of this, and to linchpin insight into the subcellular membraneless organelle assembly, gene activation and biological reactions catalyzed by enzymes, and the downstream physiological functions, and how all these events are precisely facilitated by LLPS inducing organelle function, epigenetic modulation of gene expression in this scenario, and how it goes awry in cancer progression are summarized and presented in this article.
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Affiliation(s)
- Subhajit Chakraborty
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Jagdish Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Tirthankar Baral
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Piyasa Nandi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Subhajit Patra
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India.
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McLaurin DM, Tucker SK, Hebert MD. Coilin mediates m6A RNA methylation through phosphorylation of METTL3. Biol Open 2023; 12:bio060116. [PMID: 38050869 PMCID: PMC10714142 DOI: 10.1242/bio.060116] [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: 08/10/2023] [Accepted: 11/14/2023] [Indexed: 12/07/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of noncoding RNAs that regulate gene expression. An important step in miRNA biogenesis occurs when primary miRNAs are bound and cleaved by the microprocessor to generate precursor miRNAs. Regulation at this step is essential and one such regulator includes m6A RNA methylation, an RNA modification found on primary miRNAs that is installed by METTL3 and bound by hnRNPA2B1. Our lab has recently discovered that the Cajal body marker protein coilin also participates in miRNA biogenesis and hypothesized that coilin may be influencing miRNA biogenesis through m6A RNA methylation. Here we report that coilin suppression reduces m6A on primary Let7a and miR-21. We also found that coilin suppression reduced the protein expression of hnRNPA2B1 and METTL3. We observed an interaction between coilin and ectopically expressed METTL3 and found that coilin suppression reduced the nucleoplasmic portion of METTL3 and blunted ectopic METTL3 phosphorylation. Finally, coilin suppression disrupted the greater METTL3 complex with cofactors METTL14 and WTAP. Collectively, our work has uncovered a role for coilin in mediating m6A RNA methylation and provides an avenue by which coilin participates in miRNA biogenesis.
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Affiliation(s)
- Douglas M. McLaurin
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Sara K. Tucker
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Michael D. Hebert
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
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5
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Suzuki H, Furugori K, Abe R, Ogawa S, Ito S, Akiyama T, Horiuchi K, Takahashi H. MED26-containing Mediator may orchestrate multiple transcription processes through organization of nuclear bodies. Bioessays 2023; 45:e2200178. [PMID: 36852638 DOI: 10.1002/bies.202200178] [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: 09/07/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 03/01/2023]
Abstract
Mediator is a coregulatory complex that plays essential roles in multiple processes of transcription regulation. One of the human Mediator subunits, MED26, has a role in recruitment of the super elongation complex (SEC) to polyadenylated genes and little elongation complex (LEC) to non-polyadenylated genes, including small nuclear RNAs (snRNAs) and replication-dependent histone (RDH) genes. MED26-containing Mediator plays a role in 3' Pol II pausing at the proximal region of transcript end sites in RDH genes through recruitment of Cajal bodies (CBs) to histone locus bodies (HLBs). This finding suggests that Mediator is involved in the association of CBs with HLBs to facilitate 3' Pol II pausing and subsequent 3'-end processing by supplying 3'-end processing factors from CBs. Thus, we argue the possibility that Mediator is involved in the organization of nuclear bodies to orchestrate multiple processes of gene transcription.
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Affiliation(s)
- Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Kazuki Furugori
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Ryota Abe
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Shintaro Ogawa
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Sayaka Ito
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Tomohiko Akiyama
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Keiko Horiuchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
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6
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Bogolyubov DS, Chistyakova LV, Goodkov AV. Glomerulosomes: morphologically distinct nuclear organelles of unknown nature. PROTOPLASMA 2022; 259:1409-1415. [PMID: 35103866 DOI: 10.1007/s00709-022-01742-5] [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: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
The nucleus of some representatives of the genus Pelomyxa (Amoebozoa, Archamoebae, Pelobiontida) contains specific bodies (membrane-less organelles). They may be either embedded in the nucleolar mass or detached from the nucleolus. We termed these nuclear bodies the glomerulosomes for their characteristic ultrastructural appearance. The glomerulosomes are distinct nuclear bodies, about 1 μm in diameter. The morphological and diagnostic unit of a glomerulosome is an electron-dense thread/string, about 30-40 nm in thickness. These threads are not direct continuation of the nucleolar material. The threads create the unique geometric appearance of the glomerulosome by being organized into precisely parallel rows/cords. Each cord of the threads can curve at different angles within the glomerulosome body, but the threads themselves are not coiled. Nowadays, the glomerulosomes have been discovered in P. palustris, P. stagnalis, P. paradoxa, and Pelomyxa sp. Despite the unique appearance of glomerulosomes, their existence may be a more common phenomenon in eukaryotic cells than just a specific feature of the nucleus of elected pelomyxes.
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Affiliation(s)
- Dmitry S Bogolyubov
- Laboratory of Cell Morphology, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg, 194064, Russia.
| | | | - Andrew V Goodkov
- Laboratory of Cytology of Unicellular Organisms, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg, 194064, Russia
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7
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Suzuki H, Abe R, Shimada M, Hirose T, Hirose H, Noguchi K, Ike Y, Yasui N, Furugori K, Yamaguchi Y, Toyoda A, Suzuki Y, Yamamoto T, Saitoh N, Sato S, Tomomori-Sato C, Conaway RC, Conaway JW, Takahashi H. The 3' Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies' association with histone locus bodies. Nat Commun 2022; 13:2905. [PMID: 35614107 PMCID: PMC9133132 DOI: 10.1038/s41467-022-30632-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 05/10/2022] [Indexed: 11/09/2022] Open
Abstract
Non-polyadenylated mRNAs of replication-dependent histones (RDHs) are synthesized by RNA polymerase II (Pol II) at histone locus bodies (HLBs). HLBs frequently associate with Cajal bodies (CBs), in which 3'-end processing factors for RDH genes are enriched; however, this association's role in transcription termination of RDH genes remains unclear. Here, we show that Pol II pauses immediately upstream of transcript end sites of RDH genes and Mediator plays a role in this Pol II pausing through CBs' association with HLBs. Disruption of the Mediator docking site for Little elongation complex (LEC)-Cap binding complex (CBC)-Negative elongation factor (NELF), components of CBs, interferes with CBs' association with HLBs and 3' Pol II pausing, resulting in increased aberrant unprocessed RDH gene transcripts. Our findings suggest Mediator's involvement in CBs' association with HLBs to facilitate 3' Pol II pausing and subsequent 3'-end processing of RDH genes by supplying 3'-end processing factors.
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Affiliation(s)
- Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Ryota Abe
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Miho Shimada
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Tomonori Hirose
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Hiroko Hirose
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Keisuke Noguchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yoko Ike
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Nanami Yasui
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Kazuki Furugori
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yuki Yamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, Kanagawa, 226-8501, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Tatsuro Yamamoto
- Division of Cancer Biology, The Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Shigeo Sato
- Stowers Institute for Medical Research, 1000E 50th Street, Kansas City, MO, 64110, USA
| | - Chieri Tomomori-Sato
- Stowers Institute for Medical Research, 1000E 50th Street, Kansas City, MO, 64110, USA
| | - Ronald C Conaway
- Stowers Institute for Medical Research, 1000E 50th Street, Kansas City, MO, 64110, USA.,Department of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, MO, 66160, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, 1000E 50th Street, Kansas City, MO, 64110, USA.,Department of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, MO, 66160, USA
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan.
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Batnasan E, Koivukoski S, Kärkkäinen M, Latonen L. Nuclear Organization in Response to Stress: A Special Focus on Nucleoli. Results Probl Cell Differ 2022; 70:469-494. [PMID: 36348119 DOI: 10.1007/978-3-031-06573-6_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In this chapter, we discuss the nuclear organization and how it responds to different types of stress. A key component in these responses is molecular traffic between the different sub-nucleolar compartments, such as nucleoplasm, chromatin, nucleoli, and various speckle and body compartments. This allows specific repair and response activities in locations where they normally are not active and serve to halt sensitive functions until the stress insult passes and inflicted damage has been repaired. We focus on mammalian cells and their nuclear organization, especially describing the central role of the nucleolus in nuclear stress responses. We describe events after multiple stress types, including DNA damage, various drugs, and toxic compounds, and discuss the involvement of macromolecular traffic between dynamic, phase-separated nuclear organelles and foci. We delineate the key proteins and non-coding RNA in the formation of stress-responsive, non-membranous nuclear organelles, many of which are relevant to the formation of and utilization in cancer treatment.
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Affiliation(s)
- Enkhzaya Batnasan
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Sonja Koivukoski
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Minttu Kärkkäinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland.
- Foundation for the Finnish Cancer Institute, Helsinki, Finland.
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9
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Beneventi G, Munita R, Cao Thi Ngoc P, Madej M, Cieśla M, Muthukumar S, Krogh N, Nielsen H, Swaminathan V, Bellodi C. The small Cajal body-specific RNA 15 (SCARNA15) directs p53 and redox homeostasis via selective splicing in cancer cells. NAR Cancer 2021; 3:zcab026. [PMID: 34316713 PMCID: PMC8271217 DOI: 10.1093/narcan/zcab026] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/19/2021] [Accepted: 06/18/2021] [Indexed: 01/05/2023] Open
Abstract
Small Cajal body-specific RNAs (scaRNAs) guide post-transcriptional modification of spliceosomal RNA and, while commonly altered in cancer, have poorly defined roles in tumorigenesis. Here, we uncover that SCARNA15 directs alternative splicing (AS) and stress adaptation in cancer cells. Specifically, we find that SCARNA15 guides critical pseudouridylation (Ψ) of U2 spliceosomal RNA to fine-tune AS of distinct transcripts enriched for chromatin and transcriptional regulators in malignant cells. This critically impacts the expression and function of the key tumor suppressors ATRX and p53. Significantly, SCARNA15 loss impairs p53-mediated redox homeostasis and hampers cancer cell survival, motility and anchorage-independent growth. In sum, these findings highlight an unanticipated role for SCARNA15 and Ψ in directing cancer-associated splicing programs.
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Affiliation(s)
- Giulia Beneventi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Roberto Munita
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Phuong Cao Thi Ngoc
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Magdalena Madej
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Maciej Cieśla
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Sowndarya Muthukumar
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Vinay Swaminathan
- Division of Oncology, Department of Clinical Sciences, Lund University, 22184, Lund, Sweden
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
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10
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Ruff KM, Dar F, Pappu RV. Polyphasic linkage and the impact of ligand binding on the regulation of biomolecular condensates. BIOPHYSICS REVIEWS 2021; 2:021302. [PMID: 34179888 PMCID: PMC8211317 DOI: 10.1063/5.0050059] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 12/30/2022]
Abstract
Cellular matter can be spatially and temporally organized into membraneless biomolecular condensates. The current thinking is that these condensates form and dissolve via phase transitions driven by one or more condensate-specific multivalent macromolecules known as scaffolds. Cells likely regulate condensate formation and dissolution by exerting control over the concentrations of regulatory molecules, which we refer to as ligands. Wyman and Gill introduced the framework of polyphasic linkage to explain how ligands can exert thermodynamic control over phase transitions. This review focuses on describing the concepts of polyphasic linkage and the relevance of such a mechanism for controlling condensate formation and dissolution. We describe how ligand-mediated control over scaffold phase behavior can be quantified experimentally. Further, we build on recent studies to highlight features of ligands that make them suppressors vs drivers of phase separation. Finally, we highlight areas where advances are needed to further understand ligand-mediated control of condensates in complex cellular environments. These advances include understanding the effects of networks of ligands on condensate behavior and how ligands modulate phase transitions controlled by different combinations of homotypic and heterotypic interactions among scaffold macromolecules. Insights gained from the application of polyphasic linkage concepts should be useful for designing novel pharmaceutical ligands to regulate condensates.
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Affiliation(s)
- Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Furqan Dar
- Department of Physics, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, USA
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11
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Pathak RU, Soujanya M, Mishra RK. Deterioration of nuclear morphology and architecture: A hallmark of senescence and aging. Ageing Res Rev 2021; 67:101264. [PMID: 33540043 DOI: 10.1016/j.arr.2021.101264] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 01/04/2021] [Accepted: 01/26/2021] [Indexed: 12/15/2022]
Abstract
The metazoan nucleus is a highly structured organelle containing several well-defined sub-organelles. It is the largest organelle inside a cell taking up from one tenth to half of entire cell volume. This makes it one of the easiest organelles to identify and study under the microscope. Abnormalities in the nuclear morphology and architecture are commonly observed in an aged and senescent cell. For example, the nuclei enlarge, loose their shape, appear lobulated, harbour nuclear membrane invaginations, carry enlarged/fragmented nucleolus, loose heterochromatin, etc. In this review we discuss about the age-related changes in nuclear features and elaborate upon the molecular reasons driving the change. Many of these changes can be easily imaged under a microscope and analysed in silico. Thus, computational image analysis of nuclear features appears to be a promising tool to evaluate physiological age of a cell and offers to be a legitimate biomarker. It can be used to examine progression of age-related diseases and evaluate therapies.
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Affiliation(s)
| | - Mamilla Soujanya
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, Telangana, India
| | - Rakesh Kumar Mishra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, Telangana, India.
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12
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Vladimirova O, De Leo A, Deng Z, Wiedmer A, Hayden J, Lieberman PM. Phase separation and DAXX redistribution contribute to LANA nuclear body and KSHV genome dynamics during latency and reactivation. PLoS Pathog 2021; 17:e1009231. [PMID: 33471863 PMCID: PMC7943007 DOI: 10.1371/journal.ppat.1009231] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 03/09/2021] [Accepted: 12/08/2020] [Indexed: 12/14/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) can drive formation of diverse and essential macromolecular structures, including those specified by viruses. Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) genomes associate with the viral encoded Latency-Associated Nuclear Antigen (LANA) to form stable nuclear bodies (NBs) during latent infection. Here, we show that LANA-NB formation and KSHV genome conformation involves LLPS. Using LLPS disrupting solvents, we show that LANA-NBs are partially disrupted, while DAXX and PML foci are highly resistant. LLPS disruption altered the LANA-dependent KSHV chromosome conformation but did not stimulate lytic reactivation. We found that LANA-NBs undergo major morphological transformation during KSHV lytic reactivation to form LANA-associated replication compartments encompassing KSHV DNA. DAXX colocalizes with the LANA-NBs during latency but is evicted from the LANA-associated lytic replication compartments. These findings indicate the LANA-NBs are dynamic super-molecular nuclear structures that partly depend on LLPS and undergo morphological transitions corresponding to the different modes of viral replication. During latent infection, gamma-herpesvirus genomes are maintained as extrachromosomal circular DNA, referred to as episomes, by dedicated viral-encoded episome maintenance proteins. KSHV-encoded LANA maintains viral episomes through binding as an oligomeric protein to repetitive DNA elements in the viral terminal repeats (TRs). Viral episomes can be visualized as LANA-associated nuclear bodies (LANA-NBs). Here, we show that LANA-NBs utilize mechanisms of self-assembly through liquid-liquid phase separation (LLPS) to build dynamic structures that change during cell cycle and viral life cycle. We find that DAXX is a component of the latent phase LANA-NBs, but is evicted during the transition to lytic replication where LANA remains associated with KSHV DNA to form a ring-like replication compartment.
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Affiliation(s)
| | - Alessandra De Leo
- Department of Immunology, H. Lee Moffit Cancer and Research Center, Tampa Florida, United States of America
| | - Zhong Deng
- The Wistar Institute, Philadelphia, United States of America
| | - Andreas Wiedmer
- The Wistar Institute, Philadelphia, United States of America
| | - James Hayden
- The Wistar Institute, Philadelphia, United States of America
| | - Paul M. Lieberman
- The Wistar Institute, Philadelphia, United States of America
- * E-mail:
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13
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Grosch M, Ittermann S, Shaposhnikov D, Drukker M. Chromatin-Associated Membraneless Organelles in Regulation of Cellular Differentiation. Stem Cell Reports 2020; 15:1220-1232. [PMID: 33217325 PMCID: PMC7724471 DOI: 10.1016/j.stemcr.2020.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Membrane-free intracellular biocondensates are enclosures of proteins and nucleic acids that form by phase separation. Extensive ensembles of nuclear "membraneless organelles" indicate their involvement in genome regulation. Indeed, nuclear bodies have been linked to regulation of gene expression by formation of condensates made of chromatin and RNA processing factors. Important questions pertain to the involvement of membraneless organelles in determining cell identity through their cell-type-specific composition and function. Paraspeckles provide a prism to these questions because they exhibit striking cell-type-specific patterns and since they are crucial in embryogenesis. Here, we outline known interactions between paraspeckles and chromatin, and postulate how such interactions may be important in regulation of cell fate transitions. Moreover, we propose long non-coding RNAs (lncRNAs) as candidates for similar regulation because many form foci that resemble biocondensates and exhibit dynamic patterns during differentiation. Finally, we outline approaches that could ascertain how chromatin-associated membraneless organelles regulate cellular differentiation.
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Affiliation(s)
- Markus Grosch
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Sebastian Ittermann
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Dmitry Shaposhnikov
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Gorlaeus Building, Einsteinweg 55, 2333 CC RA Leiden, The Netherlands.
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14
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Razin SV, Ulianov SV. Divide and Rule: Phase Separation in Eukaryotic Genome Functioning. Cells 2020; 9:cells9112480. [PMID: 33203115 PMCID: PMC7696541 DOI: 10.3390/cells9112480] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
The functioning of a cell at various organizational levels is determined by the interactions between macromolecules that promote cellular organelle formation and orchestrate metabolic pathways via the control of enzymatic activities. Although highly specific and relatively stable protein-protein, protein-DNA, and protein-RNA interactions are traditionally suggested as the drivers for cellular function realization, recent advances in the discovery of weak multivalent interactions have uncovered the role of so-called macromolecule condensates. These structures, which are highly divergent in size, composition, function, and cellular localization are predominantly formed by liquid-liquid phase separation (LLPS): a physical-chemical process where an initially homogenous solution turns into two distinct phases, one of which contains the major portion of the dissolved macromolecules and the other one containing the solvent. In a living cell, LLPS drives the formation of membrane-less organelles such as the nucleolus, nuclear bodies, and viral replication factories and facilitates the assembly of complex macromolecule aggregates possessing regulatory, structural, and enzymatic functions. Here, we discuss the role of LLPS in the spatial organization of eukaryotic chromatin and regulation of gene expression in normal and pathological conditions.
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Affiliation(s)
- Sergey V. Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119017 Moscow, Russia;
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119017 Moscow, Russia
| | - Sergey V. Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119017 Moscow, Russia;
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119017 Moscow, Russia
- Correspondence: ; Tel.: +7-499-135-9787
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15
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Sabari BR, Dall'Agnese A, Young RA. Biomolecular Condensates in the Nucleus. Trends Biochem Sci 2020; 45:961-977. [PMID: 32684431 PMCID: PMC7572565 DOI: 10.1016/j.tibs.2020.06.007] [Citation(s) in RCA: 217] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 12/28/2022]
Abstract
Nuclear processes such as DNA replication, transcription, and RNA processing each depend on the concerted action of many different protein and RNA molecules. How biomolecules with shared functions find their way to specific locations has been assumed to occur largely by diffusion-mediated collisions. Recent studies have shown that many nuclear processes occur within condensates that compartmentalize and concentrate the protein and RNA molecules required for each process, typically at specific genomic loci. These condensates have common features and emergent properties that provide the cell with regulatory capabilities beyond canonical molecular regulatory mechanisms. We describe here the shared features of nuclear condensates, the components that produce locus-specific condensates, elements of specificity, and the emerging understanding of mechanisms regulating these compartments.
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Affiliation(s)
- Benjamin R Sabari
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA; Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA; Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142 USA.
| | | | - Richard A Young
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142 USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139 USA.
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16
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Nusinersen ameliorates motor function and prevents motoneuron Cajal body disassembly and abnormal poly(A) RNA distribution in a SMA mouse model. Sci Rep 2020; 10:10738. [PMID: 32612161 PMCID: PMC7330045 DOI: 10.1038/s41598-020-67569-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/08/2020] [Indexed: 11/09/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a devastating autosomal recessive neuromuscular disease characterized by degeneration of spinal cord alpha motor neurons (αMNs). SMA is caused by the homozygous deletion or mutation of the survival motor neuron 1 (SMN1) gene, resulting in reduced expression of SMN protein, which leads to αMN degeneration and muscle atrophy. The majority of transcripts of a second gene (SMN2) generate an alternative spliced isoform that lacks exon 7 and produces a truncated nonfunctional form of SMN. A major function of SMN is the biogenesis of spliceosomal snRNPs, which are essential components of the pre-mRNA splicing machinery, the spliceosome. In recent years, new potential therapies have been developed to increase SMN levels, including treatment with antisense oligonucleotides (ASOs). The ASO-nusinersen (Spinraza) promotes the inclusion of exon 7 in SMN2 transcripts and notably enhances the production of full-length SMN in mouse models of SMA. In this work, we used the intracerebroventricular injection of nusinersen in the SMN∆7 mouse model of SMA to evaluate the effects of this ASO on the behavior of Cajal bodies (CBs), nuclear structures involved in spliceosomal snRNP biogenesis, and the cellular distribution of polyadenylated mRNAs in αMNs. The administration of nusinersen at postnatal day (P) 1 normalized SMN expression in the spinal cord but not in skeletal muscle, rescued the growth curve and improved motor behavior at P12 (late symptomatic stage). Importantly, this ASO recovered the number of canonical CBs in MNs, significantly reduced the abnormal accumulation of polyadenylated RNAs in nuclear granules, and normalized the expression of the pre-mRNAs encoding chondrolectin and choline acetyltransferase, two key factors for αMN homeostasis. We propose that the splicing modulatory function of nusinersen in SMA αMN is mediated by the rescue of CB biogenesis, resulting in enhanced polyadenylated pre-mRNA transcription and splicing and nuclear export of mature mRNAs for translation. Our results support that the selective restoration of SMN expression in the spinal cord has a beneficial impact not only on αMNs but also on skeletal myofibers. However, the rescue of SMN expression in muscle appears to be necessary for the complete recovery of motor function.
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17
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Mészáros B, Erdős G, Szabó B, Schád É, Tantos Á, Abukhairan R, Horváth T, Murvai N, Kovács OP, Kovács M, Tosatto SCE, Tompa P, Dosztányi Z, Pancsa R. PhaSePro: the database of proteins driving liquid-liquid phase separation. Nucleic Acids Res 2020; 48:D360-D367. [PMID: 31612960 PMCID: PMC7145634 DOI: 10.1093/nar/gkz848] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/11/2019] [Accepted: 10/07/2019] [Indexed: 11/13/2022] Open
Abstract
Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid-liquid phase separation (LLPS), a process that relies on multivalent weak interactions of the constituent proteins and other macromolecules. Since the first discoveries of certain proteins being able to drive LLPS, it emerged as a general mechanism for the effective organization of cellular space that is exploited in all kingdoms of life. While numerous experimental studies report novel cases, the computational identification of LLPS drivers is lagging behind, and many open questions remain about the sequence determinants, composition, regulation and biological relevance of the resulting condensates. Our limited ability to overcome these issues is largely due to the lack of a dedicated LLPS database. Therefore, here we introduce PhaSePro (https://phasepro.elte.hu), an openly accessible, comprehensive, manually curated database of experimentally validated LLPS driver proteins/protein regions. It not only provides a wealth of information on such systems, but improves the standardization of data by introducing novel LLPS-specific controlled vocabularies. PhaSePro can be accessed through an appealing, user-friendly interface and thus has definite potential to become the central resource in this dynamically developing field.
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Affiliation(s)
- Bálint Mészáros
- MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Gábor Erdős
- MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Beáta Szabó
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Éva Schád
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Ágnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Rawan Abukhairan
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Tamás Horváth
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Nikoletta Murvai
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Orsolya P Kovács
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Márton Kovács
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova CNR Institute of Neuroscience, Padova, Italy
| | - Péter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Structural Biology (CSB), Brussels, Belgium; Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium
| | - Zsuzsanna Dosztányi
- MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
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18
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Sapaly D, Delers P, Coridon J, Salman B, Letourneur F, Dumont F, Lefebvre S. The Small-Molecule Flunarizine in Spinal Muscular Atrophy Patient Fibroblasts Impacts on the Gemin Components of the SMN Complex and TDP43, an RNA-Binding Protein Relevant to Motor Neuron Diseases. Front Mol Biosci 2020; 7:55. [PMID: 32363199 PMCID: PMC7181958 DOI: 10.3389/fmolb.2020.00055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/18/2020] [Indexed: 01/01/2023] Open
Abstract
The motor neurodegenerative disease spinal muscular atrophy (SMA) is caused by alterations of the survival motor neuron 1 (SMN1) gene involved in RNA metabolism. Although the disease mechanisms are not completely elucidated, SMN protein deficiency leads to abnormal small nuclear ribonucleoproteins (snRNPs) assembly responsible for widespread splicing defects. SMN protein localizes in nuclear bodies that are lost in SMA and adult onset amyotrophic lateral sclerosis (ALS) patient cells harboring TDP-43 or FUS/TLS mutations. We previously reported that flunarizine recruits SMN into nuclear bodies and improves the phenotype of an SMA mouse model. However, the precise mode of action remains elusive. Here, a marked reduction of the integral components of the SMN complex is observed in severe SMA patient fibroblast cells. We show that flunarizine increases the protein levels of a subset of components of the SMN-Gemins complex, Gemins2-4, and markedly reduces the RNA and protein levels of the pro-oxydant thioredoxin-interacting protein (TXNIP) encoded by an mRNA target of Gemin5. We further show that SMN deficiency causes a dissociation of the localization of the SMN complex components from the same nuclear bodies. The accumulation of TDP-43 in SMN-positive nuclear bodies is also perturbed in SMA cells. Notably, TDP-43 is found to co-localize with SMN in nuclear bodies of flunarizine-treated SMA cells. Our findings indicate that flunarizine reverses cellular changes caused by SMN deficiency in SMA cells and further support the view of a common pathway in RNA metabolism underlying infantile and adult motor neuron diseases.
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Affiliation(s)
- Delphine Sapaly
- INSERM UMR-S 1124, Toxicité Environnementale, Cibles Thérapeutiques, Signalisation Cellulaire et Biomarqueurs, Campus Saint-Germain-des-Prés, Université de Paris, Paris, France
| | - Perrine Delers
- INSERM UMR-S 1124, Toxicité Environnementale, Cibles Thérapeutiques, Signalisation Cellulaire et Biomarqueurs, Campus Saint-Germain-des-Prés, Université de Paris, Paris, France
| | - Jennifer Coridon
- BioMedTech Facilities INSERM US36 - CNRS UMS 2009, Campus Saint-Germain-des-Prés, Université de Paris, Paris, France
| | - Badih Salman
- INSERM UMR-S 1124, Toxicité Environnementale, Cibles Thérapeutiques, Signalisation Cellulaire et Biomarqueurs, Campus Saint-Germain-des-Prés, Université de Paris, Paris, France
| | | | - Florent Dumont
- Genom'ic Platform, INSERM U1016, Institut Cochin, Paris, France
| | - Suzie Lefebvre
- INSERM UMR-S 1124, Toxicité Environnementale, Cibles Thérapeutiques, Signalisation Cellulaire et Biomarqueurs, Campus Saint-Germain-des-Prés, Université de Paris, Paris, France
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19
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Lomonte P, Baklouti F, Binda O. The Biochemistry of Survival Motor Neuron Protein Is Paving the Way to Novel Therapies for Spinal Muscle Atrophy. Biochemistry 2020; 59:1391-1397. [PMID: 32227847 DOI: 10.1021/acs.biochem.9b01124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spinal muscle atrophy (SMA) is the leading genetic cause of infant mortality. SMA originates from the loss of functional survival motor neuron (SMN) protein. In most SMA cases, the SMN1 gene is deleted. However, in some cases, SMN is mutated, impairing its biological functions. SMN mutants could provide clues about the biological functions of SMN and the specific impact on SMA, potentially leading to the identification of new pathways and thus providing novel treatment alternatives, and even personalized care. Here, we discuss the biochemistry of SMN and the most recent SMA treatment strategies.
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Affiliation(s)
- Patrick Lomonte
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), 69008 Lyon, France
| | - Faouzi Baklouti
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), 69008 Lyon, France
| | - Olivier Binda
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), 69008 Lyon, France
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20
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Greig JA, Nguyen TA, Lee M, Holehouse AS, Posey AE, Pappu RV, Jedd G. Arginine-Enriched Mixed-Charge Domains Provide Cohesion for Nuclear Speckle Condensation. Mol Cell 2020; 77:1237-1250.e4. [PMID: 32048997 PMCID: PMC10715173 DOI: 10.1016/j.molcel.2020.01.025] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/04/2019] [Accepted: 01/23/2020] [Indexed: 12/29/2022]
Abstract
Low-complexity protein domains promote the formation of various biomolecular condensates. However, in many cases, the precise sequence features governing condensate formation and identity remain unclear. Here, we investigate the role of intrinsically disordered mixed-charge domains (MCDs) in nuclear speckle condensation. Proteins composed exclusively of arginine-aspartic acid dipeptide repeats undergo length-dependent condensation and speckle incorporation. Substituting arginine with lysine in synthetic and natural speckle-associated MCDs abolishes these activities, identifying a key role for multivalent contacts through arginine's guanidinium ion. MCDs can synergize with a speckle-associated RNA recognition motif to promote speckle specificity and residence. MCD behavior is tunable through net-charge: increasing negative charge abolishes condensation and speckle incorporation. Contrastingly, increasing positive charge through arginine leads to enhanced condensation, speckle enlargement, decreased splicing factor mobility, and defective mRNA export. Together, these results identify key sequence determinants of MCD-promoted speckle condensation and link the dynamic material properties of speckles with function in mRNA processing.
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Affiliation(s)
- Jamie A Greig
- Temasek Life Sciences Laboratory and Department of Biological Sciences, The National University of Singapore, Singapore 117604, Singapore
| | - Tu Anh Nguyen
- Temasek Life Sciences Laboratory and Department of Biological Sciences, The National University of Singapore, Singapore 117604, Singapore
| | - Michelle Lee
- Temasek Life Sciences Laboratory and Department of Biological Sciences, The National University of Singapore, Singapore 117604, Singapore
| | - Alex S Holehouse
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Ammon E Posey
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Gregory Jedd
- Temasek Life Sciences Laboratory and Department of Biological Sciences, The National University of Singapore, Singapore 117604, Singapore.
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21
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Krasikova A, Kulikova T. Identification of Genomic Loci Responsible for the Formation of Nuclear Domains Using Lampbrush Chromosomes. Noncoding RNA 2019; 6:ncrna6010001. [PMID: 31881720 PMCID: PMC7151628 DOI: 10.3390/ncrna6010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/19/2019] [Accepted: 12/22/2019] [Indexed: 12/12/2022] Open
Abstract
In the cell nuclei, various types of nuclear domains assemble as a result of transcriptional activity at specific chromosomal loci. Giant transcriptionally active lampbrush chromosomes, which form in oocyte nuclei of amphibians and birds enable the mapping of genomic sequences with high resolution and the visualization of individual transcription units. This makes avian and amphibian oocyte nuclei an advantageous model for studying locus-specific nuclear domains. We developed two strategies for identification and comprehensive analysis of the genomic loci involved in nuclear domain formation on lampbrush chromosomes. The first approach was based on the sequential FISH-mapping of BAC clones containing genomic DNA fragments with a known chromosomal position close to the locus of a nuclear domain. The second approach involved mechanical microdissection of the chromosomal region adjacent to the nuclear domain followed by the generation of FISH-probes and DNA sequencing. Furthermore, deciphering the DNA sequences from the dissected material by high throughput sequencing technologies and their mapping to the reference genome helps to identify the genomic region responsible for the formation of the nuclear domain. For those nuclear domains structured by nascent transcripts, identification of genomic loci of their formation is a crucial step in the identification of scaffold RNAs.
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22
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Van Fossen EM, Bednar RM, Mehl RA. Engineering Spatial Orthogonality into Protein Translation. Biochemistry 2019; 58:3325-3327. [PMID: 31343161 DOI: 10.1021/acs.biochem.9b00569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elise M Van Fossen
- Department of Biochemistry and Biophysics , Oregon State University , 2011 Ag Life Sciences Building , Corvallis , Oregon 97331-7305 , United States
| | - Riley M Bednar
- Department of Biochemistry and Biophysics , Oregon State University , 2011 Ag Life Sciences Building , Corvallis , Oregon 97331-7305 , United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics , Oregon State University , 2011 Ag Life Sciences Building , Corvallis , Oregon 97331-7305 , United States
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23
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Albrecht TR, Shevtsov SP, Wu Y, Mascibroda LG, Peart NJ, Huang KL, Sawyer IA, Tong L, Dundr M, Wagner EJ. Integrator subunit 4 is a 'Symplekin-like' scaffold that associates with INTS9/11 to form the Integrator cleavage module. Nucleic Acids Res 2019; 46:4241-4255. [PMID: 29471365 PMCID: PMC5934644 DOI: 10.1093/nar/gky100] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 02/17/2018] [Indexed: 12/14/2022] Open
Abstract
Integrator (INT) is a transcriptional regulatory complex associated with RNA polymerase II that is required for the 3′-end processing of both UsnRNAs and enhancer RNAs. Integrator subunits 9 (INTS9) and INTS11 constitute the catalytic core of INT and are paralogues of the cleavage and polyadenylation specificity factors CPSF100 and CPSF73. While CPSF73/100 are known to associate with a third protein called Symplekin, there is no paralog of Symplekin within INT raising the question of how INTS9/11 associate with the other INT subunits. Here, we have identified that INTS4 is a specific and conserved interaction partner of INTS9/11 that does not interact with either subunit individually. Although INTS4 has no significant homology with Symplekin, it possesses N-terminal HEAT repeats similar to Symplekin but also contains a β-sheet rich C-terminal region, both of which are important to bind INTS9/11. We assess three functions of INT including UsnRNA 3′-end processing, maintenance of Cajal body structural integrity, and formation of histone locus bodies to conclude that INTS4/9/11 are the most critical of the INT subunits for UsnRNA biogenesis. Altogether, these results indicate that INTS4/9/11 compose a heterotrimeric complex that likely represents the Integrator ‘cleavage module’ responsible for its endonucleolytic activity.
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Affiliation(s)
- Todd R Albrecht
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Sergey P Shevtsov
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, IL 60064, USA
| | - Yixuan Wu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Lauren G Mascibroda
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Natoya J Peart
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Iain A Sawyer
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, IL 60064, USA.,Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Miroslav Dundr
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, IL 60064, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
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24
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Sawyer IA, Sturgill D, Dundr M. Membraneless nuclear organelles and the search for phases within phases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1514. [DOI: 10.1002/wrna.1514] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/20/2018] [Accepted: 09/27/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Iain A. Sawyer
- Department of Cell Biology and Anatomy, Chicago Medical School Rosalind Franklin University of Medicine and Science North Chicago Illinois
- Laboratory of Receptor Biology and Gene Expression National Cancer Institute, National Institutes of Health Bethesda Maryland
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression National Cancer Institute, National Institutes of Health Bethesda Maryland
| | - Miroslav Dundr
- Department of Cell Biology and Anatomy, Chicago Medical School Rosalind Franklin University of Medicine and Science North Chicago Illinois
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25
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Sawyer IA, Dundr M. Chromatin loops and causality loops: the influence of RNA upon spatial nuclear architecture. Chromosoma 2017; 126:541-557. [PMID: 28593374 DOI: 10.1007/s00412-017-0632-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/17/2017] [Accepted: 05/23/2017] [Indexed: 01/18/2023]
Abstract
An intrinsic and essential trait exhibited by cells is the properly coordinated and integrated regulation of an astoundingly large number of simultaneous molecular decisions and reactions to maintain biochemical homeostasis. This is especially true inside the cell nucleus, where the recognition of DNA and RNA by a vast range of nucleic acid-interacting proteins organizes gene expression patterns. However, this dynamic system is not regulated by simple "on" or "off" signals. Instead, transcription factor and RNA polymerase recruitment to DNA are influenced by the local chromatin and epigenetic environment, a gene's relative position within the nucleus and the action of noncoding RNAs. In addition, major phase-separated structural features of the nucleus, such as nucleoli and paraspeckles, assemble in direct response to specific transcriptional activities and, in turn, influence global genomic function. Currently, the interpretation of these data is trapped in a causality dilemma reminiscent of the "chicken and the egg" paradox as it is unclear whether changes in nuclear architecture promote RNA function or vice versa. Here, we review recent advances that suggest a complex and interdependent interaction network between gene expression, chromatin topology, and noncoding RNA function. We also discuss the functional links between these essential nuclear processes from the nanoscale (gene looping) to the macroscale (sub-nuclear gene positioning and nuclear body function) and briefly highlight some of the challenges that researchers may encounter when studying these phenomena.
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Affiliation(s)
- Iain A Sawyer
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Miroslav Dundr
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA.
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26
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Sawyer IA, Sturgill D, Sung MH, Hager GL, Dundr M. Cajal body function in genome organization and transcriptome diversity. Bioessays 2016; 38:1197-1208. [PMID: 27767214 DOI: 10.1002/bies.201600144] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nuclear bodies contribute to non-random organization of the human genome and nuclear function. Using a major prototypical nuclear body, the Cajal body, as an example, we suggest that these structures assemble at specific gene loci located across the genome as a result of high transcriptional activity. Subsequently, target genes are physically clustered in close proximity in Cajal body-containing cells. However, Cajal bodies are observed in only a limited number of human cell types, including neuronal and cancer cells. Ultimately, Cajal body depletion perturbs splicing kinetics by reducing target small nuclear RNA (snRNA) transcription and limiting the levels of spliceosomal snRNPs, including their modification and turnover following each round of RNA splicing. As such, Cajal bodies are capable of shaping the chromatin interaction landscape and the transcriptome by influencing spliceosome kinetics. Future studies should concentrate on characterizing the direct influence of Cajal bodies upon snRNA gene transcriptional dynamics. Also see the video abstract here.
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Affiliation(s)
- Iain A Sawyer
- Department of Cell Biology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA.,Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Miroslav Dundr
- Department of Cell Biology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
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