1
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Shen A, Hencel K, Parker M, Scott R, Skukan R, Adesina A, Metheringham C, Miska E, Nam Y, Haerty W, Simpson G, Akay A. U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs. Nucleic Acids Res 2024; 52:9139-9160. [PMID: 38808663 PMCID: PMC11347140 DOI: 10.1093/nar/gkae447] [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: 09/15/2023] [Revised: 05/08/2024] [Accepted: 05/28/2024] [Indexed: 05/30/2024] Open
Abstract
pre-mRNA splicing is a critical feature of eukaryotic gene expression. Both cis- and trans-splicing rely on accurately recognising splice site sequences by spliceosomal U snRNAs and associated proteins. Spliceosomal snRNAs carry multiple RNA modifications with the potential to affect different stages of pre-mRNA splicing. Here, we show that the conserved U6 snRNA m6A methyltransferase METT-10 is required for accurate and efficient cis- and trans-splicing of C. elegans pre-mRNAs. The absence of METT-10 in C. elegans and METTL16 in humans primarily leads to alternative splicing at 5' splice sites with an adenosine at +4 position. In addition, METT-10 is required for splicing of weak 3' cis- and trans-splice sites. We identified a significant overlap between METT-10 and the conserved splicing factor SNRNP27K in regulating 5' splice sites with +4A. Finally, we show that editing endogenous 5' splice site +4A positions to +4U restores splicing to wild-type positions in a mett-10 mutant background, supporting a direct role for U6 snRNA m6A modification in 5' splice site recognition. We conclude that the U6 snRNA m6A modification is important for accurate and efficient pre-mRNA splicing.
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Affiliation(s)
- Aykut Shen
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
| | - Katarzyna Hencel
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
| | - Matthew T Parker
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Robyn Scott
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Roberta Skukan
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
| | | | | | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Rd, Cambridge CB2 1QN, UK
| | - Yunsun Nam
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wilfried Haerty
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Gordon G Simpson
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, DD2 5DA, UK
| | - Alper Akay
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
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2
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Juniku B, Mignon J, Carême R, Genco A, Obeid AM, Mottet D, Monari A, Michaux C. Intrinsic disorder and salt-dependent conformational changes of the N-terminal region of TFIP11 splicing factor. Int J Biol Macromol 2024; 277:134291. [PMID: 39089542 DOI: 10.1016/j.ijbiomac.2024.134291] [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: 05/30/2024] [Revised: 07/21/2024] [Accepted: 07/28/2024] [Indexed: 08/04/2024]
Abstract
Tuftelin Interacting Protein 11 (TFIP11) was identified as a critical human spliceosome assembly regulator, interacting with multiple proteins and localising in membrane-less organelles. However, a lack of structural information on TFIP11 limits the rationalisation of its biological role. TFIP11 is predicted as an intrinsically disordered protein (IDP), and more specifically concerning its N-terminal (N-TER) region. IDPs lack a defined tertiary structure, existing as a dynamic conformational ensemble, favouring protein-protein and protein-RNA interactions. IDPs are involved in liquid-liquid phase separation (LLPS), driving the formation of subnuclear compartments. Combining disorder prediction, molecular dynamics, and spectroscopy methods, this contribution shows the first evidence TFIP11 N-TER is a polyampholytic IDP, exhibiting a structural duality with the coexistence of ordered and disordered assemblies, depending on the ionic strength. Increasing the salt concentration enhances the protein conformational flexibility, presenting a more globule-like shape, and a fuzzier unstructured arrangement that could favour LLPS and protein-RNA interaction. The most charged and hydrophilic regions are the most impacted, including the G-Patch domain essential to TFIP11 function. This study gives a better understanding of the salt-dependent conformational behaviour of the N-TER TFIP11, supporting the hypothesis of the formation of different types of protein assembly, in line with its multiple biological roles.
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Affiliation(s)
- Blinera Juniku
- Laboratory of Physical Chemistry of Biomolecules, UCPTS, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium; Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium; Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium; GIGA-Molecular Biology of Diseases, Molecular Analysis of Gene Expression (MAGE) Laboratory, University of Liege, B34, Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Julien Mignon
- Laboratory of Physical Chemistry of Biomolecules, UCPTS, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium; Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium; Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium
| | - Rachel Carême
- Laboratory of Physical Chemistry of Biomolecules, UCPTS, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Alexia Genco
- GIGA-Molecular Biology of Diseases, Molecular Analysis of Gene Expression (MAGE) Laboratory, University of Liege, B34, Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Anna Maria Obeid
- GIGA-Molecular Biology of Diseases, Molecular Analysis of Gene Expression (MAGE) Laboratory, University of Liege, B34, Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Denis Mottet
- GIGA-Molecular Biology of Diseases, Molecular Analysis of Gene Expression (MAGE) Laboratory, University of Liege, B34, Avenue de l'Hôpital, B-4000 Liège, Belgium.
| | - Antonio Monari
- Université Paris Cité and CNRS, ITODYS, F-75006, Paris, France
| | - Catherine Michaux
- Laboratory of Physical Chemistry of Biomolecules, UCPTS, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium; Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium; Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium.
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3
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Kanwal N, Krogh N, Memet I, Lemus-Diaz N, Thomé C, Welp L, Mizi A, Hackert P, Papantonis A, Urlaub H, Nielsen H, Bohnsack K, Bohnsack M. GPATCH4 regulates rRNA and snRNA 2'-O-methylation in both DHX15-dependent and DHX15-independent manners. Nucleic Acids Res 2024; 52:1953-1974. [PMID: 38113271 PMCID: PMC10939407 DOI: 10.1093/nar/gkad1202] [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: 08/10/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
Regulation of RNA helicase activity, often accomplished by protein cofactors, is essential to ensure target specificity within the complex cellular environment. The largest family of RNA helicase cofactors are the G-patch proteins, but the cognate RNA helicases and cellular functions of numerous human G-patch proteins remain elusive. Here, we discover that GPATCH4 is a stimulatory cofactor of DHX15 that interacts with the DEAH box helicase in the nucleolus via residues in its G-patch domain. We reveal that GPATCH4 associates with pre-ribosomal particles, and crosslinks to the transcribed ribosomal DNA locus and precursor ribosomal RNAs as well as binding to small nucleolar- and small Cajal body-associated RNAs that guide rRNA and snRNA modifications. Loss of GPATCH4 impairs 2'-O-methylation at various rRNA and snRNA sites leading to decreased protein synthesis and cell growth. We demonstrate that the regulation of 2'-O-methylation by GPATCH4 is both dependent on, and independent of, its interaction with DHX15. Intriguingly, the ATPase activity of DHX15 is necessary for efficient methylation of DHX15-dependent sites, suggesting a function of DHX15 in regulating snoRNA-guided 2'-O-methylation of rRNA that requires activation by GPATCH4. Overall, our findings extend knowledge on RNA helicase regulation by G-patch proteins and also provide important new insights into the mechanisms regulating installation of rRNA and snRNA modifications, which are essential for ribosome function and pre-mRNA splicing.
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Affiliation(s)
- Nidhi Kanwal
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, 3B Blegdamsvej, 2200N Copenhagen, Denmark
| | - Indira Memet
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Nicolas Lemus-Diaz
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Chairini C Thomé
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Luisa M Welp
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077 Göttingen, Germany
- Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 35075 Göttingen, Germany
| | - Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, Robert-Koch-Straße 40, 35075 Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, Robert-Koch-Straße 40, 35075 Göttingen, Germany
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077 Göttingen, Germany
- Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 35075 Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
- Cluster of Excellence ‘Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells’ (MBExC), University of Göttingen, Göttingen
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, 3B Blegdamsvej, 2200N Copenhagen, Denmark
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
- Cluster of Excellence ‘Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells’ (MBExC), University of Göttingen, Göttingen
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
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4
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Chen J, Wu M, Yang Y, Ruan C, Luo Y, Song L, Wu T, Huang J, Yang B, Liu T. TFIP11 promotes replication fork reversal to preserve genome stability. Nat Commun 2024; 15:1262. [PMID: 38341452 PMCID: PMC10858868 DOI: 10.1038/s41467-024-45684-3] [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: 04/28/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
Replication fork reversal, a critical protective mechanism against replication stress in higher eukaryotic cells, is orchestrated via a series of coordinated enzymatic reactions. The Bloom syndrome gene product, BLM, a member of the highly conserved RecQ helicase family, is implicated in this process, yet its precise regulation and role remain poorly understood. In this study, we demonstrate that the GCFC domain-containing protein TFIP11 forms a complex with the BLM helicase. TFIP11 exhibits a preference for binding to DNA substrates that mimic the structure generated at stalled replication forks. Loss of either TFIP11 or BLM leads to the accumulation of the other protein at stalled forks. This abnormal accumulation, in turn, impairs RAD51-mediated fork reversal and slowing, sensitizes cells to replication stress-inducing agents, and enhances chromosomal instability. These findings reveal a previously unidentified regulatory mechanism that modulates the activities of BLM and RAD51 at stalled forks, thereby impacting genome integrity.
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Affiliation(s)
- Junliang Chen
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, China
| | - Mingjie Wu
- The Trauma Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Yulan Yang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Chunyan Ruan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Yi Luo
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Lizhi Song
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Ting Wu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Jun Huang
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Bing Yang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Ting Liu
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
- Department of Cell Biology, Zhejiang University School of Medicine, 310058, Hangzhou, China.
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5
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Roth JF, Braunschweig U, Wu M, Li JD, Lin ZY, Larsen B, Weatheritt RJ, Gingras AC, Blencowe BJ. Systematic analysis of alternative exon-dependent interactome remodeling reveals multitasking functions of gene regulatory factors. Mol Cell 2023; 83:4222-4238.e10. [PMID: 38065061 DOI: 10.1016/j.molcel.2023.10.034] [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: 03/02/2023] [Revised: 08/09/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Alternative splicing significantly expands biological complexity, particularly in the vertebrate nervous system. Increasing evidence indicates that developmental and tissue-dependent alternative exons often control protein-protein interactions; yet, only a minor fraction of these events have been characterized. Using affinity purification-mass spectrometry (AP-MS), we show that approximately 60% of analyzed neural-differential exons in proteins previously implicated in transcriptional regulation result in the gain or loss of interaction partners, which in some cases form unexpected links with coupled processes. Notably, a neural exon in Chtop regulates its interaction with the Prmt1 methyltransferase and DExD-Box helicases Ddx39b/a, affecting its methylation and activity in promoting RNA export. Additionally, a neural exon in Sap30bp affects interactions with RNA processing factors, modulating a critical function of Sap30bp in promoting the splicing of <100 nt "mini-introns" that control nuclear RNA levels. AP-MS is thus a powerful approach for elucidating the multifaceted functions of proteins imparted by context-dependent alternative exons.
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Affiliation(s)
- Jonathan F Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Mingkun Wu
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jack Daiyang Li
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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6
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Staněk D. Coilin and Cajal bodies. Nucleus 2023; 14:2256036. [PMID: 37682044 PMCID: PMC10494742 DOI: 10.1080/19491034.2023.2256036] [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: 07/28/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023] Open
Abstract
The nucleus of higher eukaryotes contains a number of structures that concentrate specific biomolecules and play distinct roles in nuclear metabolism. In recent years, the molecular mechanisms controlling their formation have been intensively studied. In this brief review, I focus on coilin and Cajal bodies. Coilin is a key scaffolding protein of Cajal bodies that is evolutionarily conserved in metazoans. Cajal bodies are thought to be one of the archetypal nuclear structures involved in the metabolism of several short non-coding nuclear RNAs. Yet surprisingly little is known about the structure and function of coilin, and a comprehensive model to explain the origin of Cajal bodies is also lacking. Here, I summarize recent results on Cajal bodies and coilin and discuss them in the context of the last three decades of research in this field.
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Affiliation(s)
- David Staněk
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
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7
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Wang C, Ulryck N, Herzel L, Pythoud N, Kleiber N, Guérineau V, Jactel V, Moritz C, Bohnsack M, Carapito C, Touboul D, Bohnsack K, Graille M. N 2-methylguanosine modifications on human tRNAs and snRNA U6 are important for cell proliferation, protein translation and pre-mRNA splicing. Nucleic Acids Res 2023; 51:7496-7519. [PMID: 37283053 PMCID: PMC10415138 DOI: 10.1093/nar/gkad487] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/21/2023] [Accepted: 05/22/2023] [Indexed: 06/08/2023] Open
Abstract
Modified nucleotides in non-coding RNAs, such as tRNAs and snRNAs, represent an important layer of gene expression regulation through their ability to fine-tune mRNA maturation and translation. Dysregulation of such modifications and the enzymes installing them have been linked to various human pathologies including neurodevelopmental disorders and cancers. Several methyltransferases (MTases) are regulated allosterically by human TRMT112 (Trm112 in Saccharomyces cerevisiae), but the interactome of this regulator and targets of its interacting MTases remain incompletely characterized. Here, we have investigated the interaction network of human TRMT112 in intact cells and identify three poorly characterized putative MTases (TRMT11, THUMPD3 and THUMPD2) as direct partners. We demonstrate that these three proteins are active N2-methylguanosine (m2G) MTases and that TRMT11 and THUMPD3 methylate positions 10 and 6 of tRNAs, respectively. For THUMPD2, we discovered that it directly associates with the U6 snRNA, a core component of the catalytic spliceosome, and is required for the formation of m2G, the last 'orphan' modification in U6 snRNA. Furthermore, our data reveal the combined importance of TRMT11 and THUMPD3 for optimal protein synthesis and cell proliferation as well as a role for THUMPD2 in fine-tuning pre-mRNA splicing.
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Affiliation(s)
- Can Wang
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Nathalie Ulryck
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Lydia Herzel
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Nicolas Pythoud
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI, FR2048 Strasbourg, France
| | - Nicole Kleiber
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Vincent Guérineau
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Vincent Jactel
- Laboratoire de Synthèse Organique (LSO), CNRS, École polytechnique, ENSTA, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Chloé Moritz
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI, FR2048 Strasbourg, France
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), Göttingen, Germany
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI, FR2048 Strasbourg, France
| | - David Touboul
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
- Laboratoire de Chimie Moléculaire (LCM), CNRS, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
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8
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Klimešová K, Petržílková H, Bařinka C, Staněk D. SART3 associates with a post-splicing complex. J Cell Sci 2023; 136:jcs260380. [PMID: 36620952 DOI: 10.1242/jcs.260380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 12/10/2022] [Indexed: 01/10/2023] Open
Abstract
SART3 is a multifunctional protein that acts in several steps of gene expression, including assembly and recycling of the spliceosomal U4/U6 small nuclear ribonucleoprotein particle (snRNP). In this work, we provide evidence that SART3 associates via its N-terminal HAT domain with the 12S U2 snRNP. Further analysis showed that SART3 associates with the post-splicing complex containing U2 and U5 snRNP components. In addition, we observed an interaction between SART3 and the RNA helicase DHX15, which disassembles post-splicing complexes. Based on our data, we propose a model that SART3 associates via its N-terminal HAT domain with the post-splicing complex, where it interacts with U6 snRNA to protect it and to initiate U6 snRNA recycling before a next round of splicing.
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MESH Headings
- RNA Splicing/genetics
- Spliceosomes/genetics
- Spliceosomes/metabolism
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoprotein, U5 Small Nuclear/genetics
- Ribonucleoprotein, U5 Small Nuclear/metabolism
- Ribonucleoprotein, U2 Small Nuclear/genetics
- Ribonucleoprotein, U2 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
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Affiliation(s)
- Klára Klimešová
- Department of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Hana Petržílková
- Department of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Cyril Bařinka
- Laboratory of Structural Biology, Institute of Biotechnology, Czech Academy of Sciences, 252 50 Prague, Czech Republic
| | - David Staněk
- Department of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
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9
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Zhu Y, Zhang J, Yu L, Xu S, Chen L, Wu K, Kong L, Lin W, Xue J, Wang Q, Lin Y, Chen X. SENP3 promotes tumor progression and is a novel prognostic biomarker in triple-negative breast cancer. Front Oncol 2023; 12:972969. [PMID: 36698419 PMCID: PMC9868814 DOI: 10.3389/fonc.2022.972969] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 12/14/2022] [Indexed: 01/12/2023] Open
Abstract
Background The clinical outcome of triple-negative breast cancer (TNBC) is poor. Finding more targets for the treatment of TNBC is an urgent need. SENPs are SUMO-specific proteins that play an important role in SUMO modification. Among several tumor types, SENPs have been identified as relevant biomarkers for progression and prognosis. The role of SENPs in TNBC is not yet clear. Methods The expression and prognosis of SENPs in TNBC were analyzed by TCGA and GEO data. SENP3 coexpression regulatory networks were determined by weighted gene coexpression network analysis (WGCNA). Least absolute shrinkage and selection operator (LASSO) and Cox univariate analyses were used to develop a risk signature based on genes associated with SENP3. A time-dependent receiver operating characteristic (ROC) analysis was employed to evaluate a risk signature's predictive accuracy and sensitivity. Moreover, a nomogram was constructed to facilitate clinical application. Results The prognostic and expression effects of SENP family genes were validated using the TCGA and GEO databases. SENP3 was found to be the only gene in the SENP family that was highly expressed and associated with an unfavorable prognosis in TNBC patients. Cell functional experiments showed that knockdown of SENP3 leads to growth, invasion, and migration inhibition of TNBC cells in vitro. By using WGCNA, 273 SENP3-related genes were identified. Finally, 11 SENP3-related genes were obtained from Cox univariate analysis and LASSO regression. Based on this, a prognostic risk prediction model was established. The risk signature of SENP3-related genes was verified as an independent prognostic marker for TNBC patients. Conclusion Among SENP family genes, we found that SENP3 was overexpressed in TNBC and associated with a worse prognosis. SENP3 knockdown can inhibit tumor proliferation, invasion, and migration. In TNBC patients, a risk signature based on the expression of 11 SENP3-related genes may improve prognosis prediction. The established risk markers may be promising prognostic biomarkers that can guide the individualized treatment of TNBC patients.
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Affiliation(s)
- Youzhi Zhu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Jiasheng Zhang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Liangfei Yu
- Department of Breast Surgery, the First Hospital of Fuzhou, Fuzhou, China
| | - Sunwang Xu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Ling Chen
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Kunlin Wu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Lingjun Kong
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Wei Lin
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Jiajie Xue
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Qingshui Wang
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China,*Correspondence: Xiangjin Chen, ; Yao Lin, ; Qingshui Wang,
| | - Yao Lin
- Central Laboratory at The Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, China,*Correspondence: Xiangjin Chen, ; Yao Lin, ; Qingshui Wang,
| | - Xiangjin Chen
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China,*Correspondence: Xiangjin Chen, ; Yao Lin, ; Qingshui Wang,
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10
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Webster SF, Ghalei H. Maturation of small nucleolar RNAs: from production to function. RNA Biol 2023; 20:715-736. [PMID: 37796118 PMCID: PMC10557570 DOI: 10.1080/15476286.2023.2254540] [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] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
Small Nucleolar RNAs (snoRNAs) are an abundant group of non-coding RNAs with well-defined roles in ribosomal RNA processing, folding and chemical modification. Besides their classic roles in ribosome biogenesis, snoRNAs are also implicated in several other cellular activities including regulation of splicing, transcription, RNA editing, cellular trafficking, and miRNA-like functions. Mature snoRNAs must undergo a series of processing steps tightly regulated by transiently associating factors and coordinated with other cellular processes including transcription and splicing. In addition to their mature forms, snoRNAs can contribute to gene expression regulation through their derivatives and degradation products. Here, we review the current knowledge on mechanisms of snoRNA maturation, including the different pathways of processing, and the regulatory mechanisms that control snoRNA levels and complex assembly. We also discuss the significance of studying snoRNA maturation, highlight the gaps in the current knowledge and suggest directions for future research in this area.
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Affiliation(s)
- Sarah F. Webster
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia, USA
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Homa Ghalei
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
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11
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DHX15 is involved in SUGP1-mediated RNA missplicing by mutant SF3B1 in cancer. Proc Natl Acad Sci U S A 2022; 119:e2216712119. [PMID: 36459648 PMCID: PMC9894173 DOI: 10.1073/pnas.2216712119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
SF3B1 is the most frequently mutated spliceosomal gene in cancer. Several hotspot mutations are known to disrupt the interaction of SF3B1 with another splicing factor, SUGP1, resulting in the RNA missplicing that characterizes mutant SF3B1 cancers. Properties of SUGP1, especially the presence of a G-patch motif, a structure known to function by activating DEAH-box RNA helicases, suggest the requirement of such an enzyme in SUGP1 function in splicing. However, the identity of this putative helicase has remained an important unanswered question. Here, using a variety of protein-protein interaction assays, we identify DHX15 as the critical helicase. We further show that depletion of DHX15 or expression of any of several DHX15 mutants, including one implicated in acute myeloid leukemia, partially recapitulates the splicing defects of mutant SF3B1. Moreover, a DHX15-SUGP1 G-patch fusion protein is able to incorporate into the spliceosome to rescue the splicing defects of mutant SF3B1. We also present the crystal structure of the human DHX15-SUGP1 G-patch complex, which reveals the molecular basis of their direct interaction. Our data thus demonstrate that DHX15 is the RNA helicase that functions with SUGP1 and additionally provide important insight into how mutant SF3B1 disrupts splicing in cancer.
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12
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Yang J, Miao RR, Li YN, Pan T, Wu SH, Qu XJ, Cui SX. Atypical chemokine receptor 3 induces colorectal tumorigenesis in mice by promoting β-arrestin-NOLC1-fibrillarin-dependent rRNA biogenesis. Acta Pharmacol Sin 2022; 43:2967-2976. [PMID: 35365782 PMCID: PMC9622750 DOI: 10.1038/s41401-022-00901-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/13/2022] [Indexed: 01/27/2023] Open
Abstract
Atypical chemokine receptor 3 (ACKR3) has emerged as a key player in various biological processes. Its atypical "intercepting receptor" properties have established ACKR3 as the major regulator in the pathophysiological processes in many diseases. In this study, we investigated the role of ACKR3 activation in promoting colorectal tumorigenesis. We showed that ACKR3 expression levels were significantly increased in human colon cancer tissues, and high levels of ACKR3 predicted the increased severity of cancer. In Villin-ACKR3 transgenic mice with a high expression level of CKR3 in their intestinal epithelial cells, administration of AOM/DSS induced more severe colorectal tumorigenesis than their WT littermates. Cancer cells of Villin-ACKR3 transgenic mice were characterised by the nuclear β-arrestin-1 (β-arr1)-activated perturbation of rRNA biogenesis. In HCT116 cells, cotreatment with CXCL12 and AMD3100 selectively activated ACKR3 and induced nuclear translocation of β-arr1, leading to an interaction of β-arr1 with nucleolar and coiled-body phosphoprotein 1 (NOLC1). NOLC1, as the phosphorylated protein, further interacted with fibrillarin, a conserved nucleolar methyltransferase responsible for ribosomal RNA methylation in the nucleolus, thereby increasing the methylation in histone H2A and promoting rRNA transcription in ribosome biogenesis. In conclusion, ACKR3 promotes colorectal tumorigenesis through the perturbation of rRNA biogenesis by the β-arr1-induced interaction of NOLC1 with fibrillarin.
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Affiliation(s)
- Juan Yang
- Beijing Key Laboratory of Environmental Toxicology, Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, 100069, China
- Department of Comprehensive Ward, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Rong-Rong Miao
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Ya-Nan Li
- Beijing Key Laboratory of Environmental Toxicology, Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, 100069, China
| | - Ting Pan
- Beijing Key Laboratory of Environmental Toxicology, Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, 100069, China
| | - Shu-Hua Wu
- Department of Pathology, Hospital of Bin Zhou Medical College, Binzhou, 256603, China
| | - Xian-Jun Qu
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Shu-Xiang Cui
- Beijing Key Laboratory of Environmental Toxicology, Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, 100069, China.
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Bohnsack KE, Kanwal N, Bohnsack MT. Prp43/DHX15 exemplify RNA helicase multifunctionality in the gene expression network. Nucleic Acids Res 2022; 50:9012-9022. [PMID: 35993807 PMCID: PMC9458436 DOI: 10.1093/nar/gkac687] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Dynamic regulation of RNA folding and structure is critical for the biogenesis and function of RNAs and ribonucleoprotein (RNP) complexes. Through their nucleotide triphosphate-dependent remodelling functions, RNA helicases are key modulators of RNA/RNP structure. While some RNA helicases are dedicated to a specific target RNA, others are multifunctional and engage numerous substrate RNAs in different aspects of RNA metabolism. The discovery of such multitasking RNA helicases raises the intriguing question of how these enzymes can act on diverse RNAs but also maintain specificity for their particular targets within the RNA-dense cellular environment. Furthermore, the identification of RNA helicases that sit at the nexus between different aspects of RNA metabolism raises the possibility that they mediate cross-regulation of different cellular processes. Prominent and extensively characterized multifunctional DEAH/RHA-box RNA helicases are DHX15 and its Saccharomyces cerevisiae (yeast) homologue Prp43. Due to their central roles in key cellular processes, these enzymes have also served as prototypes for mechanistic studies elucidating the mode of action of this type of enzyme. Here, we summarize the current knowledge on the structure, regulation and cellular functions of Prp43/DHX15, and discuss the general concept and implications of RNA helicase multifunctionality.
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Affiliation(s)
- Katherine E Bohnsack
- Correspondence may also be addressed to Katherine E. Bohnsack. Tel: +49 551 3969305; Fax: +49 551 395960;
| | - Nidhi Kanwal
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- To whom correspondence should be addressed. Tel: +49 551 395968; Fax: +49 551 395960;
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