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Li C, Li CQ, Chen ZB, Liu BQ, Sun X, Wei KH, Li CY, Luan JB. Wolbachia symbionts control sex in a parasitoid wasp using a horizontally acquired gene. Curr Biol 2024; 34:2359-2372.e9. [PMID: 38692276 DOI: 10.1016/j.cub.2024.04.035] [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: 02/15/2024] [Revised: 03/26/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024]
Abstract
Host reproduction can be manipulated by bacterial symbionts in various ways. Parthenogenesis induction is the most effective type of reproduction manipulation by symbionts for their transmission. Insect sex is determined by regulation of doublesex (dsx) splicing through transformer2 (tra2) and transformer (tra) interaction. Although parthenogenesis induction by symbionts has been studied since the 1970s, its underlying molecular mechanism is unknown. Here we identify a Wolbachia parthenogenesis-induction feminization factor gene (piff) that targets sex-determining genes and causes female-producing parthenogenesis in the haplodiploid parasitoid Encarsia formosa. We found that Wolbachia elimination repressed expression of female-specific dsx and enhanced expression of male-specific dsx, which led to the production of wasp haploid male offspring. Furthermore, we found that E. formosa tra is truncated and non-functional, and Wolbachia has a functional tra homolog, termed piff, with an insect origin. Wolbachia PIFF can colocalize and interact with wasp TRA2. Moreover, Wolbachia piff has coordinated expression with tra2 and dsx of E. formosa. Our results demonstrate the bacterial symbiont Wolbachia has acquired an insect gene to manipulate the host sex determination cascade and induce parthenogenesis in wasps. This study reveals insect-to-bacteria horizontal gene transfer drives the evolution of animal sex determination systems, elucidating a striking mechanism of insect-microbe symbiosis.
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Affiliation(s)
- Ce Li
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Chu-Qiao Li
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhan-Bo Chen
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Bing-Qi Liu
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiang Sun
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Kai-Heng Wei
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Chen-Yi Li
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Jun-Bo Luan
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
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2
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Garg A, Shang R, Cvetanovic T, Lai EC, Joshua-Tor L. The structural landscape of Microprocessor Mediated pri- let-7 miRNAs processing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593372. [PMID: 38766155 PMCID: PMC11100773 DOI: 10.1101/2024.05.09.593372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
miRNA biogenesis is initiated upon cleavage of a primary miRNA (pri-miRNA) hairpin by Microprocessor (MP), composed of the Drosha RNase III enzyme and its partner DGCR8. Multiple pri-miRNA sequence motifs affect MP recognition, fidelity, and efficiency. Here, we performed cryo-EM and biochemical studies of several let-7 family pri-miRNAs in complex with human MP. We show that MP has structural plasticity to accommodate different pri-miRNAs. These also revealed key structural features of the 5' UG sequence motif, more comprehensively represented as the "fUN" motif. Our analysis explains how the bulged nucleotide in class-II pri-let-7 members alters Drosha cleavage, generating a noncanonical precursor with 1-nt 3' overhang. Finally, the MP-SRSF3-pri-let-7f1 structure reveals how SRSF3 interacts with the CNNC motif and Drosha's PAZ-like domain, to promote proper Drosha loading onto the basal hairpin junction. Overall, our work illuminates the mechanisms for flexible recognition, accurate cleavage, and regulated processing of different pri-miRNAs by MP.
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Affiliation(s)
- Ankur Garg
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road,Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
| | - Renfu Shang
- Developmental Biology Program, Sloan Kettering Institute, 430 East 67th St, ROC-10, New York, NY 10065, USA
| | - Todor Cvetanovic
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road,Cold Spring Harbor, New York, 11724 USA
| | - Eric C. Lai
- Developmental Biology Program, Sloan Kettering Institute, 430 East 67th St, ROC-10, New York, NY 10065, USA
| | - Leemor Joshua-Tor
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road,Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
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3
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Martínez-Lumbreras S, Träger LK, Mulorz MM, Payr M, Dikaya V, Hipp C, König J, Sattler M. Intramolecular autoinhibition regulates the selectivity of PRPF40A tandem WW domains for proline-rich motifs. Nat Commun 2024; 15:3888. [PMID: 38719828 PMCID: PMC11079029 DOI: 10.1038/s41467-024-48004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
PRPF40A plays an important role in the regulation of pre-mRNA splicing by mediating protein-protein interactions in the early steps of spliceosome assembly. By binding to proteins at the 5´ and 3´ splice sites, PRPF40A promotes spliceosome assembly by bridging the recognition of the splices. The PRPF40A WW domains are expected to recognize proline-rich sequences in SF1 and SF3A1 in the early spliceosome complexes E and A, respectively. Here, we combine NMR, SAXS and ITC to determine the structure of the PRPF40A tandem WW domains in solution and characterize the binding specificity and mechanism for proline-rich motifs recognition. Our structure of the PRPF40A WW tandem in complex with a high-affinity SF1 peptide reveals contributions of both WW domains, which also enables tryptophan sandwiching by two proline residues in the ligand. Unexpectedly, a proline-rich motif in the N-terminal region of PRPF40A mediates intramolecular interactions with the WW tandem. Using NMR, ITC, mutational analysis in vitro, and immunoprecipitation experiments in cells, we show that the intramolecular interaction acts as an autoinhibitory filter for proof-reading of high-affinity proline-rich motifs in bona fide PRPF40A binding partners. We propose that similar autoinhibitory mechanisms are present in most WW tandem-containing proteins to enhance binding selectivity and regulation of WW/proline-rich peptide interaction networks.
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Affiliation(s)
- Santiago Martínez-Lumbreras
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany.
| | - Lena K Träger
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Miriam M Mulorz
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128, Mainz, Germany
| | - Marco Payr
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Varvara Dikaya
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Clara Hipp
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Julian König
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128, Mainz, Germany
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany.
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4
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Bouton L, Ecoutin A, Malard F, Campagne S. Small molecules modulating RNA splicing: a review of targets and future perspectives. RSC Med Chem 2024; 15:1109-1126. [PMID: 38665842 PMCID: PMC11042171 DOI: 10.1039/d3md00685a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/03/2024] [Indexed: 04/28/2024] Open
Abstract
In eukaryotic cells, RNA splicing is crucial for gene expression. Dysregulation of this process can result in incorrect mRNA processing, leading to aberrant gene expression patterns. Such abnormalities are implicated in many inherited diseases and cancers. Historically, antisense oligonucleotides, which bind to specific RNA targets, have been used to correct these splicing abnormalities. Despite their high specificity of action, these oligonucleotides have drawbacks, such as lack of oral bioavailability and the need for chemical modifications to enhance cellular uptake and stability. As a result, recent efforts focused on the development of small organic molecules that can correct abnormal RNA splicing event under disease conditions. This review discusses known and potential targets of these molecules, including RNA structures, trans-acting splicing factors, and the spliceosome - the macromolecular complex responsible for RNA splicing. We also rely on recent advances to discuss therapeutic applications of RNA-targeting small molecules in splicing correction. Overall, this review presents an update on strategies for RNA splicing modulation, emphasizing the therapeutic promise of small molecules.
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Affiliation(s)
- Léa Bouton
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Agathe Ecoutin
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
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5
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Fukumura K, Sperotto L, Seuß S, Kang HS, Yoshimoto R, Sattler M, Mayeda A. SAP30BP interacts with RBM17/SPF45 to promote splicing in a subset of human short introns. Cell Rep 2023; 42:113534. [PMID: 38065098 DOI: 10.1016/j.celrep.2023.113534] [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: 03/13/2023] [Revised: 11/03/2023] [Accepted: 11/16/2023] [Indexed: 12/30/2023] Open
Abstract
Human pre-mRNA splicing requires the removal of introns with highly variable lengths, from tens to over a million nucleotides. Therefore, mechanisms of intron recognition and splicing are likely not universal. Recently, we reported that splicing in a subset of human short introns with truncated polypyrimidine tracts depends on RBM17 (SPF45), instead of the canonical splicing factor U2 auxiliary factor (U2AF) heterodimer. Here, we demonstrate that SAP30BP, a factor previously implicated in transcriptional control, is an essential splicing cofactor for RBM17. In vitro binding and nuclear magnetic resonance analyses demonstrate that a U2AF-homology motif (UHM) in RBM17 binds directly to a newly identified UHM-ligand motif in SAP30BP. We show that this RBM17-SAP30BP interaction is required to specifically recruit RBM17 to phosphorylated SF3B1 (SF3b155), a U2 small nuclear ribonucleoprotein (U2 snRNP) component in active spliceosomes. We propose a mechanism for splicing in a subset of short introns, in which SAP30BP guides RBM17 in the assembly of active spliceosomes.
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Affiliation(s)
- Kazuhiro Fukumura
- Division of Gene Expression Mechanism, Center for Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan.
| | - Luca Sperotto
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Bavarian NMR Center, TUM School of Natural Sciences, 85748 Garching, Germany
| | - Stefanie Seuß
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Bavarian NMR Center, TUM School of Natural Sciences, 85748 Garching, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Bavarian NMR Center, TUM School of Natural Sciences, 85748 Garching, Germany
| | - Rei Yoshimoto
- Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, Hirakata, Osaka 673-0101, Japan
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Bavarian NMR Center, TUM School of Natural Sciences, 85748 Garching, Germany
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Center for Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan.
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6
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Feng Q, Krick K, Chu J, Burge CB. Splicing quality control mediated by DHX15 and its G-patch activator SUGP1. Cell Rep 2023; 42:113223. [PMID: 37805921 PMCID: PMC10842378 DOI: 10.1016/j.celrep.2023.113223] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 07/27/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023] Open
Abstract
Pre-mRNA splicing is surveilled at different stages by quality control (QC) mechanisms. The leukemia-associated DExH-box family helicase hDHX15/scPrp43 is known to disassemble spliceosomes after splicing. Here, using rapid protein depletion and analysis of nascent and mature RNA to enrich for direct effects, we identify a widespread splicing QC function for DHX15 in human cells, consistent with recent in vitro studies. We find that suboptimal introns with weak splice sites, multiple branch points, and cryptic introns are repressed by DHX15, suggesting a general role in promoting splicing fidelity. We identify SUGP1 as a G-patch factor that activates DHX15's splicing QC function. This interaction is dependent on both DHX15's ATPase activity and on SUGP1's U2AF ligand motif (ULM) domain. Together, our results support a model in which DHX15 plays a major role in splicing QC when recruited and activated by SUGP1.
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Affiliation(s)
- Qing Feng
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA.
| | - Keegan Krick
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA
| | - Jennifer Chu
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA.
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7
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Feng Y, Zhu S, Liu T, Zhi G, Shao B, Liu J, Li B, Jiang C, Feng Q, Wu P, Wang D. Surmounting Cancer Drug Resistance: New Perspective on RNA-Binding Proteins. Pharmaceuticals (Basel) 2023; 16:1114. [PMID: 37631029 PMCID: PMC10458901 DOI: 10.3390/ph16081114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
RNA-binding proteins (RBPs), being pivotal elements in both physiological and pathological processes, possess the ability to directly impact RNA, thereby exerting a profound influence on cellular life. Furthermore, the dysregulation of RBPs not only induces alterations in the expression levels of genes associated with cancer but also impairs the occurrence of post-transcriptional regulatory mechanisms. Consequently, these circumstances can give rise to aberrations in cellular processes, ultimately resulting in alterations within the proteome. An aberrant proteome can disrupt the equilibrium between oncogenes and tumor suppressor genes, promoting cancer progression. Given their significant role in modulating gene expression and post-transcriptional regulation, directing therapeutic interventions towards RBPs represents a viable strategy for combating drug resistance in cancer treatment. RBPs possess significant potential as diagnostic and prognostic markers for diverse cancer types. Gaining comprehensive insights into the structure and functionality of RBPs, along with delving deeper into the molecular mechanisms underlying RBPs in tumor drug resistance, can enhance cancer treatment strategies and augment the prognostic outcomes for individuals afflicted with cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Peijie Wu
- School of Basic Medical Sciences and State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.F.); (S.Z.); (T.L.); (G.Z.); (B.S.); (J.L.); (B.L.); (C.J.); (Q.F.)
| | - Dong Wang
- School of Basic Medical Sciences and State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.F.); (S.Z.); (T.L.); (G.Z.); (B.S.); (J.L.); (B.L.); (C.J.); (Q.F.)
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8
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Ebersberger S, Hipp C, Mulorz MM, Buchbender A, Hubrich D, Kang HS, Martínez-Lumbreras S, Kristofori P, Sutandy FXR, Llacsahuanga Allcca L, Schönfeld J, Bakisoglu C, Busch A, Hänel H, Tretow K, Welzel M, Di Liddo A, Möckel MM, Zarnack K, Ebersberger I, Legewie S, Luck K, Sattler M, König J. FUBP1 is a general splicing factor facilitating 3' splice site recognition and splicing of long introns. Mol Cell 2023:S1097-2765(23)00516-6. [PMID: 37506698 DOI: 10.1016/j.molcel.2023.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/19/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023]
Abstract
Splicing of pre-mRNAs critically contributes to gene regulation and proteome expansion in eukaryotes, but our understanding of the recognition and pairing of splice sites during spliceosome assembly lacks detail. Here, we identify the multidomain RNA-binding protein FUBP1 as a key splicing factor that binds to a hitherto unknown cis-regulatory motif. By collecting NMR, structural, and in vivo interaction data, we demonstrate that FUBP1 stabilizes U2AF2 and SF1, key components at the 3' splice site, through multivalent binding interfaces located within its disordered regions. Transcriptional profiling and kinetic modeling reveal that FUBP1 is required for efficient splicing of long introns, which is impaired in cancer patients harboring FUBP1 mutations. Notably, FUBP1 interacts with numerous U1 snRNP-associated proteins, suggesting a unique role for FUBP1 in splice site bridging for long introns. We propose a compelling model for 3' splice site recognition of long introns, which represent 80% of all human introns.
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Affiliation(s)
| | - Clara Hipp
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Miriam M Mulorz
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | | | - Dalmira Hubrich
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Santiago Martínez-Lumbreras
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Panajot Kristofori
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, 70569 Stuttgart, Germany
| | | | | | - Jonas Schönfeld
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Cem Bakisoglu
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Heike Hänel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Kerstin Tretow
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Mareen Welzel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | | | - Martin M Möckel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; CardioPulmonary Institute (CPI), 35392 Gießen, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; Senckenberg Biodiversity and Climate Research Center (S-BIK-F), 60325 Frankfurt am Main, Germany; LOEWE Center for Translational Biodiversity Genomics (TBG), 60325 Frankfurt am Main, Germany
| | - Stefan Legewie
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, 70569 Stuttgart, Germany; Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, 70569 Stuttgart, Germany
| | - Katja Luck
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany.
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany.
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9
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Carico C, Placzek WJ. Reviewing PTBP1 Domain Modularity in the Pre-Genomic Era: A Foundation to Guide the Next Generation of Exploring PTBP1 Structure-Function Relationships. Int J Mol Sci 2023; 24:11218. [PMID: 37446395 DOI: 10.3390/ijms241311218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023] Open
Abstract
Polypyrimidine tract binding protein 1 (PTBP1) is one of the most well-described RNA binding proteins, known initially for its role as a splicing repressor before later studies revealed its numerous roles in RNA maturation, stability, and translation. While PTBP1's various biological roles have been well-described, it remains unclear how its four RNA recognition motif (RRM) domains coordinate these functions. The early PTBP1 literature saw extensive effort placed in detailing structures of each of PTBP1's RRMs, as well as their individual RNA sequence and structure preferences. However, limitations in high-throughput and high-resolution genomic approaches (i.e., next-generation sequencing had not yet been developed) precluded the functional translation of these findings into a mechanistic understanding of each RRM's contribution to overall PTBP1 function. With the emergence of new technologies, it is now feasible to begin elucidating the individual contributions of each RRM to PTBP1 biological functions. Here, we review all the known literature describing the apo and RNA bound structures of each of PTBP1's RRMs, as well as the emerging literature describing the dependence of specific RNA processing events on individual RRM domains. Our goal is to provide a framework of the structure-function context upon which to facilitate the interpretation of future studies interrogating the dynamics of PTBP1 function.
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Affiliation(s)
- Christine Carico
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - William J Placzek
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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10
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Panzeri V, Pieraccioli M, Cesari E, de la Grange P, Sette C. CDK12/13 promote splicing of proximal introns by enhancing the interaction between RNA polymerase II and the splicing factor SF3B1. Nucleic Acids Res 2023; 51:5512-5526. [PMID: 37026485 PMCID: PMC10287901 DOI: 10.1093/nar/gkad258] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/17/2023] [Accepted: 03/28/2023] [Indexed: 04/08/2023] Open
Abstract
Transcription-associated cyclin-dependent kinases (CDKs) regulate the transcription cycle through sequential phosphorylation of RNA polymerase II (RNAPII). Herein, we report that dual inhibition of the highly homologous CDK12 and CDK13 impairs splicing of a subset of promoter-proximal introns characterized by weak 3' splice sites located at larger distance from the branchpoint. Nascent transcript analysis indicated that these introns are selectively retained upon pharmacological inhibition of CDK12/13 with respect to downstream introns of the same pre-mRNAs. Retention of these introns was also triggered by pladienolide B (PdB), an inhibitor of the U2 small nucelar ribonucleoprotein (snRNP) factor SF3B1 that recognizes the branchpoint. CDK12/13 activity promotes the interaction of SF3B1 with RNAPII phosphorylated on Ser2, and disruption of this interaction by treatment with the CDK12/13 inhibitor THZ531 impairs the association of SF3B1 with chromatin and its recruitment to the 3' splice site of these introns. Furthermore, by using suboptimal doses of THZ531 and PdB, we describe a synergic effect of these inhibitors on intron retention, cell cycle progression and cancer cell survival. These findings uncover a mechanism by which CDK12/13 couple RNA transcription and processing, and suggest that combined inhibition of these kinases and the spliceosome represents an exploitable anticancer approach.
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Affiliation(s)
- Valentina Panzeri
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
| | - Marco Pieraccioli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
- Gemelli Science and Technology Park (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Eleonora Cesari
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
- Gemelli Science and Technology Park (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | | | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
- Gemelli Science and Technology Park (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
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11
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Yuan X, Howie KL, Kazemi Sabzvar M, Chinnaswamy K, Stuckey JA, Yang CY. Profiling the Binding Activities of Peptides and Inhibitors to the U2 Auxiliary Factor Homology Motif (UHM) Domains. ACS Med Chem Lett 2023; 14:450-457. [PMID: 37077390 PMCID: PMC10107908 DOI: 10.1021/acsmedchemlett.2c00537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/17/2023] [Indexed: 04/21/2023] Open
Abstract
RNA splicing is a biological process to generate mature mRNA (mRNA) by removing introns and annexing exons in the nascent RNA transcript and is executed by a multiprotein complex called spliceosome. To aid RNA splicing, a class of splicing factors use an atypical RNA recognition domain (UHM) to bind with U2AF ligand motifs (ULMs) in proteins to form modules that recognize splice sites and splicing regulatory elements on mRNA. Mutations of UHM containing splicing factors have been found frequently in myeloid neoplasms. To profile the selectivity of UHMs for inhibitor development, we established binding assays to measure the binding activities between UHM domains and ULM peptides and a set of small-molecule inhibitors. Additionally, we computationally analyzed the targeting potential of the UHM domains by small-molecule inhibitors. Our study provided the binding assessment of UHM domains to diverse ligands that may guide development of selective UHM domain inhibitors in the future.
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Affiliation(s)
- Xinrui Yuan
- Departments
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Kathryn L. Howie
- Departments
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Mona Kazemi Sabzvar
- Departments
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | | | - Jeanne A. Stuckey
- Life
Science Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chao-Yie Yang
- Departments
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
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12
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Hasenahuer MA, Sanchis-Juan A, Laskowski RA, Baker JA, Stephenson JD, Orengo CA, Raymond FL, Thornton JM. Mapping the Constrained Coding Regions in the Human Genome to Their Corresponding Proteins. J Mol Biol 2023; 435:167892. [PMID: 36410474 PMCID: PMC9875310 DOI: 10.1016/j.jmb.2022.167892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022]
Abstract
Constrained Coding Regions (CCRs) in the human genome have been derived from DNA sequencing data of large cohorts of healthy control populations, available in the Genome Aggregation Database (gnomAD) [1]. They identify regions depleted of protein-changing variants and thus identify segments of the genome that have been constrained during human evolution. By mapping these DNA-defined regions from genomic coordinates onto the corresponding protein positions and combining this information with protein annotations, we have explored the distribution of CCRs and compared their co-occurrence with different protein functional features, previously annotated at the amino acid level in public databases. As expected, our results reveal that functional amino acids involved in interactions with DNA/RNA, protein-protein contacts and catalytic sites are the protein features most likely to be highly constrained for variation in the control population. More surprisingly, we also found that linear motifs, linear interacting peptides (LIPs), disorder-order transitions upon binding with other protein partners and liquid-liquid phase separating (LLPS) regions are also strongly associated with high constraint for variability. We also compared intra-species constraints in the human CCRs with inter-species conservation and functional residues to explore how such CCRs may contribute to the analysis of protein variants. As has been previously observed, CCRs are only weakly correlated with conservation, suggesting that intraspecies constraints complement interspecies conservation and can provide more information to interpret variant effects.
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Affiliation(s)
- Marcia A. Hasenahuer
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK,Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK,Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK,Corresponding author at: European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK. @MarHasenahuer
| | - Alba Sanchis-Juan
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge CB2 0XY, UK,NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Roman A. Laskowski
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - James A. Baker
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - James D. Stephenson
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Christine A. Orengo
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - F. Lucy Raymond
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK,NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Janet M. Thornton
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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13
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Keil P, Wulf A, Kachariya N, Reuscher S, Hühn K, Silbern I, Altmüller J, Keller M, Stehle R, Zarnack K, Sattler M, Urlaub H, Sträßer K. Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA. Nucleic Acids Res 2022; 51:831-851. [PMID: 36583366 PMCID: PMC9881175 DOI: 10.1093/nar/gkac1206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/25/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022] Open
Abstract
RNA-binding proteins (RBPs) control every RNA metabolic process by multiple protein-RNA and protein-protein interactions. Their roles have largely been analyzed by crude mutations, which abrogate multiple functions at once and likely impact the structural integrity of the large ribonucleoprotein particles (RNPs) these proteins function in. Using UV-induced RNA-protein crosslinking of entire cells, protein complex purification and mass spectrometric analysis, we identified >100 in vivo RNA crosslinks in 16 nuclear mRNP components in Saccharomyces cerevisiae. For functional analysis, we chose Npl3, which displayed crosslinks in its two RNA recognition motifs (RRMs) and in the connecting flexible linker region. Both RRM domains and the linker uniquely contribute to RNA recognition as revealed by NMR and structural analyses. Interestingly, mutations in these regions cause different phenotypes, indicating distinct functions of the different RNA-binding domains. Notably, an npl3-Linker mutation strongly impairs recruitment of several mRNP components to chromatin and incorporation of other mRNP components into nuclear mRNPs, establishing a so far unknown function of Npl3 in nuclear mRNP assembly. Taken together, our integrative analysis uncovers a specific function of the RNA-binding activity of the nuclear mRNP component Npl3. This approach can be readily applied to RBPs in any RNA metabolic process.
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Affiliation(s)
| | | | | | - Samira Reuscher
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt a.M., Germany
| | - Kristin Hühn
- Institute of Biochemistry, FB08, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Ivan Silbern
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Goettingen, University Medical Center Goettingen, Institute of Clinical Chemistry, Robert-Koch-Strasse 40, 37075 Goettingen, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, 50931 Cologne, Germany,Technology platform genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Mario Keller
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt a.M., Germany
| | - Ralf Stehle
- Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany,Institute of Structural Biology, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt a.M., Germany,Cardio-Pulmonary Institute (CPI), EXC 2026, 35392 Giessen, Germany
| | | | | | - Katja Sträßer
- To whom correspondence should be addressed. Tel: +49 641 99 35400; Fax: +49 641 99 35409;
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14
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Galardi JW, Bela VN, Jeffery N, He X, Glasser E, Loerch S, Jenkins JL, Pulvino MJ, Boutz PL, Kielkopf CL. A UHM - ULM interface with unusual structural features contributes to U2AF2 and SF3B1 association for pre-mRNA splicing. J Biol Chem 2022; 298:102224. [PMID: 35780835 PMCID: PMC9364107 DOI: 10.1016/j.jbc.2022.102224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 11/30/2022] Open
Abstract
During spliceosome assembly, the 3′ splice site is recognized by sequential U2AF2 complexes, first with Splicing Factor 1 (SF1) and second by the SF3B1 subunit of the U2 small nuclear ribonuclear protein particle. The U2AF2–SF1 interface is well characterized, comprising a U2AF homology motif (UHM) of U2AF2 bound to a U2AF ligand motif (ULM) of SF1. However, the structure of the U2AF2–SF3B1 interface and its importance for pre-mRNA splicing are unknown. To address this knowledge gap, we determined the crystal structure of the U2AF2 UHM bound to a SF3B1 ULM site at 1.8-Å resolution. We discovered a distinctive trajectory of the SF3B1 ULM across the U2AF2 UHM surface, which differs from prior UHM/ULM structures and is expected to modulate the orientations of the full-length proteins. We established that the binding affinity of the U2AF2 UHM for the cocrystallized SF3B1 ULM rivals that of a nearly full-length U2AF2 protein for an N-terminal SF3B1 region. An additional SF3B6 subunit had no detectable effect on the U2AF2–SF3B1 binding affinities. We further showed that key residues at the U2AF2 UHM–SF3B1 ULM interface contribute to coimmunoprecipitation of the splicing factors. Moreover, disrupting the U2AF2–SF3B1 interface changed splicing of representative human transcripts. From analysis of genome-wide data, we found that many of the splice sites coregulated by U2AF2 and SF3B1 differ from those coregulated by U2AF2 and SF1. Taken together, these findings support distinct structural and functional roles for the U2AF2—SF1 and U2AF2—SF3B1 complexes during the pre-mRNA splicing process.
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Affiliation(s)
- Justin W Galardi
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Victoria N Bela
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Nazish Jeffery
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Xueyang He
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Eliezra Glasser
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Sarah Loerch
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Jermaine L Jenkins
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Mary J Pulvino
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Paul L Boutz
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Clara L Kielkopf
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.
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15
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Sette C, Paronetto MP. Somatic Mutations in Core Spliceosome Components Promote Tumorigenesis and Generate an Exploitable Vulnerability in Human Cancer. Cancers (Basel) 2022; 14:cancers14071827. [PMID: 35406598 PMCID: PMC8997811 DOI: 10.3390/cancers14071827] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary High throughput exome sequencing approaches have disclosed recurrent cancer-associated mutations in spliceosomal components, which drive aberrant pre-mRNA processing events and support the tumor phenotype. At the same time, mutations in spliceosome genes and aberrant splicing regulation establish a selective vulnerability of cancer cells to splicing-targeting approaches, which could be exploited therapeutically. It is conceivable that a better understanding of the mechanisms and roles of abnormal splicing in tumor metabolism will facilitate the development of a novel generation of tumor-targeting drugs. In this review, we describe recent advances in the elucidation of the biological impact and biochemical effects of somatic mutations in core spliceosome components on splicing choices and their associated targetable vulnerabilities. Abstract Alternative pre-mRNA processing enables the production of distinct mRNA and protein isoforms from a single gene, thus greatly expanding the coding potential of eukaryotic genomes and fine-tuning gene expression programs. Splicing is carried out by the spliceosome, a complex molecular machinery which assembles step-wise on mRNA precursors in the nucleus of eukaryotic cells. In the last decade, exome sequencing technologies have allowed the identification of point mutations in genes encoding splicing factors as a recurrent hallmark of human cancers, with higher incidence in hematological malignancies. These mutations lead to production of splicing factors that reduce the fidelity of the splicing process and yield splicing variants that are often advantageous for cancer cells. However, at the same time, these mutations increase the sensitivity of transformed cells to splicing inhibitors, thus offering a therapeutic opportunity for novel targeted strategies. Herein, we review the recent literature documenting cancer-associated mutations in components of the early spliceosome complex and discuss novel therapeutic strategies based on small-molecule spliceosome inhibitors that exhibit strong anti-tumor effects, particularly against cancer cells harboring mutations in spliceosomal components.
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Affiliation(s)
- Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy;
- GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Piazza Lauro De Bosis, 6, 00135 Rome, Italy
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, IRCCS, Via del Fosso di Fiorano 64, 00143 Rome, Italy
- Correspondence:
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16
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Biancon G, Joshi P, Zimmer JT, Hunck T, Gao Y, Lessard MD, Courchaine E, Barentine AES, Machyna M, Botti V, Qin A, Gbyli R, Patel A, Song Y, Kiefer L, Viero G, Neuenkirchen N, Lin H, Bewersdorf J, Simon MD, Neugebauer KM, Tebaldi T, Halene S. Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. Mol Cell 2022; 82:1107-1122.e7. [PMID: 35303483 PMCID: PMC8988922 DOI: 10.1016/j.molcel.2022.02.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/21/2021] [Accepted: 02/15/2022] [Indexed: 12/13/2022]
Abstract
Splicing factor mutations are common among cancers, recently emerging as drivers of myeloid malignancies. U2AF1 carries hotspot mutations in its RNA-binding motifs; however, how they affect splicing and promote cancer remain unclear. The U2AF1/U2AF2 heterodimer is critical for 3' splice site (3'SS) definition. To specifically unmask changes in U2AF1 function in vivo, we developed a crosslinking and immunoprecipitation procedure that detects contacts between U2AF1 and the 3'SS AG at single-nucleotide resolution. Our data reveal that the U2AF1 S34F and Q157R mutants establish new 3'SS contacts at -3 and +1 nucleotides, respectively. These effects compromise U2AF2-RNA interactions, resulting predominantly in intron retention and exon exclusion. Integrating RNA binding, splicing, and turnover data, we predicted that U2AF1 mutations directly affect stress granule components, which was corroborated by single-cell RNA-seq. Remarkably, U2AF1-mutant cell lines and patient-derived MDS/AML blasts displayed a heightened stress granule response, pointing to a novel role for biomolecular condensates in adaptive oncogenic strategies.
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Affiliation(s)
- Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA.
| | - Poorval Joshi
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Joshua T Zimmer
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Torben Hunck
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Yimeng Gao
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Mark D Lessard
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Edward Courchaine
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew E S Barentine
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Martin Machyna
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Valentina Botti
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Ashley Qin
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Rana Gbyli
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Amisha Patel
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Yuanbin Song
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Department of Hematologic Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Lea Kiefer
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Nils Neuenkirchen
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Haifan Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Toma Tebaldi
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
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17
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Martín E, Vivori C, Rogalska M, Herrero-Vicente J, Valcárcel J. Alternative splicing regulation of cell-cycle genes by SPF45/SR140/CHERP complex controls cell proliferation. RNA (NEW YORK, N.Y.) 2021; 27:1557-1576. [PMID: 34544891 PMCID: PMC8594467 DOI: 10.1261/rna.078935.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/11/2021] [Indexed: 06/10/2023]
Abstract
The regulation of pre-mRNA processing has important consequences for cell division and the control of cancer cell proliferation, but the underlying molecular mechanisms remain poorly understood. We report that three splicing factors, SPF45, SR140, and CHERP, form a tight physical and functionally coherent complex that regulates a variety of alternative splicing events, frequently by repressing short exons flanked by suboptimal 3' splice sites. These comprise alternative exons embedded in genes with important functions in cell-cycle progression, including the G2/M key regulator FOXM1 and the spindle regulator SPDL1. Knockdown of either of the three factors leads to G2/M arrest and to enhanced apoptosis in HeLa cells. Promoting the changes in FOXM1 or SPDL1 splicing induced by SPF45/SR140/CHERP knockdown partially recapitulates the effects on cell growth, arguing that the complex orchestrates a program of alternative splicing necessary for efficient cell proliferation.
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Affiliation(s)
- Elena Martín
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Claudia Vivori
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Malgorzata Rogalska
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Jorge Herrero-Vicente
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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18
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Borao S, Ayté J, Hümmer S. Evolution of the Early Spliceosomal Complex-From Constitutive to Regulated Splicing. Int J Mol Sci 2021; 22:ijms222212444. [PMID: 34830325 PMCID: PMC8624252 DOI: 10.3390/ijms222212444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/14/2022] Open
Abstract
Pre-mRNA splicing is a major process in the regulated expression of genes in eukaryotes, and alternative splicing is used to generate different proteins from the same coding gene. Splicing is a catalytic process that removes introns and ligates exons to create the RNA sequence that codifies the final protein. While this is achieved in an autocatalytic process in ancestral group II introns in prokaryotes, the spliceosome has evolved during eukaryogenesis to assist in this process and to finally provide the opportunity for intron-specific splicing. In the early stage of splicing, the RNA 5' and 3' splice sites must be brought within proximity to correctly assemble the active spliceosome and perform the excision and ligation reactions. The assembly of this first complex, termed E-complex, is currently the least understood process. We focused in this review on the formation of the E-complex and compared its composition and function in three different organisms. We highlight the common ancestral mechanisms in S. cerevisiae, S. pombe, and mammals and conclude with a unifying model for intron definition in constitutive and regulated co-transcriptional splicing.
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Affiliation(s)
- Sonia Borao
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
- Correspondence: (J.A.); (S.H.)
| | - Stefan Hümmer
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
- Translational Molecular Pathology, Vall d’Hebron Research Institute (VHIR), CIBERONC, 08035 Barcelona, Spain
- Correspondence: (J.A.); (S.H.)
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19
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Zhang X, Bustos MA, Gross R, Ramos RI, Takeshima T, Mills GB, Yu Q, Hoon DSB. Interleukin enhancer-binding factor 2 promotes cell proliferation and DNA damage response in metastatic melanoma. Clin Transl Med 2021; 11:e608. [PMID: 34709752 PMCID: PMC8516365 DOI: 10.1002/ctm2.608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND 1q21.3 amplification, which is frequently observed in metastatic melanoma, is associated with cancer progression. Interleukin enhancer-binding factor 2 (ILF2) is located in the 1q21.3 amplified region, but its functional role or contribution to tumour aggressiveness in cutaneous melanoma is unknown. METHODS In silico analyses were performed using the TCGA SKCM dataset with clinical annotations and three melanoma microarray cohorts from the GEO datasets. RNA in situ hybridisation and immunohistochemistry were utilised to validate the gene expression in melanoma tissues. Four stable melanoma cell lines were established for in vitro ILF2 functional characterisation. RESULTS Our results showed that the ILF2 copy number variation (CNV) is positively correlated with ILF2 mRNA expression (r = 0.68, p < .0001). Additionally, ILF2 expression is significantly increased with melanoma progression (p < .0001), and significantly associated with poor overall survival for metastatic melanoma patients (p = .026). The overexpression of ILF2 (ILF2-OV) promotes proliferation in metastatic melanoma cells, whereas ILF2 knockdown decreases proliferation by blocking the cell cycle. Mechanistically, we demonstrated the interaction between ILF2 and the splicing factor U2AF2, whose knockdown reverses the proliferation effects mediated by ILF2-OV. Stage IIIB-C melanoma patients with high ILF2-U2AF2 expression showed significantly shorter overall survival (p = .024). Enhanced ILF2/U2AF2 expression promotes a more efficient DNA-damage repair by increasing RAD50 and ATM mRNA expression. Paradoxically, metastatic melanoma cells with ILF2-OV were more sensitive to ATM inhibitors. CONCLUSION Our study uncovered that ILF2 amplification of the 1q21.3 chromosome is associated with melanoma progression and triggers a functional downstream pathway in metastatic melanoma promoting drug resistance.
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Affiliation(s)
- Xiaoqing Zhang
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Matias A. Bustos
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Rebecca Gross
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Romela Irene Ramos
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Teh‐Ling Takeshima
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Gordon B. Mills
- Department of Cell Development and Cancer BiologyKnight Cancer InstituteOregon Health and Science UniversityPortlandOregon
| | - Qiang Yu
- Agency for Science Technology and Research (A*STAR)Genome Institute of SingaporeBiopolisSingapore
| | - Dave S. B. Hoon
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
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20
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Kobayashi A, Clément MJ, Craveur P, El Hage K, Salone JDM, Bollot G, Pastré D, Maucuer A. Identification of a small molecule splicing inhibitor targeting UHM domains. FEBS J 2021; 289:682-698. [PMID: 34520118 DOI: 10.1111/febs.16199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/10/2021] [Accepted: 09/13/2021] [Indexed: 01/07/2023]
Abstract
Splicing factor mutations are frequent in myeloid neoplasms, blood cancers, and solid tumors. Cancer cells harboring these mutations present a particular vulnerability to drugs that target splicing factors such as SF3b155 or CAPERα. Still, the arsenal of chemical probes that target the spliceosome is very limited. U2AF homology motifs (UHMs) are common protein interaction domains among splicing factors. They present a hydrophobic pocket ideally suited to anchor small molecules with the aim to inhibit protein-protein interaction. Here, we combined a virtual screening of a small molecules database and an in vitro competition assay and identified a small molecule, we named UHMCP1 that prevents the SF3b155/U2AF65 interaction. NMR analyses and molecular dynamics simulations confirmed the binding of this molecule in the hydrophobic pocket of the U2AF65 UHM domain. We further provide evidence that UHMCP1 impacts RNA splicing and cell viability and is therefore an interesting novel compound targeting an UHM domain with potential anticancer properties.
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Affiliation(s)
- Asaki Kobayashi
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France.,SYNSIGHT, Genopole Entreprises, Evry, France
| | | | | | - Krystel El Hage
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | | | | | - David Pastré
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Alexandre Maucuer
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
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21
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A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex. Cell Chem Biol 2021; 28:1145-1157.e6. [PMID: 33689684 PMCID: PMC8380659 DOI: 10.1016/j.chembiol.2021.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/25/2021] [Accepted: 02/11/2021] [Indexed: 12/20/2022]
Abstract
Dysregulated pre-mRNA splicing is an emerging Achilles heel of cancers and myelodysplasias. To expand the currently limited portfolio of small-molecule drug leads, we screened for chemical modulators of the U2AF complex, which nucleates spliceosome assembly and is mutated in myelodysplasias. A hit compound specifically enhances RNA binding by a U2AF2 subunit. Remarkably, the compound inhibits splicing of representative substrates and stalls spliceosome assembly at the stage of U2AF function. Computational docking, together with structure-guided mutagenesis, indicates that the compound bridges the tandem U2AF2 RNA recognition motifs via hydrophobic and electrostatic moieties. Cells expressing a cancer-associated U2AF1 mutant are preferentially killed by treatment with the compound. Altogether, our results highlight the potential of trapping early spliceosome assembly as an effective pharmacological means to manipulate pre-mRNA splicing. By extension, we suggest that stabilizing assembly intermediates may offer a useful approach for small-molecule inhibition of macromolecular machines.
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22
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Fukumura K, Yoshimoto R, Sperotto L, Kang HS, Hirose T, Inoue K, Sattler M, Mayeda A. SPF45/RBM17-dependent, but not U2AF-dependent, splicing in a distinct subset of human short introns. Nat Commun 2021; 12:4910. [PMID: 34389706 PMCID: PMC8363638 DOI: 10.1038/s41467-021-24879-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 07/06/2021] [Indexed: 11/11/2022] Open
Abstract
Human pre-mRNA introns vary in size from under fifty to over a million nucleotides. We searched for essential factors involved in the splicing of human short introns by screening siRNAs against 154 human nuclear proteins. The splicing activity was assayed with a model HNRNPH1 pre-mRNA containing short 56-nucleotide intron. We identify a known alternative splicing regulator SPF45 (RBM17) as a constitutive splicing factor that is required to splice out this 56-nt intron. Whole-transcriptome sequencing of SPF45-deficient cells reveals that SPF45 is essential in the efficient splicing of many short introns. To initiate the spliceosome assembly on a short intron with the truncated poly-pyrimidine tract, the U2AF-homology motif (UHM) of SPF45 competes out that of U2AF65 (U2AF2) for binding to the UHM-ligand motif (ULM) of the U2 snRNP protein SF3b155 (SF3B1). We propose that splicing in a distinct subset of human short introns depends on SPF45 but not U2AF heterodimer. The length distribution of human pre-mRNA introns is very extensive. The authors demonstrate that splicing in a subset of short introns is dependent on SPF45 (RBM17), which replaces authentic U2AF-heterodimer on the truncated poly-pyrimidine tracts and interacts with the U2 snRNP protein SF3b155.
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Affiliation(s)
- Kazuhiro Fukumura
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan.
| | - Rei Yoshimoto
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan.,Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, Hirakata, Osaka, Japan
| | - Luca Sperotto
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Bavarian NMR Center (BNMRZ), Chemistry Department, Technical University of Munich, Garching, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Bavarian NMR Center (BNMRZ), Chemistry Department, Technical University of Munich, Garching, Germany
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Kunio Inoue
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Hyogo, Japan
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Bavarian NMR Center (BNMRZ), Chemistry Department, Technical University of Munich, Garching, Germany
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan.
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23
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Joseph B, Lai EC. The Exon Junction Complex and intron removal prevent re-splicing of mRNA. PLoS Genet 2021; 17:e1009563. [PMID: 34033644 PMCID: PMC8184009 DOI: 10.1371/journal.pgen.1009563] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/07/2021] [Accepted: 04/26/2021] [Indexed: 01/23/2023] Open
Abstract
Accurate splice site selection is critical for fruitful gene expression. Recently, the mammalian EJC was shown to repress competing, cryptic, splice sites (SS). However, the evolutionary generality of this remains unclear. Here, we demonstrate the Drosophila EJC suppresses hundreds of functional cryptic SS, even though most bear weak splicing motifs and are seemingly incompetent. Mechanistically, the EJC directly conceals cryptic splicing elements by virtue of its position-specific recruitment, preventing aberrant SS definition. Unexpectedly, we discover the EJC inhibits scores of regenerated 5' and 3' recursive SS on segments that have already undergone splicing, and that loss of EJC regulation triggers faulty resplicing of mRNA. An important corollary is that certain intronless cDNA constructs yield unanticipated, truncated transcripts generated by resplicing. We conclude the EJC has conserved roles to defend transcriptome fidelity by (1) repressing illegitimate splice sites on pre-mRNAs, and (2) preventing inadvertent activation of such sites on spliced segments.
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Affiliation(s)
- Brian Joseph
- Developmental Biology Program, Sloan Kettering Institute, New York, New York, United States of America
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Eric C. Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, New York, United States of America
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
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24
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Mendel M, Delaney K, Pandey RR, Chen KM, Wenda JM, Vågbø CB, Steiner FA, Homolka D, Pillai RS. Splice site m 6A methylation prevents binding of U2AF35 to inhibit RNA splicing. Cell 2021; 184:3125-3142.e25. [PMID: 33930289 PMCID: PMC8208822 DOI: 10.1016/j.cell.2021.03.062] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 02/16/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
The N6-methyladenosine (m6A) RNA modification is used widely to alter the fate of mRNAs. Here we demonstrate that the C. elegans writer METT-10 (the ortholog of mouse METTL16) deposits an m6A mark on the 3′ splice site (AG) of the S-adenosylmethionine (SAM) synthetase pre-mRNA, which inhibits its proper splicing and protein production. The mechanism is triggered by a rich diet and acts as an m6A-mediated switch to stop SAM production and regulate its homeostasis. Although the mammalian SAM synthetase pre-mRNA is not regulated via this mechanism, we show that splicing inhibition by 3′ splice site m6A is conserved in mammals. The modification functions by physically preventing the essential splicing factor U2AF35 from recognizing the 3′ splice site. We propose that use of splice-site m6A is an ancient mechanism for splicing regulation. m6A deposited at 3′ splice site by worm METT-10 inhibits splicing Methylation blocks 3′ splice site recognition by splicing factor U2AF35 Methylation and splicing inhibition is a response to change in worm diet Splicing inhibition by 3′ splice site m6A is conserved in mammals
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Affiliation(s)
- Mateusz Mendel
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Kamila Delaney
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Radha Raman Pandey
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Kuan-Ming Chen
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Joanna M Wenda
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Cathrine Broberg Vågbø
- Proteomics and Modomics Experimental Core (PROMEC), Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU) and St. Olavs Hospital Central Staff, Trondheim, Norway
| | - Florian A Steiner
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - David Homolka
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland.
| | - Ramesh S Pillai
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland.
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25
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Tong D. The role of JMJD6/U2AF65/AR-V7 axis in castration-resistant prostate cancer progression. Cancer Cell Int 2021; 21:45. [PMID: 33430885 PMCID: PMC7802141 DOI: 10.1186/s12935-020-01739-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/25/2020] [Indexed: 12/19/2022] Open
Abstract
Castration-resistant prostate cancer (CRPC) remains prostate cancer research and treatment bottleneck. Abnormal androgen receptor (AR) activation still has a pivotal role in CRPC. Multiple mechanisms involve the process, of which overabundant AR-V7 mRNA splicing production is currently focused and increasingly studied. However, factually, there is no definite conclusion about regulation of AR-V7 mRNA splicing. Recently developed knowledge has demonstrated that JMJD6 and U2AF65 as a hopeful approach in mRNA splicing regulation. The authors propose a novel possible mechanism elucidating AR mRNA splicing for CRPC progression using dual-function enzyme JMJD6 and its induced JMJD6/U2AF65/AR-V7 axis. In this hypothesis JMJD6 introduces to AR promoter to demethylate H3R or H4R and promotes AR mRNA transcription via its demethylase activity and interaction with U2AF65. It is expected that JMJD6 could further effectively perform U2AF65 hydroxylation to achieve AR-V7 mRNA splicing via its hydroxylase activity.
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Affiliation(s)
- Dali Tong
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, People's Republic of China.
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26
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Identification of phenothiazine derivatives as UHM-binding inhibitors of early spliceosome assembly. Nat Commun 2020; 11:5621. [PMID: 33159082 PMCID: PMC7648758 DOI: 10.1038/s41467-020-19514-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/16/2020] [Indexed: 12/31/2022] Open
Abstract
Interactions between U2AF homology motifs (UHMs) and U2AF ligand motifs (ULMs) play a crucial role in early spliceosome assembly in eukaryotic gene regulation. UHM-ULM interactions mediate heterodimerization of the constitutive splicing factors U2AF65 and U2AF35 and between other splicing factors that regulate spliceosome assembly at the 3′ splice site, where UHM domains of alternative splicing factors, such as SPF45 and PUF60, contribute to alternative splicing regulation. Here, we performed high-throughput screening using fluorescence polarization assays with hit validation by NMR and identified phenothiazines as general inhibitors of UHM-ULM interactions. NMR studies show that these compounds occupy the tryptophan binding pocket of UHM domains. Co-crystal structures of the inhibitors with the PUF60 UHM domain and medicinal chemistry provide structure-activity-relationships and reveal functional groups important for binding. These inhibitors inhibit early spliceosome assembly on pre-mRNA substrates in vitro. Our data show that spliceosome assembly can be inhibited by targeting UHM-ULM interactions by small molecules, thus extending the toolkit of splicing modulators for structural and biochemical studies of the spliceosome and splicing regulation. So far only a few compounds have been reported as splicing modulators. Here, the authors combine high-throughput screening, chemical synthesis, NMR, X-ray crystallography with functional studies and develop phenothiazines as inhibitors for the U2AF Homology Motif (UHM) domains of proteins that regulate splicing and show that they inhibit early spliceosome assembly on pre-mRNA substrates in vitro.
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27
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Yoshida H, Park SY, Sakashita G, Nariai Y, Kuwasako K, Muto Y, Urano T, Obayashi E. Elucidation of the aberrant 3' splice site selection by cancer-associated mutations on the U2AF1. Nat Commun 2020; 11:4744. [PMID: 32958768 PMCID: PMC7505975 DOI: 10.1038/s41467-020-18559-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 08/24/2020] [Indexed: 12/14/2022] Open
Abstract
The accurate exclusion of introns by RNA splicing is critical for the production of mature mRNA. U2AF1 binds specifically to the 3´ splice site, which includes an essential AG dinucleotide. Even a single amino acid mutation of U2AF1 can cause serious disease such as certain cancers or myelodysplastic syndromes. Here, we describe the first crystal structures of wild-type and pathogenic mutant U2AF1 complexed with target RNA, revealing the mechanism of 3´ splice site selection, and how aberrant splicing results from clinically important mutations. Unexpected features of this mechanism may assist the future development of new treatments against diseases caused by splicing errors. U2AF1 binds to the 3’ splice site of introns and its mutation lead to abnormal splicing. Here the authors solve the crystal structures of wild type and pathogenic mutant U2AF1 bound to target RNA, showing that different target sequence is preferred by pathogenic mutant.
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Affiliation(s)
- Hisashi Yoshida
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Sam-Yong Park
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Gyosuke Sakashita
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, 693-8501, Japan
| | - Yuko Nariai
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, 693-8501, Japan
| | - Kanako Kuwasako
- Faculty of Pharmacy and Research institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shin-machi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Yutaka Muto
- Faculty of Pharmacy and Research institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shin-machi, Nishitokyo-shi, Tokyo, 202-8585, Japan.
| | - Takeshi Urano
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, 693-8501, Japan
| | - Eiji Obayashi
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, 693-8501, Japan.
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28
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Warnasooriya C, Feeney CF, Laird KM, Ermolenko DN, Kielkopf CL. A splice site-sensing conformational switch in U2AF2 is modulated by U2AF1 and its recurrent myelodysplasia-associated mutation. Nucleic Acids Res 2020; 48:5695-5709. [PMID: 32343311 PMCID: PMC7261175 DOI: 10.1093/nar/gkaa293] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/09/2020] [Accepted: 04/17/2020] [Indexed: 02/02/2023] Open
Abstract
An essential heterodimer of the U2AF1 and U2AF2 pre-mRNA splicing factors nucleates spliceosome assembly at polypyrimidine (Py) signals preceding the major class of 3′ splice sites. U2AF1 frequently acquires an S34F-encoding mutation among patients with myelodysplastic syndromes (MDS). The influence of the U2AF1 subunit and its S34F mutation on the U2AF2 conformations remains unknown. Here, we employ single molecule Förster resonance energy transfer (FRET) to determine the influence of wild-type or S34F-substituted U2AF1 on the conformational dynamics of U2AF2 and its splice site RNA complexes. In the absence of RNA, the U2AF1 subunit stabilizes a high FRET value, which by structure-guided mutagenesis corresponds to a closed conformation of the tandem U2AF2 RNA recognition motifs (RRMs). When the U2AF heterodimer is bound to a strong, uridine-rich splice site, U2AF2 switches to a lower FRET value characteristic of an open, side-by-side arrangement of the RRMs. Remarkably, the U2AF heterodimer binds weak, uridine-poor Py tracts as a mixture of closed and open U2AF2 conformations, which are modulated by the S34F mutation. Shifts between open and closed U2AF2 may underlie U2AF1-dependent splicing of degenerate Py tracts and contribute to a subset of S34F-dysregulated splicing events in MDS patients.
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Affiliation(s)
- Chandani Warnasooriya
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Callen F Feeney
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Kholiswa M Laird
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Dmitri N Ermolenko
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Clara L Kielkopf
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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29
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An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2. Proc Natl Acad Sci U S A 2020; 117:7140-7149. [PMID: 32188783 DOI: 10.1073/pnas.1913483117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The recognition of cis-regulatory RNA motifs in human transcripts by RNA binding proteins (RBPs) is essential for gene regulation. The molecular features that determine RBP specificity are often poorly understood. Here, we combined NMR structural biology with high-throughput iCLIP approaches to identify a regulatory mechanism for U2AF2 RNA recognition. We found that the intrinsically disordered linker region connecting the two RNA recognition motif (RRM) domains of U2AF2 mediates autoinhibitory intramolecular interactions to reduce nonproductive binding to weak Py-tract RNAs. This proofreading favors binding of U2AF2 at stronger Py-tracts, as required to define 3' splice sites at early stages of spliceosome assembly. Mutations that impair the linker autoinhibition enhance the affinity for weak Py-tracts result in promiscuous binding of U2AF2 along mRNAs and impact on splicing fidelity. Our findings highlight an important role of intrinsically disordered linkers to modulate RNA interactions of multidomain RBPs.
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30
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Herdt O, Reich S, Medenbach J, Timmermann B, Olofsson D, Preußner M, Heyd F. The zinc finger domains in U2AF26 and U2AF35 have diverse functionalities including a role in controlling translation. RNA Biol 2020; 17:843-856. [PMID: 32116123 DOI: 10.1080/15476286.2020.1732701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Recent work has associated point mutations in both zinc fingers (ZnF) of the spliceosome component U2AF35 with malignant transformation. However, surprisingly little is known about the functionality of the U2AF35 ZnF domains in general. Here we have analysed key functionalities of the ZnF domains of mammalian U2AF35 and its paralog U2AF26. Both ZnFs are required for splicing regulation, whereas only ZnF2 controls protein stability and contributes to the interaction with U2AF65. These features are confirmed in a naturally occurring splice variant of U2AF26 lacking ZnF2, that is strongly induced upon activation of primary mouse T cells and localized in the cytoplasm. Using Ribo-Seq in a model T cell line we provide evidence for a role of U2AF26 in activating cytoplasmic steps in gene expression, notably translation. Consistently, an MS2 tethering assay shows that cytoplasmic U2AF26/35 increase translation when localized to the 5'UTR of a model mRNA. This regulation is partially dependent on ZnF1 thus providing a connection between a core splicing factor, the ZnF domains and the regulation of translation. Altogether, our work reveals unexpected functions of U2AF26/35 and their ZnF domains, thereby contributing to a better understanding of their role and regulation in mammalian cells.
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Affiliation(s)
- Olga Herdt
- Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Freie Universität Berlin , Berlin, Germany
| | - Stefan Reich
- Institute of Biochemistry I, University of Regensburg , Regensburg, Germany
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg , Regensburg, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max-Planck-Institute for Molecular Genetics , Berlin, Germany
| | - Didrik Olofsson
- Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Freie Universität Berlin , Berlin, Germany
| | - Marco Preußner
- Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Freie Universität Berlin , Berlin, Germany
| | - Florian Heyd
- Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Freie Universität Berlin , Berlin, Germany
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31
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Esfahani MS, Lee LJ, Jeon YJ, Flynn RA, Stehr H, Hui AB, Ishisoko N, Kildebeck E, Newman AM, Bratman SV, Porteus MH, Chang HY, Alizadeh AA, Diehn M. Functional significance of U2AF1 S34F mutations in lung adenocarcinomas. Nat Commun 2019; 10:5712. [PMID: 31836708 PMCID: PMC6911043 DOI: 10.1038/s41467-019-13392-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 11/07/2019] [Indexed: 12/23/2022] Open
Abstract
The functional role of U2AF1 mutations in lung adenocarcinomas (LUADs) remains incompletely understood. Here, we report a significant co-occurrence of U2AF1 S34F mutations with ROS1 translocations in LUADs. To characterize this interaction, we profiled effects of S34F on the transcriptome-wide distribution of RNA binding and alternative splicing in cells harboring the ROS1 translocation. Compared to its wild-type counterpart, U2AF1 S34F preferentially binds and modulates splicing of introns containing CAG trinucleotides at their 3' splice junctions. The presence of S34F caused a shift in cross-linking at 3' splice sites, which was significantly associated with alternative splicing of skipped exons. U2AF1 S34F induced expression of genes involved in the epithelial-mesenchymal transition (EMT) and increased tumor cell invasion. Finally, S34F increased splicing of the long over the short SLC34A2-ROS1 isoform, which was also associated with enhanced invasiveness. Taken together, our results suggest a mechanistic interaction between mutant U2AF1 and ROS1 in LUAD.
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Affiliation(s)
- Mohammad S Esfahani
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, USA
- Department of Radiation Oncology, Stanford University, Stanford, USA
| | - Luke J Lee
- Stanford Cancer Institute, Stanford University, Stanford, USA
| | - Young-Jun Jeon
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Department of Radiation Oncology, Stanford University, Stanford, USA
| | - Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Angela B Hui
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Department of Radiation Oncology, Stanford University, Stanford, USA
| | - Noriko Ishisoko
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Eric Kildebeck
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, USA
- Department of Biomedical Data Science, Stanford University, Stanford, USA
| | - Scott V Bratman
- Department of Radiation Oncology, Stanford University, Stanford, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, USA
- Department of Radiation Oncology, University of Toronto, Toronto, CA, USA
| | | | - Howard Y Chang
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, USA
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, USA.
- Division of Oncology, Department of Medicine, Stanford University, Stanford, USA.
- Division of Hematology, Department of Medicine, Stanford University, Stanford, USA.
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, USA.
- Department of Radiation Oncology, Stanford University, Stanford, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, USA.
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32
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Chang JW, Yeh HS, Park M, Erber L, Sun J, Cheng S, Bui AM, Fahmi NA, Nasti R, Kuang R, Chen Y, Zhang W, Yong J. mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control. Nucleic Acids Res 2019; 47:10373-10387. [PMID: 31504847 PMCID: PMC6821156 DOI: 10.1093/nar/gkz761] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/23/2019] [Accepted: 08/23/2019] [Indexed: 01/13/2023] Open
Abstract
U2 auxiliary factor 1 (U2AF1) functions in 3′-splice site selection during pre-mRNA processing. Alternative usage of duplicated tandem exons in U2AF1 produces two isoforms, U2AF1a and U2AF1b, but their functional differences are unappreciated due to their homology. Through integrative approaches of genome editing, customized-transcriptome profiling and crosslinking-mediated interactome analyses, we discovered that the expression of U2AF1 isoforms is controlled by mTOR and they exhibit a distinctive molecular profile for the splice site and protein interactomes. Mechanistic dissection of mutually exclusive alternative splicing events revealed that U2AF1 isoforms’ inherent differential preferences of nucleotide sequences and their stoichiometry determine the 3′-splice site. Importantly, U2AF1a-driven transcriptomes feature alternative splicing events in the 5′-untranslated region (5′-UTR) that are favorable for translation. These findings unveil distinct roles of duplicated tandem exon-derived U2AF1 isoforms in the regulation of the transcriptome and suggest U2AF1a-driven 5′-UTR alternative splicing as a molecular mechanism of mTOR-regulated translational control.
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Affiliation(s)
- Jae-Woong Chang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Hsin-Sung Yeh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Meeyeon Park
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Luke Erber
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Jiao Sun
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Sze Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Alexander M Bui
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Naima Ahmed Fahmi
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Ryan Nasti
- Department of Genetics, Cell and Developmental Biology, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Rui Kuang
- Department of Computer Science and Engineering, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Wei Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
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33
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Pabis M, Corsini L, Vincendeau M, Tripsianes K, Gibson TJ, Brack-Werner R, Sattler M. Modulation of HIV-1 gene expression by binding of a ULM motif in the Rev protein to UHM-containing splicing factors. Nucleic Acids Res 2019; 47:4859-4871. [PMID: 30892606 PMCID: PMC6511859 DOI: 10.1093/nar/gkz185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/04/2019] [Accepted: 03/18/2019] [Indexed: 12/01/2022] Open
Abstract
The HIV-1 protein Rev is essential for virus replication and ensures the expression of partially spliced and unspliced transcripts. We identified a ULM (UHM ligand motif) motif in the Arginine-Rich Motif (ARM) of the Rev protein. ULMs (UHM ligand motif) mediate protein interactions during spliceosome assembly by binding to UHM (U2AF homology motifs) domains. Using NMR, biophysical methods and crystallography we show that the Rev ULM binds to the UHMs of U2AF65 and SPF45. The highly conserved Trp45 in the Rev ULM is crucial for UHM binding in vitro, for Rev co-precipitation with U2AF65 in human cells and for proper processing of HIV transcripts. Thus, Rev-ULM interactions with UHM splicing factors contribute to the regulation of HIV-1 transcript processing, also at the splicing level. The Rev ULM is an example of viral mimicry of host short linear motifs that enables the virus to interfere with the host molecular machinery.
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Affiliation(s)
- Marta Pabis
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85 764, Germany.,Center for Integrated Protein Science Munich, Department Chemie, TU München, Garching 85748, Germany
| | - Lorenzo Corsini
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85 764, Germany.,Center for Integrated Protein Science Munich, Department Chemie, TU München, Garching 85748, Germany
| | - Michelle Vincendeau
- Institute of Virology, Helmholtz Zentrum München, Neuherberg 85 764, Germany.,Research Unit Cellular Signal Integration, Helmholtz Zentrum München, Neuherberg, 85 764, Germany
| | - Konstantinos Tripsianes
- CEITEC - Central European Institute of Technology, Masaryk University, Brno 62 500, Czech Republic
| | | | - Ruth Brack-Werner
- Institute of Virology, Helmholtz Zentrum München, Neuherberg 85 764, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85 764, Germany.,Center for Integrated Protein Science Munich, Department Chemie, TU München, Garching 85748, Germany
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34
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Talkish J, Igel H, Hunter O, Horner SW, Jeffery NN, Leach JR, Jenkins JL, Kielkopf CL, Ares M. Cus2 enforces the first ATP-dependent step of splicing by binding to yeast SF3b1 through a UHM-ULM interaction. RNA (NEW YORK, N.Y.) 2019; 25:1020-1037. [PMID: 31110137 PMCID: PMC6633205 DOI: 10.1261/rna.070649.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/15/2019] [Indexed: 05/16/2023]
Abstract
Stable recognition of the intron branchpoint (BP) by the U2 snRNP to form the pre-spliceosome is the first ATP-dependent step of splicing. Genetic and biochemical data from yeast indicate that Cus2 aids U2 snRNA folding into the stem IIa conformation prior to pre-spliceosome formation. Cus2 must then be removed by an ATP-dependent function of Prp5 before assembly can progress. However, the location from which Cus2 is displaced and the nature of its binding to the U2 snRNP are unknown. Here, we show that Cus2 contains a conserved UHM (U2AF homology motif) that binds Hsh155, the yeast homolog of human SF3b1, through a conserved ULM (U2AF ligand motif). Mutations in either motif block binding and allow pre-spliceosome formation without ATP. A 2.0 Å resolution structure of the Hsh155 ULM in complex with the UHM of Tat-SF1, the human homolog of Cus2, and complementary binding assays show that the interaction is highly similar between yeast and humans. Furthermore, we show that Tat-SF1 can replace Cus2 function by enforcing ATP dependence of pre-spliceosome formation in yeast extracts. Cus2 is removed before pre-spliceosome formation, and both Cus2 and its Hsh155 ULM binding site are absent from available cryo-EM structure models. However, our data are consistent with the apparent location of the disordered Hsh155 ULM between the U2 stem-loop IIa and the HEAT repeats of Hsh155 that interact with Prp5. We propose a model in which Prp5 uses ATP to remove Cus2 from Hsh155 such that extended base-pairing between U2 snRNA and the intron BP can occur.
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Affiliation(s)
- Jason Talkish
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Haller Igel
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Oarteze Hunter
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Steven W Horner
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Nazish N Jeffery
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Justin R Leach
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Jermaine L Jenkins
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Clara L Kielkopf
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Manuel Ares
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
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35
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Královicová J, Ševcíková I, Stejskalová E, Obuca M, Hiller M, Stanek D, Vorechovský I. PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RRM. Nucleic Acids Res 2019; 46:6166-6187. [PMID: 29788428 PMCID: PMC6093180 DOI: 10.1093/nar/gky389] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/01/2018] [Indexed: 12/27/2022] Open
Abstract
PUF60 is a splicing factor that binds uridine (U)-rich tracts and facilitates association of the U2 small nuclear ribonucleoprotein with primary transcripts. PUF60 deficiency (PD) causes a developmental delay coupled with intellectual disability and spinal, cardiac, ocular and renal defects, but PD pathogenesis is not understood. Using RNA-Seq, we identify human PUF60-regulated exons and show that PUF60 preferentially acts as their activator. PUF60-activated internal exons are enriched for Us upstream of their 3′ splice sites (3′ss), are preceded by longer AG dinucleotide exclusion zones and more distant branch sites, with a higher probability of unpaired interactions across a typical branch site location as compared to control exons. In contrast, PUF60-repressed exons show U-depletion with lower estimates of RNA single-strandedness. We also describe PUF60-regulated, alternatively spliced isoforms encoding other U-bound splicing factors, including PUF60 partners, suggesting that they are co-regulated in the cell, and identify PUF60-regulated exons derived from transposed elements. PD-associated amino-acid substitutions, even within a single RNA recognition motif (RRM), altered selection of competing 3′ss and branch points of a PUF60-dependent exon and the 3′ss choice was also influenced by alternative splicing of PUF60. Finally, we propose that differential distribution of RNA processing steps detected in cells lacking PUF60 and the PUF60-paralog RBM39 is due to the RBM39 RS domain interactions. Together, these results provide new insights into regulation of exon usage by the 3′ss organization and reveal that germline mutation heterogeneity in RRMs can enhance phenotypic variability at the level of splice-site and branch-site selection.
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Affiliation(s)
- Jana Královicová
- University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK.,Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Ivana Ševcíková
- Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Eva Stejskalová
- Czech Academy of Sciences, Institute of Molecular Genetics, 142 20 Prague, Czech Republic
| | - Mina Obuca
- Czech Academy of Sciences, Institute of Molecular Genetics, 142 20 Prague, Czech Republic
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics and Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - David Stanek
- Czech Academy of Sciences, Institute of Molecular Genetics, 142 20 Prague, Czech Republic
| | - Igor Vorechovský
- University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK
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36
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Miyazono KI, Ohno Y, Wada H, Ito T, Fukatsu Y, Kurisaki A, Asashima M, Tanokura M. Structural basis for receptor-regulated SMAD recognition by MAN1. Nucleic Acids Res 2019; 46:12139-12153. [PMID: 30321401 PMCID: PMC6294489 DOI: 10.1093/nar/gky925] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/04/2018] [Indexed: 01/15/2023] Open
Abstract
Receptor-regulated SMAD (R-SMAD: SMAD1, SMAD2, SMAD3, SMAD5 and SMAD8) proteins are key transcription factors of the transforming growth factor-β (TGF-β) superfamily of cytokines. MAN1, an integral protein of the inner nuclear membrane, is a SMAD cofactor that terminates TGF-β superfamily signals. Heterozygous loss-of-function mutations in MAN1 result in osteopoikilosis, Buschke-Ollendorff syndrome and melorheostosis. MAN1 interacts with MAD homology 2 (MH2) domains of R-SMAD proteins using its C-terminal U2AF homology motif (UHM) domain and UHM ligand motif (ULM) and facilitates R-SMAD dephosphorylation. Here, we report the structural basis for R-SMAD recognition by MAN1. The SMAD2–MAN1 and SMAD1–MAN1 complex structures show that an intramolecular UHM–ULM interaction of MAN1 forms a hydrophobic surface that interacts with a hydrophobic surface among the H2 helix, the strands β8 and β9, and the L3 loop of the MH2 domains of R-SMAD proteins. The complex structures also show the mechanism by which SMAD cofactors distinguish R-SMAD proteins that possess a highly conserved molecular surface.
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Affiliation(s)
- Ken-Ichi Miyazono
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Yosuke Ohno
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Hikaru Wada
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Tomoko Ito
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Yui Fukatsu
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Akira Kurisaki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan.,Biotechnology Research Institute for Drug Discovery (BRD), National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Makoto Asashima
- Biotechnology Research Institute for Drug Discovery (BRD), National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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37
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Tari M, Manceau V, de Matha Salone J, Kobayashi A, Pastré D, Maucuer A. U2AF 65 assemblies drive sequence-specific splice site recognition. EMBO Rep 2019; 20:e47604. [PMID: 31271494 DOI: 10.15252/embr.201847604] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/21/2019] [Accepted: 05/28/2019] [Indexed: 02/06/2023] Open
Abstract
The essential splicing factor U2AF65 is known to help anchoring U2 snRNP at the branch site. Its C-terminal UHM domain interacts with ULM motifs of SF3b155, an U2 snRNP protein. Here, we report a cooperative binding of U2AF65 and the related protein CAPERα to the multi-ULM domain of SF3b155. In addition, we show that the RS domain of U2AF65 drives a liquid-liquid phase separation that is amplified by intronic RNA with repeated pyrimidine tracts. In cells, knockdown of either U2AF65 or CAPERα improves the inclusion of cassette exons that are preceded by such repeated pyrimidine-rich motifs. These results support a model in which liquid-like assemblies of U2AF65 and CAPERα on repetitive pyrimidine-rich RNA sequences are driven by their RS domains, and facilitate the recruitment of the multi-ULM domain of SF3b155. We anticipate that posttranslational modifications and proteins recruited in dynamical U2AF65 and CAPERα condensates may further contribute to the complex mechanisms leading to specific splice site choice that occurs in cells.
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Affiliation(s)
- Manel Tari
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Valérie Manceau
- Institut Necker Enfants Malades (INEM), Inserm U1151 - CNRS UMR 8253, Université Paris Descartes, Paris, France
| | | | - Asaki Kobayashi
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - David Pastré
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Alexandre Maucuer
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
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38
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Loerch S, Leach JR, Horner SW, Maji D, Jenkins JL, Pulvino MJ, Kielkopf CL. The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface. J Biol Chem 2018; 294:2892-2902. [PMID: 30567737 DOI: 10.1074/jbc.ra118.006764] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/10/2018] [Indexed: 01/09/2023] Open
Abstract
The transcription elongation and pre-mRNA splicing factor Tat-SF1 associates with the U2 small nuclear ribonucleoprotein (snRNP) of the spliceosome. However, the direct binding partner and underlying interactions mediating the Tat-SF1-U2 snRNP association remain unknown. Here, we identified SF3b1 as a Tat-SF1-interacting subunit of the U2 snRNP. Our 1.1 Å resolution crystal structure revealed that Tat-SF1 contains a U2AF homology motif (UHM) protein-protein interaction module. We demonstrated that Tat-SF1 preferentially and directly binds the SF3b1 subunit compared with other U2AF ligand motif (ULM)-containing splicing factors, and further established that SF3b1 association depends on the integrity of the Tat-SF1 UHM. We next compared the Tat-SF1-binding affinities for each of the five known SF3b1 ULMs and then determined the structures of representative high- and low-affinity SF3b1 ULM complexes with the Tat-SF1 UHM at 1.9 Å and 2.1 Å resolutions, respectively. These structures revealed a canonical UHM-ULM interface, comprising a Tat-SF1 binding pocket for a ULM tryptophan (SF3b1 Trp338) and electrostatic interactions with a basic ULM tail. Importantly, we found that SF3b1 regulates Tat-SF1 levels and that these two factors influence expression of overlapping representative transcripts, consistent with a functional partnership of Tat-SF1 and SF3b1. Altogether, these results define a new molecular interface of the Tat-SF1-U2 snRNP complex for gene regulation.
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Affiliation(s)
- Sarah Loerch
- From the Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Justin R Leach
- From the Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Steven W Horner
- From the Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Debanjana Maji
- From the Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Jermaine L Jenkins
- From the Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Mary J Pulvino
- From the Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Clara L Kielkopf
- From the Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
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39
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Sawazaki R, Imai S, Yokogawa M, Hosoda N, Hoshino SI, Mio M, Mio K, Shimada I, Osawa M. Characterization of the multimeric structure of poly(A)-binding protein on a poly(A) tail. Sci Rep 2018; 8:1455. [PMID: 29362417 PMCID: PMC5780489 DOI: 10.1038/s41598-018-19659-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/05/2018] [Indexed: 11/24/2022] Open
Abstract
Eukaryotic mature mRNAs possess a poly adenylate tail (poly(A)), to which multiple molecules of poly(A)-binding protein C1 (PABPC1) bind. PABPC1 regulates translation and mRNA metabolism by binding to regulatory proteins. To understand functional mechanism of the regulatory proteins, it is necessary to reveal how multiple molecules of PABPC1 exist on poly(A). Here, we characterize the structure of the multiple molecules of PABPC1 on poly(A), by using transmission electron microscopy (TEM), chemical cross-linking, and NMR spectroscopy. The TEM images and chemical cross-linking results indicate that multiple PABPC1 molecules form a wormlike structure in the PABPC1-poly(A) complex, in which the PABPC1 molecules are linearly arrayed. NMR and cross-linking analyses indicate that PABPC1 forms a multimer by binding to the neighbouring PABPC1 molecules via interactions between the RNA recognition motif (RRM) 2 in one molecule and the middle portion of the linker region of another molecule. A PABPC1 mutant lacking the interaction site in the linker, which possesses an impaired ability to form the multimer, reduced the in vitro translation activity, suggesting the importance of PABPC1 multimer formation in the translation process. We therefore propose a model of the PABPC1 multimer that provides clues to comprehensively understand the regulation mechanism of mRNA translation.
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Affiliation(s)
- Ryoichi Sawazaki
- Graduate School of Pharmaceutical Sciences, Keio University, Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Shunsuke Imai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mariko Yokogawa
- Graduate School of Pharmaceutical Sciences, Keio University, Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Nao Hosoda
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Shin-Ichi Hoshino
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Muneyo Mio
- Molecular Profiling Research Center for Drug Discovery and OPERANDO Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuhiro Mio
- Molecular Profiling Research Center for Drug Discovery and OPERANDO Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo, 135-0064, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, Keio University, Shibakoen, Minato-ku, Tokyo, 105-8512, Japan. .,Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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40
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Kielkopf CL. Insights from structures of cancer-relevant pre-mRNA splicing factors. Curr Opin Genet Dev 2017; 48:57-66. [PMID: 29128695 DOI: 10.1016/j.gde.2017.10.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 10/10/2017] [Accepted: 10/13/2017] [Indexed: 12/21/2022]
Abstract
Pre-mRNA splicing factors recognize consensus signals within preliminary transcripts, and as cogs of the spliceosome machine, orchestrate the excision and rejoining of pre-mRNA regions for gene expression. Large-scale sequencing has demonstrated that mutations in key genes encoding pre-mRNA splicing factors are common among myeloid neoplasms and also occur in a variety of other cancers. This revelation offers new therapeutic opportunities to target pre-mRNA splicing vulnerabilities in hematologic and other malignancies. The mutated residues typically alter 3' splice site choice for a subset of transcripts. In this review, we highlight mechanistic insights from recent 3D structures that reveal the affected residues poised for pre-mRNA recognition.
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Affiliation(s)
- Clara L Kielkopf
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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41
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Glasser E, Agrawal AA, Jenkins JL, Kielkopf CL. Cancer-Associated Mutations Mapped on High-Resolution Structures of the U2AF2 RNA Recognition Motifs. Biochemistry 2017; 56:4757-4761. [PMID: 28850223 DOI: 10.1021/acs.biochem.7b00551] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Acquired point mutations of pre-mRNA splicing factors recur among cancers, leukemias, and related neoplasms. Several studies have established that somatic mutations of a U2AF1 subunit, which normally recognizes 3' splice site junctions, recur among myelodysplastic syndromes. The U2AF2 splicing factor recognizes polypyrimidine signals that precede most 3' splice sites as a heterodimer with U2AF1. In contrast with those of the well-studied U2AF1 subunit, descriptions of cancer-relevant U2AF2 mutations and their structural relationships are lacking. Here, we survey databases of cancer-associated mutations and identify recurring missense mutations in the U2AF2 gene. We determine ultra-high-resolution structures of the U2AF2 RNA recognition motifs (RRM1 and RRM2) at 1.1 Å resolution and map the structural locations of the mutated U2AF2 residues. Comparison with prior, lower-resolution structures of the tandem U2AF2 RRMs in the RNA-bound and apo states reveals clusters of cancer-associated mutations at the U2AF2 RRM-RNA or apo-RRM1-RRM2 interfaces. Although the role of U2AF2 mutations in malignant transformation remains uncertain, our results show that cancer-associated mutations correlate with functionally important surfaces of the U2AF2 splicing factor.
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Affiliation(s)
- Eliezra Glasser
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Anant A Agrawal
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Jermaine L Jenkins
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Clara L Kielkopf
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
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42
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Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins. Biochem Soc Trans 2017; 44:1058-65. [PMID: 27528752 DOI: 10.1042/bst20160080] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Indexed: 02/04/2023]
Abstract
Polypyrimidine tract binding protein (PTBP1) is a heterogeneous nuclear ribonucleoprotein (hnRNP) that plays roles in most stages of the life-cycle of pre-mRNA and mRNAs in the nucleus and cytoplasm. PTBP1 has four RNA binding domains of the RNA recognition motif (RRM) family, each of which can bind to pyrimidine motifs. In addition, RRM2 can interact via its dorsal surface with proteins containing short peptide ligands known as PTB RRM2 interacting (PRI) motifs, originally found in the protein Raver1. Here we review our recent progress in understanding the interactions of PTB with RNA and with various proteins containing PRI ligands.
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43
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Wedel C, Förstner KU, Derr R, Siegel TN. GT-rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes. EMBO J 2017; 36:2581-2594. [PMID: 28701485 PMCID: PMC5579346 DOI: 10.15252/embj.201695323] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 01/25/2023] Open
Abstract
Genome‐wide transcription studies are revealing an increasing number of “dispersed promoters” that, unlike “focused promoters”, lack well‐conserved sequence motifs and tight regulation. Dispersed promoters are nevertheless marked by well‐defined chromatin structures, suggesting that specific sequence elements must exist in these unregulated promoters. Here, we have analyzed regions of transcription initiation in the eukaryotic parasite Trypanosoma brucei, in which RNA polymerase II transcription initiation occurs over broad regions without distinct promoter motifs and lacks regulation. Using a combination of site‐specific and genome‐wide assays, we identified GT‐rich promoters that can drive transcription and promote the targeted deposition of the histone variant H2A.Z in a genomic context‐dependent manner. In addition, upon mapping nucleosome occupancy at high resolution, we find nucleosome positioning to correlate with RNA pol II enrichment and gene expression, pointing to a role in RNA maturation. Nucleosome positioning may thus represent a previously unrecognized layer of gene regulation in trypanosomes. Our findings show that even highly dispersed, unregulated promoters contain specific DNA elements that are able to induce transcription and changes in chromatin structure.
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Affiliation(s)
- Carolin Wedel
- Research Center for Infectious Diseases, Universität Würzburg, Würzburg, Germany
| | | | - Ramona Derr
- Research Center for Infectious Diseases, Universität Würzburg, Würzburg, Germany
| | - T Nicolai Siegel
- Research Center for Infectious Diseases, Universität Würzburg, Würzburg, Germany .,Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, München, Germany.,Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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44
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Chatrikhi R, Wang W, Gupta A, Loerch S, Maucuer A, Kielkopf CL. SF1 Phosphorylation Enhances Specific Binding to U2AF 65 and Reduces Binding to 3'-Splice-Site RNA. Biophys J 2017; 111:2570-2586. [PMID: 28002734 DOI: 10.1016/j.bpj.2016.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/02/2016] [Accepted: 11/08/2016] [Indexed: 12/25/2022] Open
Abstract
Splicing factor 1 (SF1) recognizes 3' splice sites of the major class of introns as a ternary complex with U2AF65 and U2AF35 splicing factors. A conserved SPSP motif in a coiled-coil domain of SF1 is highly phosphorylated in proliferating human cells and is required for cell proliferation. The UHM kinase 1 (UHMK1), also called KIS, double-phosphorylates both serines of this SF1 motif. Here, we use isothermal titration calorimetry to demonstrate that UHMK1 phosphorylation of the SF1 SPSP motif slightly enhances specific binding of phospho-SF1 to its cognate U2AF65 protein partner. Conversely, quantitative fluorescence anisotropy RNA binding assays and isothermal titration calorimetry experiments establish that double-SPSP phosphorylation reduces phospho-SF1 and phospho-SF1-U2AF65 binding affinities for either optimal or suboptimal splice-site RNAs. Domain-substitution and mutagenesis experiments further demonstrate that arginines surrounding the phosphorylated SF1 loop are required for cooperative 3' splice site recognition by the SF1-U2AF65 complex (where cooperativity is defined as a nonadditive increase in RNA binding by the protein complex relative to the individual proteins). In the context of local, intracellular concentrations, the subtle effects of SF1 phosphorylation on its associations with U2AF65 and splice-site RNAs are likely to influence pre-mRNA splicing. However, considering roles for SF1 in pre-mRNA retention and transcriptional repression, as well as in splicing, future comprehensive investigations are needed to fully explain the requirement for SF1 SPSP phosphorylation in proliferating human cells.
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Affiliation(s)
- Rakesh Chatrikhi
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York
| | - Wenhua Wang
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York
| | - Ankit Gupta
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York
| | - Sarah Loerch
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York
| | | | - Clara L Kielkopf
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York.
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45
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van Roon AMM, Oubridge C, Obayashi E, Sposito B, Newman AJ, Séraphin B, Nagai K. Crystal structure of U2 snRNP SF3b components: Hsh49p in complex with Cus1p-binding domain. RNA (NEW YORK, N.Y.) 2017; 23:968-981. [PMID: 28348170 PMCID: PMC5435868 DOI: 10.1261/rna.059378.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 03/17/2017] [Indexed: 05/02/2023]
Abstract
Spliceosomal proteins Hsh49p and Cus1p are components of SF3b, which together with SF3a, Msl1p/Lea1p, Sm proteins, and U2 snRNA, form U2 snRNP, which plays a crucial role in pre-mRNA splicing. Hsh49p, comprising two RRMs, forms a heterodimer with Cus1p. We determined the crystal structures of Saccharomyces cerevisiae full-length Hsh49p as well as its RRM1 in complex with a minimal binding region of Cus1p (residues 290-368). The structures show that the Cus1 fragment binds to the α-helical surface of Hsh49p RRM1, opposite the four-stranded β-sheet, leaving the canonical RNA-binding surface available to bind RNA. Hsh49p binds the 5' end region of U2 snRNA via RRM1. Its affinity is increased in complex with Cus1(290-368)p, partly because an extended RNA-binding surface forms across the protein-protein interface. The Hsh49p RRM1-Cus1(290-368)p structure fits well into cryo-EM density of the Bact spliceosome, corroborating the biological relevance of our crystal structure.
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Affiliation(s)
| | - Chris Oubridge
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Eiji Obayashi
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Benedetta Sposito
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Bertrand Séraphin
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé et de la Recherche Médicale (INSERM), U964/Université de Strasbourg, 67404 Illkirch, France
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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46
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Aberrant splicing in maize rough endosperm3 reveals a conserved role for U12 splicing in eukaryotic multicellular development. Proc Natl Acad Sci U S A 2017; 114:E2195-E2204. [PMID: 28242684 PMCID: PMC5358371 DOI: 10.1073/pnas.1616173114] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA splicing of U12-type introns functions in human cell differentiation, but it is not known whether this class of introns has a similar role in plants. The maize ROUGH ENDOSPERM3 (RGH3) protein is orthologous to the human splicing factor, ZRSR2. ZRSR2 mutations are associated with myelodysplastic syndrome (MDS) and cause U12 splicing defects. Maize rgh3 mutants have aberrant endosperm cell differentiation and proliferation. We found that most U12-type introns are retained or misspliced in rgh3 Genes affected in rgh3 and ZRSR2 mutants identify cell cycle and protein glycosylation as common pathways disrupted. Transcripts with retained U12-type introns can be found in polysomes, suggesting that splicing efficiency can alter protein isoforms. The rgh3 mutant protein disrupts colocalization with a known ZRSR2-interacting protein, U2AF2. These results indicate conserved function for RGH3/ZRSR2 in U12 splicing and a deeply conserved role for the minor spliceosome to promote cell differentiation from stem cells to terminal fates.
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47
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Loerch S, Kielkopf CL. Unmasking the U2AF homology motif family: a bona fide protein-protein interaction motif in disguise. RNA (NEW YORK, N.Y.) 2016; 22:1795-1807. [PMID: 27852923 PMCID: PMC5113200 DOI: 10.1261/rna.057950.116] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
U2AF homology motifs (UHM) that recognize U2AF ligand motifs (ULM) are an emerging family of protein-protein interaction modules. UHM-ULM interactions recur in pre-mRNA splicing factors including U2AF1 and SF3b1, which are frequently mutated in myelodysplastic syndromes. The core topology of the UHM resembles an RNA recognition motif and is often mistakenly classified within this large family. Here, we unmask the charade and review recent discoveries of UHM-ULM modules for protein-protein interactions. Diverse polypeptide extensions and selective phosphorylation of UHM and ULM family members offer new molecular mechanisms for the assembly of specific partners in the early-stage spliceosome.
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Affiliation(s)
- Sarah Loerch
- Center for RNA Biology and Department for Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Clara L Kielkopf
- Center for RNA Biology and Department for Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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48
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Falk S, Finogenova K, Melko M, Benda C, Lykke-Andersen S, Jensen TH, Conti E. Structure of the RBM7-ZCCHC8 core of the NEXT complex reveals connections to splicing factors. Nat Commun 2016; 7:13573. [PMID: 27905398 PMCID: PMC5146272 DOI: 10.1038/ncomms13573] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 10/13/2016] [Indexed: 01/24/2023] Open
Abstract
The eukaryotic RNA exosome participates extensively in RNA processing and degradation. In human cells, three accessory factors (RBM7, ZCCHC8 and hMTR4) interact to form the nuclear exosome targeting (NEXT) complex, which directs a subset of non-coding RNAs for exosomal degradation. Here we elucidate how RBM7 is incorporated in the NEXT complex. We identify a proline-rich segment of ZCCHC8 as the interaction site for the RNA-recognition motif (RRM) of RBM7 and present the crystal structure of the corresponding complex at 2.0 Å resolution. On the basis of the structure, we identify a proline-rich segment within the splicing factor SAP145 with strong similarity to ZCCHC8. We show that this segment of SAP145 not only binds the RRM region of another splicing factor SAP49 but also the RRM of RBM7. These dual interactions of RBM7 with the exosome and the spliceosome suggest a model whereby NEXT might recruit the exosome to degrade intronic RNAs. RBM7 and ZCCHC8 are two core subunits of the Nuclear Exosome Targeting complex, which regulates the degradation of selected non-coding RNAs in human cells. Here, the authors use structural and biochemical methods to show how ZCCHC8 recruits RBM7 in the complex, leaving the RNA binding site accessible and revealing possible implications for splicing.
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Affiliation(s)
- Sebastian Falk
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Ksenia Finogenova
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Mireille Melko
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, 8000C Aarhus, Denmark
| | - Christian Benda
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Søren Lykke-Andersen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, 8000C Aarhus, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, 8000C Aarhus, Denmark
| | - Elena Conti
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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49
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Jagtap PKA, Garg D, Kapp TG, Will CL, Demmer O, Lührmann R, Kessler H, Sattler M. Rational Design of Cyclic Peptide Inhibitors of U2AF Homology Motif (UHM) Domains To Modulate Pre-mRNA Splicing. J Med Chem 2016; 59:10190-10197. [PMID: 27753493 DOI: 10.1021/acs.jmedchem.6b01118] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
U2AF homology motifs (UHMs) are atypical RNA recognition motif domains that mediate critical protein-protein interactions during the regulation of alternative pre-mRNA splicing and other processes. The recognition of UHM domains by UHM ligand motif (ULM) peptide sequences plays important roles during early steps of spliceosome assembly. Splicing factor 45 kDa (SPF45) is an alternative splicing factor implicated in breast and lung cancers, and splicing regulation of apoptosis-linked pre-mRNAs by SPF45 was shown to depend on interactions between its UHM domain and ULM motifs in constitutive splicing factors. We have developed cyclic peptide inhibitors that target UHM domains. By screening a focused library of linear and cyclic peptides and performing structure-activity relationship analysis, we designed cyclic peptides with 4-fold improved binding affinity for the SPF45 UHM domain compared to native ULM ligands and 270-fold selectivity to discriminate UHM domains from alternative and constitutive splicing factors. These inhibitors are useful tools to modulate and dissect mechanisms of alternative splicing regulation.
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Affiliation(s)
- Pravin Kumar Ankush Jagtap
- Institute of Structural Biology, Helmholtz Zentrum München , Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany.,Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München , Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Divita Garg
- Institute of Structural Biology, Helmholtz Zentrum München , Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany.,Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München , Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Tobias G Kapp
- Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München , Lichtenbergstrasse 4, 85747 Garching, Germany.,Institute for Advanced Study (IAS), Technische Universität München , Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Cindy L Will
- Max Planck Institute for Biophysical Chemistry , Department of Cellular Biochemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Oliver Demmer
- Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München , Lichtenbergstrasse 4, 85747 Garching, Germany.,Institute for Advanced Study (IAS), Technische Universität München , Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Reinhard Lührmann
- Max Planck Institute for Biophysical Chemistry , Department of Cellular Biochemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Horst Kessler
- Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München , Lichtenbergstrasse 4, 85747 Garching, Germany.,Institute for Advanced Study (IAS), Technische Universität München , Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München , Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany.,Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München , Lichtenbergstrasse 4, 85747 Garching, Germany
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50
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Recognition of the 3' splice site RNA by the U2AF heterodimer involves a dynamic population shift. Proc Natl Acad Sci U S A 2016; 113:E7169-E7175. [PMID: 27799531 DOI: 10.1073/pnas.1605873113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An essential early step in the assembly of human spliceosomes onto pre-mRNA involves the recognition of regulatory RNA cis elements in the 3' splice site by the U2 auxiliary factor (U2AF). The large (U2AF65) and small (U2AF35) subunits of the U2AF heterodimer contact the polypyrimidine tract (Py-tract) and the AG-dinucleotide, respectively. The tandem RNA recognition motif domains (RRM1,2) of U2AF65 adopt closed/inactive and open/active conformations in the free form and when bound to bona fide Py-tract RNA ligands. To investigate the molecular mechanism and dynamics of 3' splice site recognition by U2AF65 and the role of U2AF35 in the U2AF heterodimer, we have combined single-pair FRET and NMR experiments. In the absence of RNA, the RRM1,2 domain arrangement is highly dynamic on a submillisecond time scale, switching between closed and open conformations. The addition of Py-tract RNA ligands with increasing binding affinity (strength) gradually shifts the equilibrium toward an open conformation. Notably, the protein-RNA complex is rigid in the presence of a strong Py-tract but exhibits internal motion with weak Py-tracts. Surprisingly, the presence of U2AF35, whose UHM domain interacts with U2AF65 RRM1, increases the population of the open arrangement of U2AF65 RRM1,2 in the absence and presence of a weak Py-tract. These data indicate that the U2AF heterodimer promotes spliceosome assembly by a dynamic population shift toward the open conformation of U2AF65 to facilitate the recognition of weak Py-tracts at the 3' splice site. The structure and RNA binding of the heterodimer was unaffected by cancer-linked myelodysplastic syndrome mutants.
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