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Bensaude O, Barbosa I, Morillo L, Dikstein R, Le Hir H. Exon-junction complex association with stalled ribosomes and slow translation-independent disassembly. Nat Commun 2024; 15:4209. [PMID: 38760352 PMCID: PMC11101648 DOI: 10.1038/s41467-024-48371-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
Exon junction complexes are deposited at exon-exon junctions during splicing. They are primarily known to activate non-sense mediated degradation of transcripts harbouring premature stop codons before the last intron. According to a popular model, exon-junction complexes accompany mRNAs to the cytoplasm where the first translating ribosome pushes them out. However, they are also removed by uncharacterized, translation-independent mechanisms. Little is known about kinetic and transcript specificity of these processes. Here we tag core subunits of exon-junction complexes with complementary split nanoluciferase fragments to obtain sensitive and quantitative assays for complex formation. Unexpectedly, exon-junction complexes form large stable mRNPs containing stalled ribosomes. Complex assembly and disassembly rates are determined after an arrest in transcription and/or translation. 85% of newly deposited exon-junction complexes are disassembled by a translation-dependent mechanism. However as this process is much faster than the translation-independent one, only 30% of the exon-junction complexes present in cells at steady state require translation for disassembly. Deep RNA sequencing shows a bias of exon-junction complex bound transcripts towards microtubule and centrosome coding ones and demonstrate that the lifetimes of exon-junction complexes are transcript-specific. This study provides a dynamic vision of exon-junction complexes and uncovers their unexpected stable association with ribosomes.
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Affiliation(s)
- Olivier Bensaude
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.
| | - Isabelle Barbosa
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Lucia Morillo
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Rivka Dikstein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.
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2
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Schulz D, Feulner L, Santos Rubenich D, Heimer S, Rohrmüller S, Reinders Y, Falchetti M, Wetzel M, Braganhol E, Lummertz da Rocha E, Schäfer N, Stöckl S, Brockhoff G, Wege AK, Fritsch J, Pohl F, Reichert TE, Ettl T, Bauer RJ. Subcellular localization of PD-L1 and cell-cycle-dependent expression of nuclear PD-L1 variants: implications for head and neck cancer cell functions and therapeutic efficacy. Mol Oncol 2024; 18:431-452. [PMID: 38103190 PMCID: PMC10850815 DOI: 10.1002/1878-0261.13567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/24/2023] [Accepted: 12/13/2023] [Indexed: 12/18/2023] Open
Abstract
The programmed cell death 1 ligand 1 (PD-L1)/programmed cell death protein 1 (PD-1) axis is primarily associated with immunosuppression in cytotoxic T lymphocytes (CTLs). However, mounting evidence is supporting the thesis that PD-L1 not only functions as a ligand but mediates additional cellular functions in tumor cells. Moreover, it has been demonstrated that PD-L1 is not exclusively localized at the cellular membrane. Subcellular fractionation revealed the presence of PD-L1 in various cellular compartments of six well-characterized head and neck cancer (HNC) cell lines, including the nucleus. Via Western blotting, we detected PD-L1 in its well-known glycosylated/deglycosylated state at 40-55 kDa. In addition, we detected previously unknown PD-L1 variants with a molecular weight at approximately 70 and > 150 kDa exclusively in nuclear protein fractions. These in vitro findings were confirmed with primary tumor samples from head and neck squamous cell carcinoma (HNSCC) patients. Furthermore, we demonstrated that nuclear PD-L1 variant expression is cell-cycle-dependent. Immunofluorescence staining of PD-L1 in different cell cycle phases of synchronized HNC cells supported these observations. Mechanisms of nuclear PD-L1 trafficking remain less understood; however, proximity ligation assays showed a cell-cycle-dependent interaction of the cytoskeletal protein vimentin with PD-L1, whereas vimentin could serve as a potential shuttle for nuclear PD-L1 transportation. Mass spectrometry after PD-L1 co-immunoprecipitation, followed by gene ontology analysis, indicated interaction of nuclear PD-L1 with proteins involved in DNA remodeling and messenger RNA (mRNA) splicing. Our results in HNC cells suggest a highly complex regulation of PD-L1 and multiple tumor cell-intrinsic functions, independent of immune regulation. These observations bear significant implications for the therapeutic efficacy of immune checkpoint inhibition.
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Affiliation(s)
- Daniela Schulz
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
- Department of Oral and Maxillofacial Surgery, Experimental Oral and Maxillofacial Surgery, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
| | - Laura Feulner
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
- Department of Oral and Maxillofacial Surgery, Experimental Oral and Maxillofacial Surgery, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
| | - Dominique Santos Rubenich
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
- Department of Oral and Maxillofacial Surgery, Experimental Oral and Maxillofacial Surgery, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
- Postgraduation program in BiosciencesFederal University of Health Sciences from Porto AlegreBrazil
| | - Sina Heimer
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
| | - Sophia Rohrmüller
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
- Department of Oral and Maxillofacial Surgery, Experimental Oral and Maxillofacial Surgery, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
| | - Yvonne Reinders
- Leibniz‐Institute for Analytical Sciences, ISAS e.V.DortmundGermany
| | - Marcelo Falchetti
- Department of Microbiology, Immunology and ParasitologyFederal University of Santa CatarinaFlorianópolisBrazil
| | - Martin Wetzel
- Department of Oral and Maxillofacial Surgery, Experimental Oral and Maxillofacial Surgery, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
| | - Elizandra Braganhol
- Department of Basic Health SciencesFederal University of Health Sciences from Porto AlegreBrazil
| | - Edroaldo Lummertz da Rocha
- Department of Microbiology, Immunology and ParasitologyFederal University of Santa CatarinaFlorianópolisBrazil
| | - Nicole Schäfer
- Department of Orthopaedic Surgery, Experimental OrthopaedicsUniversity of RegensburgGermany
- Department of Orthopaedic Surgery, Experimental Orthopaedics, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
| | - Sabine Stöckl
- Department of Orthopaedic Surgery, Experimental OrthopaedicsUniversity of RegensburgGermany
- Department of Orthopaedic Surgery, Experimental Orthopaedics, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
| | - Gero Brockhoff
- Department of Gynecology and ObstetricsUniversity Medical Center RegensburgGermany
| | - Anja K. Wege
- Department of Gynecology and ObstetricsUniversity Medical Center RegensburgGermany
| | - Jürgen Fritsch
- Department of Infection Prevention and Infectious DiseasesUniversity Medical Center RegensburgGermany
| | - Fabian Pohl
- Department of RadiotherapyUniversity Medical Center RegensburgGermany
| | - Torsten E. Reichert
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
| | - Tobias Ettl
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
| | - Richard J. Bauer
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
- Department of Oral and Maxillofacial Surgery, Experimental Oral and Maxillofacial Surgery, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
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3
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Monaghan L, Longman D, Cáceres JF. Translation-coupled mRNA quality control mechanisms. EMBO J 2023; 42:e114378. [PMID: 37605642 PMCID: PMC10548175 DOI: 10.15252/embj.2023114378] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/23/2023] Open
Abstract
mRNA surveillance pathways are essential for accurate gene expression and to maintain translation homeostasis, ensuring the production of fully functional proteins. Future insights into mRNA quality control pathways will enable us to understand how cellular mRNA levels are controlled, how defective or unwanted mRNAs can be eliminated, and how dysregulation of these can contribute to human disease. Here we review translation-coupled mRNA quality control mechanisms, including the non-stop and no-go mRNA decay pathways, describing their mechanisms, shared trans-acting factors, and differences. We also describe advances in our understanding of the nonsense-mediated mRNA decay (NMD) pathway, highlighting recent mechanistic findings, the discovery of novel factors, as well as the role of NMD in cellular physiology and its impact on human disease.
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Affiliation(s)
- Laura Monaghan
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Dasa Longman
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
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4
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Bohnsack KE, Yi S, Venus S, Jankowsky E, Bohnsack MT. Cellular functions of eukaryotic RNA helicases and their links to human diseases. Nat Rev Mol Cell Biol 2023; 24:749-769. [PMID: 37474727 DOI: 10.1038/s41580-023-00628-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/22/2023]
Abstract
RNA helicases are highly conserved proteins that use nucleoside triphosphates to bind or remodel RNA, RNA-protein complexes or both. RNA helicases are classified into the DEAD-box, DEAH/RHA, Ski2-like, Upf1-like and RIG-I families, and are the largest class of enzymes active in eukaryotic RNA metabolism - virtually all aspects of gene expression and its regulation involve RNA helicases. Mutation and dysregulation of these enzymes have been linked to a multitude of diseases, including cancer and neurological disorders. In this Review, we discuss the regulation and functional mechanisms of RNA helicases and their roles in eukaryotic RNA metabolism, including in transcription regulation, pre-mRNA splicing, ribosome assembly, translation and RNA decay. We highlight intriguing models that link helicase structure, mechanisms of function (such as local strand unwinding, translocation, winching, RNA clamping and displacing RNA-binding proteins) and biological roles, including emerging connections between RNA helicases and cellular condensates formed through liquid-liquid phase separation. We also discuss associations of RNA helicases with human diseases and recent efforts towards the design of small-molecule inhibitors of these pivotal regulators of eukaryotic gene expression.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
| | - Soon Yi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Moderna, Cambridge, MA, USA.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
- Göttingen Centre for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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5
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Miyashita A, Kobayashi M, Yokota T, Zochodne DW. Diabetic Polyneuropathy: New Strategies to Target Sensory Neurons in Dorsal Root Ganglia. Int J Mol Sci 2023; 24:ijms24065977. [PMID: 36983051 PMCID: PMC10051459 DOI: 10.3390/ijms24065977] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/29/2023] Open
Abstract
Diabetic polyneuropathy (DPN) is the most common type of diabetic neuropathy, rendering a slowly progressive, symmetrical, and length-dependent dying-back axonopathy with preferential sensory involvement. Although the pathogenesis of DPN is complex, this review emphasizes the concept that hyperglycemia and metabolic stressors directly target sensory neurons in the dorsal root ganglia (DRG), leading to distal axonal degeneration. In this context, we discuss the role for DRG-targeting gene delivery, specifically oligonucleotide therapeutics for DPN. Molecules including insulin, GLP-1, PTEN, HSP27, RAGE, CWC22, and DUSP1 that impact neurotrophic signal transduction (for example, phosphatidylinositol-3 kinase/phosphorylated protein kinase B [PI3/pAkt] signaling) and other cellular networks may promote regeneration. Regenerative strategies may be essential in maintaining axon integrity during ongoing degeneration in diabetes mellitus (DM). We discuss specific new findings that relate to sensory neuron function in DM associated with abnormal dynamics of nuclear bodies such as Cajal bodies and nuclear speckles in which mRNA transcription and post-transcriptional processing occur. Manipulating noncoding RNAs such as microRNA and long-noncoding RNA (specifically MALAT1) that regulate gene expression through post-transcriptional modification are interesting avenues to consider in supporting neurons during DM. Finally, we present therapeutic possibilities around the use of a novel DNA/RNA heteroduplex oligonucleotide that provides more efficient gene knockdown in DRG than the single-stranded antisense oligonucleotide.
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Affiliation(s)
- Akiko Miyashita
- Department of Neurology, Neurological Science, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Masaki Kobayashi
- Department of Neurology, Neurological Science, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
- Department of Neurology, Nissan Tamagawa Hospital, Tokyo 158-0095, Japan
| | - Takanori Yokota
- Department of Neurology, Neurological Science, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Douglas W. Zochodne
- Division of Neurology and Department of Medicine, Faculty of Medicine and Dentistry, The Neuroscience and Mental Health Institute and The Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G 2G3, Canada
- Correspondence: ; Tel.: +1-780-248-1928; Fax: +1-780-248-1807
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6
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Mitra R, Rehman A, Singh KK, Jaganathan BG. Multifaceted roles of MAGOH Proteins. Mol Biol Rep 2023; 50:1931-1941. [PMID: 36396768 DOI: 10.1007/s11033-022-07904-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 07/14/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022]
Abstract
MAGOH and MAGOHB are paralog proteins that can substitute each other in the exon junction complex (EJC). The EJC is formed of core components EIF4A3, RBM8A, and MAGOH/MAGOHB. As a part of the EJC, MAGOH proteins are required for mRNA splicing, export, translation and nonsense-mediated mRNA decay (NMD). MAGOH is also essential for embryonic development and normal cellular functioning. The haploinsufficiency of MAGOH results in disorders such as microcephaly and cancer. The present review discusses the discovery of MAGOH, its paralog MAGOHB, their roles in cellular function as part of the EJC, and other cellular roles that are not directly associated with mRNA processing. We also discuss how MAGOH haploinsufficiency in cancer cells can be exploited to develop a novel targeted cancer treatment.
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Affiliation(s)
- Rumela Mitra
- Stem Cells and Cancer Biology Research Group, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, Guwahati, Assam, India
| | - Ayushi Rehman
- RNA-Binding Proteins (RBPs) Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, Guwahati, Assam, India
| | - Kusum Kumari Singh
- RNA-Binding Proteins (RBPs) Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, Guwahati, Assam, India.
| | - Bithiah Grace Jaganathan
- Stem Cells and Cancer Biology Research Group, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, Guwahati, Assam, India.
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, 781039, Guwahati, Assam, India.
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7
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Jacksi M, Schad E, Buday L, Tantos A. Absence of Scaffold Protein Tks4 Disrupts Several Signaling Pathways in Colon Cancer Cells. Int J Mol Sci 2023; 24:ijms24021310. [PMID: 36674824 PMCID: PMC9861885 DOI: 10.3390/ijms24021310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
Tks4 is a large scaffold protein in the EGFR signal transduction pathway that is involved in several cellular processes, such as cellular motility, reactive oxygen species-dependent processes, and embryonic development. It is also implicated in a rare developmental disorder, Frank-ter Haar syndrome. Loss of Tks4 resulted in the induction of an EMT-like process, with increased motility and overexpression of EMT markers in colorectal carcinoma cells. In this work, we explored the broader effects of deletion of Tks4 on the gene expression pattern of HCT116 colorectal carcinoma cells by transcriptome sequencing of wild-type and Tks4 knockout (KO) cells. We identified several protein coding genes with altered mRNA levels in the Tks4 KO cell line, as well as a set of long non-coding RNAs, and confirmed these changes with quantitative PCR on a selected set of genes. Our results show a significant perturbation of gene expression upon the deletion of Tks4, suggesting the involvement of different signal transduction pathways over the well-known EGFR signaling.
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Affiliation(s)
- Mevan Jacksi
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - László Buday
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Department of Molecular Biology, Semmelweis University Medical School, 1094 Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Correspondence:
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8
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V M DD, Sivaramakrishnan V, Arvind Kumar K. Structural systems biology approach delineate the functional implications of SNPs in exon junction complex interaction network. J Biomol Struct Dyn 2023; 41:11969-11986. [PMID: 36617892 DOI: 10.1080/07391102.2022.2164355] [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: 02/03/2022] [Accepted: 12/26/2022] [Indexed: 01/10/2023]
Abstract
In eukaryotes, transcripts that carry premature termination codons (PTC) leading to truncated proteins are degraded by the Nonsense Mediated Decay (NMD) machinery. Missense and nonsense Single Nucleotide Polymorphisms (SNPs) in proteins belonging to Exon junction complex (EJC) and up-frameshift protein (UPF) will compromise NMD leading to the accumulation of truncated proteins in various diseases. The EJC and UPF which are involved in NMD is a good model system to study the effect of SNPs at a system level. Despite the availability of crystal structures, computational tools, and data on mutational and deletion studies, with functional implications, an integrated effort to understand the impact of SNPs at the systems level is lacking. To study the functional consequences of missense SNPs, sequence-based techniques like SIFT and PolyPhen which classify SNPs as deleterious or non-deleterious and structure-based methods like FoldX which calculate the Delta Delta G, (ddGs, ∆∆G) are used. Using FoldX, the ddG for mutations with experimentally validated functional effects is calculated and compared with those calculated for SNPs in the same protein-protein interaction interface. Further, a model is conceived to explain the functional implications of SNPs based on the effects observed for known mutants. The results are visualized in a network format. The effects of nonsense mutations are discerned by comparing with deletion mutation studies and loss of interaction in the crystal structure. The present work not only integrates genomics, proteomics, and classical genetics with 'Structural Biology' but also helps to integrate it into a 'systems-level functional network'.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Datta Darshan V M
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - K Arvind Kumar
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
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9
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Zhao Q, Chen Y, Qu L. Combined Transcriptomic and Proteomic Analyses Reveal the Different Responses to UVA and UVB Radiation in Human Keratinocytes. Photochem Photobiol 2023; 99:137-152. [PMID: 35638308 DOI: 10.1111/php.13658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/25/2022] [Indexed: 01/25/2023]
Abstract
Ultraviolet (UV) radiation from sunlight is a major risk factor for many cutaneous pathologies including skin aging and cancers. Despite decades of research, the different responses to UVA and UVB in human keratinocytes have not been systemically investigated. Here, we performed multi-omics to characterize the common and different changes in gene transcription and protein expression after exposure to UVB and UVA, respectively. Keratinocyte cells, treated with or without UV, were analyzed by TMT-labeled MS/MS spectra and RNA-sequencing. A common set of genes/proteins was found to be impacted by both UVA and UVB and the other differential genes/proteins showed wavelength specificity. The common set of genes/proteins were mainly involved in keratinization, lipid metabolic processes and stimulus response. The UVB specifically responsive genes/proteins were mainly related to RNA processing, gene silencing regulation and cytoskeleton organization. The UVA specifically responsive genes/proteins were mainly involved in vesicle-mediated transport and oxygen-containing compound response. Meanwhile, the hub differential genes/proteins in each set were identified by protein-protein interaction networks and cluster analysis. This work provided a global view of the similar and differential molecular mechanisms of UVB- and UVA-induced cell damage in keratinocytes, which would be beneficial for further studies in the prevention or treatment of UV-related pathologies.
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Affiliation(s)
- Qinqin Zhao
- Characteristic Plants Research and Development Center, Botanee Research Institute, Shanghai Jiyan Bio-Pharmaceutical Development Co., Ltd., Shanghai, China
| | - Yueyue Chen
- Characteristic Plants Research and Development Center, Botanee Research Institute, Shanghai Jiyan Bio-Pharmaceutical Development Co., Ltd., Shanghai, China.,Yunnan Characteristic Plant Extraction Laboratory, Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Kunming, China
| | - Liping Qu
- Characteristic Plants Research and Development Center, Botanee Research Institute, Shanghai Jiyan Bio-Pharmaceutical Development Co., Ltd., Shanghai, China.,Yunnan Characteristic Plant Extraction Laboratory, Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Kunming, China.,Yunnan Botanee Bio-technology Group Co., Ltd., Kunming, China
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10
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Bohnsack KE, Kanwal N, Bohnsack MT. Prp43/DHX15 exemplify RNA helicase multifunctionality in the gene expression network. Nucleic Acids Res 2022; 50:9012-9022. [PMID: 35993807 PMCID: PMC9458436 DOI: 10.1093/nar/gkac687] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Dynamic regulation of RNA folding and structure is critical for the biogenesis and function of RNAs and ribonucleoprotein (RNP) complexes. Through their nucleotide triphosphate-dependent remodelling functions, RNA helicases are key modulators of RNA/RNP structure. While some RNA helicases are dedicated to a specific target RNA, others are multifunctional and engage numerous substrate RNAs in different aspects of RNA metabolism. The discovery of such multitasking RNA helicases raises the intriguing question of how these enzymes can act on diverse RNAs but also maintain specificity for their particular targets within the RNA-dense cellular environment. Furthermore, the identification of RNA helicases that sit at the nexus between different aspects of RNA metabolism raises the possibility that they mediate cross-regulation of different cellular processes. Prominent and extensively characterized multifunctional DEAH/RHA-box RNA helicases are DHX15 and its Saccharomyces cerevisiae (yeast) homologue Prp43. Due to their central roles in key cellular processes, these enzymes have also served as prototypes for mechanistic studies elucidating the mode of action of this type of enzyme. Here, we summarize the current knowledge on the structure, regulation and cellular functions of Prp43/DHX15, and discuss the general concept and implications of RNA helicase multifunctionality.
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Affiliation(s)
- Katherine E Bohnsack
- Correspondence may also be addressed to Katherine E. Bohnsack. Tel: +49 551 3969305; Fax: +49 551 395960;
| | - Nidhi Kanwal
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- To whom correspondence should be addressed. Tel: +49 551 395968; Fax: +49 551 395960;
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11
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Ho CH, Paolantoni C, Bawankar P, Tang Z, Brown S, Roignant J, Treisman JE. An exon junction complex-independent function of Barentsz in neuromuscular synapse growth. EMBO Rep 2022; 23:e53231. [PMID: 34726300 PMCID: PMC8728599 DOI: 10.15252/embr.202153231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 01/07/2023] Open
Abstract
The exon junction complex controls the translation, degradation, and localization of spliced mRNAs, and three of its core subunits also play a role in splicing. Here, we show that a fourth subunit, Barentsz, has distinct functions within and separate from the exon junction complex in Drosophila neuromuscular development. The distribution of mitochondria in larval muscles requires Barentsz as well as other exon junction complex subunits and is not rescued by a Barentsz transgene in which residues required for binding to the core subunit eIF4AIII are mutated. In contrast, interactions with the exon junction complex are not required for Barentsz to promote the growth of neuromuscular synapses. We find that the Activin ligand Dawdle shows reduced expression in barentsz mutants and acts downstream of Barentsz to control synapse growth. Both barentsz and dawdle are required in motor neurons, muscles, and glia for normal synapse growth, and exogenous Dawdle can rescue synapse growth in the absence of barentsz. These results identify a biological function for Barentsz that is independent of the exon junction complex.
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Affiliation(s)
- Cheuk Hei Ho
- Skirball Institute for Biomolecular Medicine and Department of Cell BiologyNYU School of MedicineNew YorkNYUSA
| | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Praveen Bawankar
- Institute of Pharmaceutical and Biomedical SciencesJohannes Gutenberg‐University MainzMainzGermany
| | - Zuojian Tang
- Center for Health Informatics and BioinformaticsNYU Langone Medical CenterNew YorkNYUSA
- Present address:
Computational Biology at Ridgefield US, Global Computational Biology and Digital ScienceBoehringer IngelheimRidgefieldCTUSA
| | - Stuart Brown
- Center for Health Informatics and BioinformaticsNYU Langone Medical CenterNew YorkNYUSA
- Present address:
ExxonMobil Corporate Strategic ResearchAnnandaleNJUSA
| | - Jean‐Yves Roignant
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- Institute of Pharmaceutical and Biomedical SciencesJohannes Gutenberg‐University MainzMainzGermany
| | - Jessica E Treisman
- Skirball Institute for Biomolecular Medicine and Department of Cell BiologyNYU School of MedicineNew YorkNYUSA
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12
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Covelo-Molares H, Obrdlik A, Poštulková I, Dohnálková M, Gregorová P, Ganji R, Potěšil D, Gawriyski L, Varjosalo M, Vaňáčová Š. The comprehensive interactomes of human adenosine RNA methyltransferases and demethylases reveal distinct functional and regulatory features. Nucleic Acids Res 2021; 49:10895-10910. [PMID: 34634806 PMCID: PMC8565353 DOI: 10.1093/nar/gkab900] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 12/26/2022] Open
Abstract
N6-methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am) are two abundant modifications found in mRNAs and ncRNAs that can regulate multiple aspects of RNA biology. They function mainly by regulating interactions with specific RNA-binding proteins. Both modifications are linked to development, disease and stress response. To date, three methyltransferases and two demethylases have been identified that modify adenosines in mammalian mRNAs. Here, we present a comprehensive analysis of the interactomes of these enzymes. PCIF1 protein network comprises mostly factors involved in nascent RNA synthesis by RNA polymerase II, whereas ALKBH5 is closely linked with most aspects of pre-mRNA processing and mRNA export to the cytoplasm. METTL16 resides in subcellular compartments co-inhabited by several other RNA modifiers and processing factors. FTO interactome positions this demethylase at a crossroad between RNA transcription, RNA processing and DNA replication and repair. Altogether, these enzymes share limited spatial interactomes, pointing to specific molecular mechanisms of their regulation.
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Affiliation(s)
- Helena Covelo-Molares
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Ales Obrdlik
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Ivana Poštulková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Michaela Dohnálková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Pavlína Gregorová
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Ranjani Ganji
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - David Potěšil
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Lisa Gawriyski
- Institute of Biotechnology & HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
| | - Markku Varjosalo
- Institute of Biotechnology & HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
| | - Štěpánka Vaňáčová
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
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13
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Ye J, She X, Liu Z, He Z, Gao X, Lu L, Liang R, Lin Y. Eukaryotic Initiation Factor 4A-3: A Review of Its Physiological Role and Involvement in Oncogenesis. Front Oncol 2021; 11:712045. [PMID: 34458150 PMCID: PMC8386015 DOI: 10.3389/fonc.2021.712045] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/27/2021] [Indexed: 12/30/2022] Open
Abstract
EIF4A3, a member of the DEAD-box protein family, is a nuclear matrix protein and a core component of the exon junction complex (EJC). Under physiological conditions, EIF4A3 participates in post-transcriptional gene regulation by promoting EJC control of precursor mRNA splicing, thus influencing nonsense-mediated mRNA decay. In addition, EIF4A3 maintains the expression of significant selenoproteins, including phospholipid hydroperoxide glutathione peroxidase and thioredoxin reductase 1. Several recent studies have shown that EIF4A3 promotes tumor growth in multiple human cancers such as glioblastoma, hepatocellular carcinoma, pancreatic cancer, and ovarian cancer. Molecular biology studies also showed that EIF4A3 is recruited by long non-coding RNAs to regulate the expression of certain proteins in tumors. However, its tumor-related functions and underlying mechanisms are not well understood. Here, we review the physiological role of EIF4A3 and the potential association between EIF4A3 overexpression and tumorigenesis. We also evaluate the protein's potential utility as a diagnosis biomarker, therapeutic target, and prognosis indicator, hoping to provide new ideas for future research.
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Affiliation(s)
- Jiazhou Ye
- Guangxi Medical University Cancer Hospital, Nanning, China
| | | | - Ziyu Liu
- Guangxi Medical University, Nanning, China
| | - Ziqin He
- Guangxi Medical University, Nanning, China
| | - Xing Gao
- Guangxi Medical University Cancer Hospital, Nanning, China
| | - Lu Lu
- Guangxi Medical University Cancer Hospital, Nanning, China
| | - Rong Liang
- Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yan Lin
- Guangxi Medical University Cancer Hospital, Nanning, China
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14
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Cheruiyot A, Li S, Nonavinkere Srivatsan S, Ahmed T, Chen Y, Lemacon DS, Li Y, Yang Z, Wadugu BA, Warner WA, Pruett-Miller SM, Obeng EA, Link DC, He D, Xiao F, Wang X, Bailis JM, Walter MJ, You Z. Nonsense-Mediated RNA Decay Is a Unique Vulnerability of Cancer Cells Harboring SF3B1 or U2AF1 Mutations. Cancer Res 2021; 81:4499-4513. [PMID: 34215620 DOI: 10.1158/0008-5472.can-20-4016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/26/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is recognized as an RNA surveillance pathway that targets aberrant mRNAs with premature translation termination codons (PTC) for degradation, however, its molecular mechanisms and roles in health and disease remain incompletely understood. In this study, we developed a novel reporter system to accurately measure NMD activity in individual cells. A genome-wide CRISPR-Cas9 knockout screen using this reporter system identified novel NMD-promoting factors, including multiple components of the SF3B complex and other U2 spliceosome factors. Interestingly, cells with mutations in the spliceosome genes SF3B1 and U2AF1, which are commonly found in myelodysplastic syndrome (MDS) and cancers, have overall attenuated NMD activity. Compared with wild-type (WT) cells, SF3B1- and U2AF1-mutant cells were more sensitive to NMD inhibition, a phenotype that is accompanied by elevated DNA replication obstruction, DNA damage, and chromosomal instability. Remarkably, the sensitivity of spliceosome mutant cells to NMD inhibition was rescued by overexpression of RNase H1, which removes R-loops in the genome. Together, these findings shed new light on the functional interplay between NMD and RNA splicing and suggest a novel synthetic lethal strategy for the treatment of MDS and cancers with spliceosome mutations. SIGNIFICANCE: This study has developed a novel NMD reporter system and identified a potential therapeutic approach of targeting the NMD pathway to treat cancer with spliceosome gene mutations.
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Affiliation(s)
- Abigael Cheruiyot
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Shan Li
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Sridhar Nonavinkere Srivatsan
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Tanzir Ahmed
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Yuhao Chen
- Department of Radiation Oncology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Delphine S Lemacon
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Ying Li
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.,Clinical Biobank, The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Zheng Yang
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.,Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, China
| | - Brian A Wadugu
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Wayne A Warner
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Esther A Obeng
- Molecular Oncology Division, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Daniel C Link
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Dalin He
- Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, China
| | - Fei Xiao
- Clinical Biobank, The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Xiaowei Wang
- Department of Radiation Oncology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | | | - Matthew J Walter
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Zhongsheng You
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.
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15
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Zhu Y, Ren C, Yang L. Effect of eukaryotic translation initiation factor 4A3 in malignant tumors. Oncol Lett 2021; 21:358. [PMID: 33747215 PMCID: PMC7967930 DOI: 10.3892/ol.2021.12619] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/19/2021] [Indexed: 01/03/2023] Open
Abstract
Eukaryotic translation initiation factor 4A3 (EIF4A3), a key component of the exon junction complex, is widely involved in RNA splicing and nonsense-mediated mRNA decay. EIF4A3 has also been reported to be involved in cell cycle regulation and apoptosis. Thus, EIF4A3 may serve as a pivotal regulatory factor involved in the occurrence and development of multiple diseases. Previous studies have demonstrated that EIF4A3 is mutated in neuromuscular degenerative lesions and is differentially expressed in several tumors, serving as a non-coding RNA binding protein to regulate its expression. In addition, studies have reported that inhibiting EIF4A3 can prevent tumor cell proliferation, thus, several researchers are trying to design and synthesize potent and selective EIF4A3 inhibitors. The present review summarizes the function of EIF4A3 in cell cycle and discusses it underlying molecular mechanisms that contribute to the occurrence of malignant diseases. In addition, EIF4A3 selective inhibitors, and bioinformatics analyses performed to analyze the expression and mutations of EIF4A3 in gynecological tumors and breast cancer, are also discussed.
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Affiliation(s)
- Yuanhang Zhu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Chenchen Ren
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Li Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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16
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Kwon OS, Mishra R, Safieddine A, Coleno E, Alasseur Q, Faucourt M, Barbosa I, Bertrand E, Spassky N, Le Hir H. Exon junction complex dependent mRNA localization is linked to centrosome organization during ciliogenesis. Nat Commun 2021; 12:1351. [PMID: 33649372 PMCID: PMC7921557 DOI: 10.1038/s41467-021-21590-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 01/14/2021] [Indexed: 12/17/2022] Open
Abstract
Exon junction complexes (EJCs) mark untranslated spliced mRNAs and are crucial for the mRNA lifecycle. An imbalance in EJC dosage alters mouse neural stem cell (mNSC) division and is linked to human neurodevelopmental disorders. In quiescent mNSC and immortalized human retinal pigment epithelial (RPE1) cells, centrioles form a basal body for ciliogenesis. Here, we report that EJCs accumulate at basal bodies of mNSC or RPE1 cells and decline when these cells differentiate or resume growth. A high-throughput smFISH screen identifies two transcripts accumulating at centrosomes in quiescent cells, NIN and BICD2. In contrast to BICD2, the localization of NIN transcripts is EJC-dependent. NIN mRNA encodes a core component of centrosomes required for microtubule nucleation and anchoring. We find that EJC down-regulation impairs both pericentriolar material organization and ciliogenesis. An EJC-dependent mRNA trafficking towards centrosome and basal bodies might contribute to proper mNSC division and brain development. Exon junction complexes (EJCs) that mark untranslated mRNA are involved in transport, translation and nonsense-mediated mRNA decay. Here the authors show centrosomal localization of EJCs which appears to be required for both the localization of NIN mRNA around centrosomes and ciliogenesis.
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Affiliation(s)
- Oh Sung Kwon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Rahul Mishra
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Adham Safieddine
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.,Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Emeline Coleno
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.,Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Quentin Alasseur
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Marion Faucourt
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Isabelle Barbosa
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.,Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Nathalie Spassky
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.
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17
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Abstract
The passage of mRNAs through the nuclear pores into the cytoplasm is essential in all eukaryotes. For regulation, mRNA export is tightly connected to the full machinery of nuclear mRNA processing, starting at transcription. Export competence of pre-mRNAs gradually increases by both transient and permanent interactions with multiple RNA processing and export factors. mRNA export is best understood in opisthokonts, with limited knowledge in plants and protozoa. Here, I review and compare nuclear mRNA processing and export between opisthokonts and Trypanosoma brucei. The parasite has many unusual features in nuclear mRNA processing, such as polycistronic transcription and trans-splicing. It lacks several nuclear complexes and nuclear-pore-associated proteins that in opisthokonts play major roles in mRNA export. As a consequence, trypanosome mRNA export control is not tight and export can even start co-transcriptionally. Whether trypanosomes regulate mRNA export at all, or whether leakage of immature mRNA to the cytoplasm is kept to a low level by a fast kinetics of mRNA processing remains to be investigated. mRNA export had to be present in the last common ancestor of eukaryotes. Trypanosomes are evolutionary very distant from opisthokonts and a comparison helps understanding the evolution of mRNA export.
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18
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Wong ML, Arcos-Burgos M, Liu S, Licinio AW, Yu C, Chin EWM, Yao WD, Lu XY, Bornstein SR, Licinio J. Rare Functional Variants Associated with Antidepressant Remission in Mexican-Americans: Short title: Antidepressant remission and pharmacogenetics in Mexican-Americans. J Affect Disord 2021; 279:491-500. [PMID: 33128939 PMCID: PMC7953425 DOI: 10.1016/j.jad.2020.10.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 08/24/2020] [Accepted: 10/11/2020] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Rare genetic functional variants can contribute to 30-40% of functional variability in genes relevant to drug action. Therefore, we investigated the role of rare functional variants in antidepressant response. METHOD Mexican-American individuals meeting the Diagnostic and Statistical Manual-IV criteria for major depressive disorder (MDD) participated in a prospective randomized, double-blind study with desipramine or fluoxetine. The rare variant analysis was performed using whole-exome genotyping data. Network and pathway analyses were carried out with the list of significant genes. RESULTS The Kernel-Based Adaptive Cluster method identified functional rare variants in 35 genes significantly associated with treatment remission (False discovery rate, FDR <0.01). Pathway analysis of these genes supports the involvement of the following gene ontology processes: olfactory/sensory transduction, regulation of response to cytokine stimulus, and meiotic cell cycleprocess. LIMITATIONS Our study did not have a placebo arm. We were not able to use antidepressant blood level as a covariate. Our study is based on a small sample size of only 65 Mexican-American individuals. Further studies using larger cohorts are warranted. CONCLUSION Our data identified several rare functional variants in antidepressant drug response in MDD patients. These have the potential to serve as genetic markers for predicting drug response. TRIAL REGISTRATION ClinicalTrials.gov NCT00265291.
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Affiliation(s)
- Ma-Li Wong
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, USA; Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY, USA; Mind & Brain Theme, South Australian Health and Medical Research Institute Adelaide, South Australia, Australia; Department of Psychiatry, Flinders University College of Medicine and Public Health, Bedford Park, South Australia, Australia.
| | - Mauricio Arcos-Burgos
- Grupo de Investigación en Psiquiatría, Departamento de Psiquiatría, Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellin, Antioquia, Colombia
| | - Sha Liu
- Mind & Brain Theme, South Australian Health and Medical Research Institute Adelaide, South Australia, Australia
| | - Alice W Licinio
- Mind & Brain Theme, South Australian Health and Medical Research Institute Adelaide, South Australia, Australia
| | - Chenglong Yu
- Mind & Brain Theme, South Australian Health and Medical Research Institute Adelaide, South Australia, Australia; Department of Psychiatry, Flinders University College of Medicine and Public Health, Bedford Park, South Australia, Australia
| | - Eunice W M Chin
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Wei-Dong Yao
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, USA; Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Xin-Yun Lu
- Department of Neuroscience & Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Stefan R Bornstein
- Medical Clinic III, Carl Gustav Carus University Hospital, Dresden University of Technology, Dresden, Germany
| | - Julio Licinio
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, USA; Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY, USA; Mind & Brain Theme, South Australian Health and Medical Research Institute Adelaide, South Australia, Australia; Department of Psychiatry, Flinders University College of Medicine and Public Health, Bedford Park, South Australia, Australia.
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19
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Gerbracht JV, Boehm V, Britto-Borges T, Kallabis S, Wiederstein JL, Ciriello S, Aschemeier DU, Krüger M, Frese CK, Altmüller J, Dieterich C, Gehring NH. CASC3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex. Nucleic Acids Res 2020; 48:8626-8644. [PMID: 32621609 PMCID: PMC7470949 DOI: 10.1093/nar/gkaa564] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/20/2020] [Accepted: 07/01/2020] [Indexed: 01/08/2023] Open
Abstract
The exon junction complex (EJC) is an essential constituent and regulator of spliced messenger ribonucleoprotein particles (mRNPs) in metazoans. As a core component of the EJC, CASC3 was described to be pivotal for EJC-dependent nuclear and cytoplasmic processes. However, recent evidence suggests that CASC3 functions differently from other EJC core proteins. Here, we have established human CASC3 knockout cell lines to elucidate the cellular role of CASC3. In the knockout cells, overall EJC composition and EJC-dependent splicing are unchanged. A transcriptome-wide analysis reveals that hundreds of mRNA isoforms targeted by nonsense-mediated decay (NMD) are upregulated. Mechanistically, recruiting CASC3 to reporter mRNAs by direct tethering or via binding to the EJC stimulates mRNA decay and endonucleolytic cleavage at the termination codon. Building on existing EJC-NMD models, we propose that CASC3 equips the EJC with the persisting ability to communicate with the NMD machinery in the cytoplasm. Collectively, our results characterize CASC3 as a peripheral EJC protein that tailors the transcriptome by promoting the degradation of EJC-dependent NMD substrates.
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Affiliation(s)
| | - Volker Boehm
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Thiago Britto-Borges
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, 69120 Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Sebastian Kallabis
- CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Janica L Wiederstein
- CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Simona Ciriello
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | | | - Marcus Krüger
- CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Christian K Frese
- CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50937 Cologne, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, 69120 Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50937 Cologne, Germany
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20
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Obrdlik A, Lin G, Haberman N, Ule J, Ephrussi A. The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila. Cell Rep 2020; 28:1219-1236.e11. [PMID: 31365866 DOI: 10.1016/j.celrep.2019.06.088] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/30/2019] [Accepted: 06/24/2019] [Indexed: 12/27/2022] Open
Abstract
Exon junction complex (EJC) assembles after splicing at specific positions upstream of exon-exon junctions in mRNAs of all higher eukaryotes, affecting major regulatory events. In mammalian cell cytoplasm, EJC is essential for efficient RNA surveillance, while in Drosophila, EJC is essential for localization of oskar mRNA. Here we developed a method for isolation of protein complexes and associated RNA targets (ipaRt) to explore the EJC RNA-binding landscape in a transcriptome-wide manner in adult Drosophila. We find the EJC at canonical positions, preferably on mRNAs from genes comprising multiple splice sites and long introns. Moreover, EJC occupancy is highest at junctions adjacent to strong splice sites, CG-rich hexamers, and RNA structures. Highly occupied mRNAs tend to be maternally localized and derive from genes involved in differentiation or development. These modalities, which have not been reported in mammals, specify EJC assembly on a biologically coherent set of transcripts in Drosophila.
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Affiliation(s)
- Ales Obrdlik
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Gen Lin
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Nejc Haberman
- Department for Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Jernej Ule
- Department for Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK; The Francis Crick Institute, London NW1 1AT, UK
| | - Anne Ephrussi
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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21
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Busetto V, Barbosa I, Basquin J, Marquenet É, Hocq R, Hennion M, Paternina JA, Namane A, Conti E, Bensaude O, Le Hir H. Structural and functional insights into CWC27/CWC22 heterodimer linking the exon junction complex to spliceosomes. Nucleic Acids Res 2020; 48:5670-5683. [PMID: 32329775 PMCID: PMC7261170 DOI: 10.1093/nar/gkaa267] [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: 02/13/2020] [Revised: 04/01/2020] [Accepted: 04/22/2020] [Indexed: 11/22/2022] Open
Abstract
Human CWC27 is an uncharacterized splicing factor and mutations in its gene are linked to retinal degeneration and other developmental defects. We identify the splicing factor CWC22 as the major CWC27 partner. Both CWC27 and CWC22 are present in published Bact spliceosome structures, but no interacting domains are visible. Here, the structure of a CWC27/CWC22 heterodimer bound to the exon junction complex (EJC) core component eIF4A3 is solved at 3Å-resolution. According to spliceosomal structures, the EJC is recruited in the C complex, once CWC27 has left. Our 3D structure of the eIF4A3/CWC22/CWC27 complex is compatible with the Bact spliceosome structure but not with that of the C complex, where a CWC27 loop would clash with the EJC core subunit Y14. A CWC27/CWC22 building block might thus form an intermediate landing platform for eIF4A3 onto the Bact complex prior to its conversion into C complex. Knock-down of either CWC27 or CWC22 in immortalized retinal pigment epithelial cells affects numerous common genes, indicating that these proteins cooperate, targeting the same pathways. As the most up-regulated genes encode factors involved in inflammation, our findings suggest a possible link to the retinal degeneration associated with CWC27 deficiencies.
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Affiliation(s)
- Virginia Busetto
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
| | - Isabelle Barbosa
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
| | - Jérôme Basquin
- Department of Structural Cell Biology, MPI of Biochemistry, Munich, Germany
| | - Émelie Marquenet
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
| | - Rémi Hocq
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
| | - Magali Hennion
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
| | - Janio Antonio Paternina
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
| | - Abdelkader Namane
- Génétique des Interactions Macromoléculaires, Genomes and Genetics Department, Institut Pasteur, 25-28 rue du docteur Roux 75015 Paris, France
| | - Elena Conti
- Department of Structural Cell Biology, MPI of Biochemistry, Munich, Germany
| | - Olivier Bensaude
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
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22
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A Day in the Life of the Exon Junction Complex. Biomolecules 2020; 10:biom10060866. [PMID: 32517083 PMCID: PMC7355637 DOI: 10.3390/biom10060866] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 12/12/2022] Open
Abstract
The exon junction complex (EJC) is an abundant messenger ribonucleoprotein (mRNP) component that is assembled during splicing and binds to mRNAs upstream of exon-exon junctions. EJCs accompany the mRNA during its entire life in the nucleus and the cytoplasm and communicate the information about the splicing process and the position of introns. Specifically, the EJC’s core components and its associated proteins regulate different steps of gene expression, including pre-mRNA splicing, mRNA export, translation, and nonsense-mediated mRNA decay (NMD). This review summarizes the most important functions and main protagonists in the life of the EJC. It also provides an overview of the latest findings on the assembly, composition and molecular activities of the EJC and presents them in the chronological order, in which they play a role in the EJC’s life cycle.
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23
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eIF4A3 Phosphorylation by CDKs Affects NMD during the Cell Cycle. Cell Rep 2020; 26:2126-2139.e9. [PMID: 30784594 DOI: 10.1016/j.celrep.2019.01.101] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/16/2018] [Accepted: 01/25/2019] [Indexed: 12/24/2022] Open
Abstract
Exon junction complexes (EJCs) loaded onto spliced mRNAs during splicing serve as molecular markers for various post-transcriptional gene-regulatory processes, including nonsense-mediated mRNA decay (NMD). Although the composition and structure of EJCs are well characterized, the mechanism regulating EJC deposition remains unknown. Here we find that threonine 163 (T163) within the RNA-binding motif of eIF4A3 (a core EJC component) is phosphorylated by cyclin-dependent protein kinases 1 and 2 in a cell cycle-dependent manner. T163 phosphorylation hinders binding of eIF4A3 to spliced mRNAs and other EJC components. Instead, it promotes association of eIF4A3 with CWC22, which guides eIF4A3 to an active spliceosome. These molecular events ensure the fidelity of specific deposition of the EJC ∼20-24 nt upstream of an exon-exon junction. Accordingly, NMD is affected by T163 phosphorylation. Collectively, our data provide evidence that T163 phosphorylation affects EJC formation and, consequently, NMD efficiency in a cell cycle-dependent manner.
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24
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Kurosaki T, Popp MW, Maquat LE. Quality and quantity control of gene expression by nonsense-mediated mRNA decay. Nat Rev Mol Cell Biol 2020; 20:406-420. [PMID: 30992545 DOI: 10.1038/s41580-019-0126-2] [Citation(s) in RCA: 421] [Impact Index Per Article: 105.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is one of the best characterized and most evolutionarily conserved cellular quality control mechanisms. Although NMD was first found to target one-third of mutated, disease-causing mRNAs, it is now known to also target ~10% of unmutated mammalian mRNAs to facilitate appropriate cellular responses - adaptation, differentiation or death - to environmental changes. Mutations in NMD genes in humans are associated with intellectual disability and cancer. In this Review, we discuss how NMD serves multiple purposes in human cells by degrading both mutated mRNAs to protect the integrity of the transcriptome and normal mRNAs to control the quantities of unmutated transcripts.
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.,Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Maximilian W Popp
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.,Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA. .,Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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25
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Zhu D, Mao F, Tian Y, Lin X, Gu L, Gu H, Qu LJ, Wu Y, Wu Z. The Features and Regulation of Co-transcriptional Splicing in Arabidopsis. MOLECULAR PLANT 2020; 13:278-294. [PMID: 31760161 DOI: 10.1016/j.molp.2019.11.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 09/29/2019] [Accepted: 11/15/2019] [Indexed: 05/20/2023]
Abstract
Precursor mRNA (pre-mRNA) splicing is essential for gene expression in most eukaryotic organisms. Previous studies from mammals, Drosophila, and yeast show that the majority of splicing events occurs co-transcriptionally. In plants, however, the features of co-transcriptional splicing (CTS) and its regulation still remain largely unknown. Here, we used chromatin-bound RNA sequencing to study CTS in Arabidopsis thaliana. We found that CTS is widespread in Arabidopsis seedlings, with a large proportion of alternative splicing events determined co-transcriptionally. CTS efficiency correlated with gene expression level, the chromatin landscape and, most surprisingly, the number of introns and exons of individual genes, but is independent of gene length. In combination with enhanced crosslinking and immunoprecipitation sequencing analysis, we further showed that the hnRNP-like proteins RZ-1B and RZ-1C promote efficient CTS globally through direct binding, frequently to exonic sequences. Notably, this general effect of RZ-1B/1C on splicing promotion is mainly observed at the chromatin level, not at the mRNA level. RZ-1C promotes CTS of multiple-exon genes in association with its binding to regions both proximal and distal to the regulated introns. We propose that RZ-1C promotes efficient CTS of genes with multiple exons through cooperative interactions with many exons, introns, and splicing factors. Our work thus reveals important features of CTS in plants and provides methodologies for the investigation of CTS and RNA-binding proteins in plants.
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Affiliation(s)
- Danling Zhu
- SUSTech-PKU Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Fei Mao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Yuanchun Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Xiaoya Lin
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hongya Gu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Li-Jia Qu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China.
| | - Zhe Wu
- SUSTech-PKU Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China.
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26
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Wu X, Zhao W, Cui Q, Zhou Y. Computational screening of potential regulators for mRNA-protein expression level discrepancy. Biochem Biophys Res Commun 2020; 523:196-201. [DOI: 10.1016/j.bbrc.2019.12.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 12/10/2019] [Indexed: 01/05/2023]
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27
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Abstract
The spliceosome removes introns from messenger RNA precursors (pre-mRNA). Decades of biochemistry and genetics combined with recent structural studies of the spliceosome have produced a detailed view of the mechanism of splicing. In this review, we aim to make this mechanism understandable and provide several videos of the spliceosome in action to illustrate the intricate choreography of splicing. The U1 and U2 small nuclear ribonucleoproteins (snRNPs) mark an intron and recruit the U4/U6.U5 tri-snRNP. Transfer of the 5' splice site (5'SS) from U1 to U6 snRNA triggers unwinding of U6 snRNA from U4 snRNA. U6 folds with U2 snRNA into an RNA-based active site that positions the 5'SS at two catalytic metal ions. The branch point (BP) adenosine attacks the 5'SS, producing a free 5' exon. Removal of the BP adenosine from the active site allows the 3'SS to bind, so that the 5' exon attacks the 3'SS to produce mature mRNA and an excised lariat intron.
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Affiliation(s)
- Max E Wilkinson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; ,
| | - Clément Charenton
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; ,
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; ,
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28
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Kastner B, Will CL, Stark H, Lührmann R. Structural Insights into Nuclear pre-mRNA Splicing in Higher Eukaryotes. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032417. [PMID: 30765414 DOI: 10.1101/cshperspect.a032417] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The spliceosome is a highly complex, dynamic ribonucleoprotein molecular machine that undergoes numerous structural and compositional rearrangements that lead to the formation of its active site. Recent advances in cyroelectron microscopy (cryo-EM) have provided a plethora of near-atomic structural information about the inner workings of the spliceosome. Aided by previous biochemical, structural, and functional studies, cryo-EM has confirmed or provided a structural basis for most of the prevailing models of spliceosome function, but at the same time allowed novel insights into splicing catalysis and the intriguing dynamics of the spliceosome. The mechanism of pre-mRNA splicing is highly conserved between humans and yeast, but the compositional dynamics and ribonucleoprotein (RNP) remodeling of the human spliceosome are more complex. Here, we summarize recent advances in our understanding of the molecular architecture of the human spliceosome, highlighting differences between the human and yeast splicing machineries.
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Affiliation(s)
- Berthold Kastner
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
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29
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Bartkowska K, Tepper B, Turlejski K, Djavadian RL. Roles of the exon junction complex components in the central nervous system: a mini review. Rev Neurosci 2019; 29:817-824. [PMID: 29791316 DOI: 10.1515/revneuro-2017-0113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 03/22/2018] [Indexed: 01/02/2023]
Abstract
The exon junction complex (EJC) consists of four core proteins: Magoh, RNA-binding motif 8A (Rbm8a, also known as Y14), eukaryotic initiation factor 4A3 (eIF4A3, also known as DDX48), and metastatic lymph node 51 (MLN51, also known as Casc3 or Barentsz), which are involved in the regulation of many processes occurring between gene transcription and protein translation. Its main role is to assemble into spliceosomes at the exon-exon junction of mRNA during splicing. It is, therefore, a range of functions concerning post-splicing events such as mRNA translocation, translation, and nonsense-mediated mRNA decay (NMD). Apart from this, proteins of the EJC control the splicing of specific pre-mRNAs, for example, splicing of the mapk transcript. Recent studies support essential functions of EJC proteins in oocytes and, after fertilization, in all stages of zygote development, as well as the growth of the embryo, including the development of the nervous system. During the development of the central nervous system (CNS), the EJC controls mitosis, regulating both symmetric and asymmetric cell divisions. Reduced levels of EJC components cause microcephaly. In the adult brain, Y14 and eIF4A3 appear to be involved in synaptic plasticity and in learning and memory. In this review, we focus on the involvement of EJC components in brain development and its functioning under normal conditions.
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Affiliation(s)
- Katarzyna Bartkowska
- Department of Molecular and Cellular Biology, Nencki Institute of Experimental Biology Polish Academy of Sciences, Warsaw, Poland
| | - Beata Tepper
- Department of Molecular and Cellular Biology, Nencki Institute of Experimental Biology Polish Academy of Sciences, Warsaw, Poland
| | - Kris Turlejski
- Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszynski University, Warsaw, Poland
| | - Ruzanna L Djavadian
- Department of Molecular and Cellular Biology, Nencki Institute of Experimental Biology Polish Academy of Sciences, Warsaw 02-093, Poland
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30
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Chung CS, Tseng CK, Lai YH, Wang HF, Newman AJ, Cheng SC. Dynamic protein-RNA interactions in mediating splicing catalysis. Nucleic Acids Res 2019; 47:899-910. [PMID: 30395327 PMCID: PMC6344849 DOI: 10.1093/nar/gky1089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/19/2018] [Indexed: 11/16/2022] Open
Abstract
The spliceosome is assembled via sequential interactions of pre-mRNA with five small nuclear RNAs and many proteins. Recent determination of cryo-EM structures for several spliceosomal complexes has provided deep insights into interactions between spliceosomal components and structural changes of the spliceosome between steps, but information on how the proteins interact with pre-mRNA to mediate the reaction is scarce. By systematic analysis of proteins interacting with the splice sites (SSs), we have identified many previously unknown interactions of spliceosomal components with the pre-mRNA. Prp8 directly binds over the 5′SS and the branch site (BS) for the first catalytic step, and the 5′SS and 3′SS for the second step. Switching the Prp8 interaction from the BS to the 3′SS requires Slu7, which interacts dynamically with pre-mRNA first, and then interacts stably with the 3′-exon after Prp16-mediated spliceosome remodeling. Our results suggest that Prp8 plays a key role in positioning the 5′SS and 3′SS, facilitated by Slu7 through interactions with Prp8 and substrate RNA to advance exon ligation. We also provide evidence that Prp16 first docks on the intron 3′ tail, then translocates in the 3′ to 5′ direction on remodeling the spliceosome.
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Affiliation(s)
- Che-Sheng Chung
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Chi-Kang Tseng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Yung-Hua Lai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China.,Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan 112, Republic of China
| | - Hui-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China.,Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan 112, Republic of China
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Soo-Chen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
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31
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Structures of the human spliceosomes before and after release of the ligated exon. Cell Res 2019; 29:274-285. [PMID: 30728453 PMCID: PMC6461851 DOI: 10.1038/s41422-019-0143-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 01/14/2019] [Indexed: 11/08/2022] Open
Abstract
Pre-mRNA splicing is executed by the spliceosome, which has eight major functional states each with distinct composition. Five of these eight human spliceosomal complexes, all preceding exon ligation, have been structurally characterized. In this study, we report the cryo-electron microscopy structures of the human post-catalytic spliceosome (P complex) and intron lariat spliceosome (ILS) at average resolutions of 3.0 and 2.9 Å, respectively. In the P complex, the ligated exon remains anchored to loop I of U5 small nuclear RNA, and the 3′-splice site is recognized by the junction between the 5′-splice site and the branch point sequence. The ATPase/helicase Prp22, along with the ligated exon and eight other proteins, are dissociated in the P-to-ILS transition. Intriguingly, the ILS complex exists in two distinct conformations, one with the ATPase/helicase Prp43 and one without. Comparison of these three late-stage human spliceosomes reveals mechanistic insights into exon release and spliceosome disassembly.
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32
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Promoter-proximal pausing mediated by the exon junction complex regulates splicing. Nat Commun 2019; 10:521. [PMID: 30705266 PMCID: PMC6355915 DOI: 10.1038/s41467-019-08381-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 01/04/2019] [Indexed: 02/08/2023] Open
Abstract
Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread transcriptional regulatory step across metazoans. Here we find that the nuclear exon junction complex (pre-EJC) is a critical and conserved regulator of this process. Depletion of pre-EJC subunits leads to a global decrease in Pol II pausing and to premature entry into elongation. This effect occurs, at least in part, via non-canonical recruitment of pre-EJC components at promoters. Failure to recruit the pre-EJC at promoters results in increased binding of the positive transcription elongation complex (P-TEFb) and in enhanced Pol II release. Notably, restoring pausing is sufficient to rescue exon skipping and the photoreceptor differentiation defect associated with depletion of pre-EJC components in vivo. We propose that the pre-EJC serves as an early transcriptional checkpoint to prevent premature entry into elongation, ensuring proper recruitment of RNA processing components that are necessary for exon definition.
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33
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Exon junction complex components Y14 and Mago still play a role in budding yeast. Sci Rep 2019; 9:849. [PMID: 30696855 PMCID: PMC6351623 DOI: 10.1038/s41598-018-36785-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/26/2018] [Indexed: 11/26/2022] Open
Abstract
Since their divergence from Pezizomycotina, the mRNA metabolism of budding yeasts have undergone regressive evolution. With the dramatic loss of introns, a number of quality control mechanisms have been simplified or lost during evolution, such as the exon junction complex (EJC). We report the identification of the core EJC components, Mago, Y14, and eIF4A3, in at least seven Saccharomycotina species, including Yarrowia lipolytica. Peripheral factors that join EJC, either to mediate its assembly (Ibp160 or Cwc22), or trigger downstream processes, are present in the same species, forming an evolutionary package. Co-immunoprecipitation studies in Y. lipolytica showed that Mago and Y14 have retained the capacity to form heterodimers, which successively bind to the peripheral factors Upf3, Aly/REF, and Pym. Phenotypes and RNA-Seq analysis of EJC mutants showed evidence of Y14 and Mago involvement in mRNA metabolism. Differences in unspliced mRNA levels suggest that Y14 binding either interferes with pre-mRNA splicing or retains mRNA in the nucleus before their export and translation. These findings indicate that yeast could be a relevant model for understanding EJC function.
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34
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Boehm V, Britto-Borges T, Steckelberg AL, Singh KK, Gerbracht JV, Gueney E, Blazquez L, Altmüller J, Dieterich C, Gehring NH. Exon Junction Complexes Suppress Spurious Splice Sites to Safeguard Transcriptome Integrity. Mol Cell 2018; 72:482-495.e7. [DOI: 10.1016/j.molcel.2018.08.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 07/24/2018] [Accepted: 08/20/2018] [Indexed: 12/14/2022]
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35
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Kobayashi M, Zochodne DW. Diabetic neuropathy and the sensory neuron: New aspects of pathogenesis and their treatment implications. J Diabetes Investig 2018; 9:1239-1254. [PMID: 29533535 PMCID: PMC6215951 DOI: 10.1111/jdi.12833] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/20/2018] [Accepted: 03/03/2018] [Indexed: 12/17/2022] Open
Abstract
Diabetic polyneuropathy (DPN) continues to be generally considered as a "microvascular" complication of diabetes mellitus alongside nephropathy and retinopathy. The microvascular hypothesis, however, might be tempered by the concept that diabetes directly targets dorsal root ganglion sensory neurons. This neuron-specific concept, supported by accumulating evidence, might account for important features of DPN, such as its early sensory neuron degeneration. Diabetic sensory neurons develop neuronal atrophy alongside a series of messenger ribonucleic acid (RNA) changes related to declines in structural proteins, increases in heat shock protein, increases in the receptor for advanced glycation end-products, declines in growth factor signaling and other changes. Insulin is recognized as a potent neurotrophic factor, and insulin ligation enhances neurite outgrowth through activation of the phosphoinositide 3-kinase-protein kinase B pathway within sensory neurons and attenuates phenotypic features of experimental DPN. Several interventions, including glucagon-like peptide-1 agonism, and phosphatase and tensin homolog inhibition to activate growth signals in sensory neurons, or heat shock protein overexpression, prevent or reverse neuropathic abnormalities in experimental DPN. Diabetic sensory neurons show a unique pattern of microRNA alterations, a key element of messenger RNA silencing. For example, let-7i is widely expressed in sensory neurons, supports their growth and is depleted in experimental DPN; its replenishment improves features of DPN models. Finally, impairment of pre-messenger RNA splicing in diabetic sensory neurons including abnormal nuclear RNA metabolism and structure with loss of survival motor neuron protein, a neuron survival molecule, and overexpression of CWC22, a splicing factor, offer further novel insights. The present review addresses these new aspects of DPN sensory neurodegeneration.
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Affiliation(s)
- Masaki Kobayashi
- Department of Neurology and Neurological ScienceGraduate School of MedicineTokyo Medical and Dental UniversityTokyoJapan
- Department of NeurologyYokufukai Geriatric HospitalTokyoJapan
| | - Douglas W Zochodne
- Division of Neurology and Department of MedicineNeuroscience and Mental Health InstituteFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlbertaCanada
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36
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Baird TD, Cheng KCC, Chen YC, Buehler E, Martin SE, Inglese J, Hogg JR. ICE1 promotes the link between splicing and nonsense-mediated mRNA decay. eLife 2018. [PMID: 29528287 PMCID: PMC5896957 DOI: 10.7554/elife.33178] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The nonsense-mediated mRNA decay (NMD) pathway detects aberrant transcripts containing premature termination codons (PTCs) and regulates expression of 5–10% of non-aberrant human mRNAs. To date, most proteins involved in NMD have been identified by genetic screens in model organisms; however, the increased complexity of gene expression regulation in human cells suggests that additional proteins may participate in the human NMD pathway. To identify proteins required for NMD, we performed a genome-wide RNAi screen against >21,000 genes. Canonical members of the NMD pathway were highly enriched as top hits in the siRNA screen, along with numerous candidate NMD factors, including the conserved ICE1/KIAA0947 protein. RNAseq studies reveal that depletion of ICE1 globally enhances accumulation and stability of NMD-target mRNAs. Further, our data suggest that ICE1 uses a putative MIF4G domain to interact with exon junction complex (EJC) proteins and promotes the association of the NMD protein UPF3B with the EJC. The DNA in our cells contains the hereditary information that makes each of us unique. Molecules called mRNAs are copies of this information and are used as templates for making proteins. When a strand of incorrectly copied mRNA, or one including errors from the original DNA template, is recognized, our cells destroy the mRNA to prevent it from producing a damaged protein. Organisms from yeast to humans have evolved a mechanism for finding and destroying faulty mRNAs, called mRNA surveillance. Animals are particularly reliant on mRNA surveillance, as their proteins are often made from cutting and pasting together mRNA from different portions of DNA, in a process known as splicing. Despite being a vital process, we still lack a good understanding of how mRNA surveillance works. Now, Baird et al. used human kidney cells that produced an error-containing mRNA that could be tracked. To investigate how efficient RNA surveillance is under different conditions, the levels of individual proteins were reduced one at a time. By tracking the amount of faulty mRNA, it was possible to find out if a single protein plays a role in human mRNA surveillance. If the number of faulty mRNAs is high when a protein is reduced, it suggests that this protein may be involved in mRNA surveillance. Baird et al. screened more than 21,000 proteins, the majority of proteins made in human cells. Many of the proteins that stood out as important in mRNA surveillance were the ones already known to be relevant in yeast and worm cells. But the experiments also identified new proteins that appear to play a role specifically in human RNA surveillance. One of the proteins, ICE1, is essential for the relationship between mRNA splicing and mRNA surveillance. Without ICE1, the mRNA surveillance machinery can no longer find and destroy faulty mRNAs. Nearly one-third of genetic diseases are caused by mutations that result in faulty mRNAs, which can be detected by mRNA surveillance pathways. Depending on the disease, destroying these error-containing mRNAs can either improve or worsen disease symptoms. A better understanding of the factors that control human RNA surveillance could one day help to develop treatments that affect mRNA surveillance to improve disease outcomes.
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Affiliation(s)
- Thomas D Baird
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Ken Chih-Chien Cheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, United States
| | - Yu-Chi Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, United States
| | - Eugen Buehler
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, United States
| | - Scott E Martin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, United States
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, United States
| | - J Robert Hogg
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
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37
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The exon junction complex: structural insights into a faithful companion of mammalian mRNPs. Biochem Soc Trans 2018; 46:153-161. [PMID: 29351963 DOI: 10.1042/bst20170059] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/13/2017] [Accepted: 12/18/2017] [Indexed: 12/21/2022]
Abstract
During splicing, the exon junction complex (EJC) is deposited upstream of exon-exon boundaries. The EJC and its peripheral bound proteins play an essential role in mediating mRNA export, translation and turnover. However, the exact sequence of EJC assembly and the involved factors during splicing remain elusive. Recently published structures of the human C* spliceosome clarified the position of the EJC at this phase of splicing and have given insight into previously unidentified interactions between the EJC and spliceosomal proteins. Here, these new observations are presented and the significance for EJC assembly is discussed. Furthermore, the vast landscape of EJC interacting proteins and their manifold functions are described. Finally, the factors involved in EJC disassembly and recycling are recapitulated. This review aims to integrate structural, biochemical and physiological data to obtain a comprehensive picture of EJC components during the lifetime of the EJC.
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38
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C-terminal short arginine/serine repeat sequence-dependent regulation of Y14 (RBM8A) localization. Sci Rep 2018; 8:612. [PMID: 29330450 PMCID: PMC5766523 DOI: 10.1038/s41598-017-18765-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/15/2017] [Indexed: 01/01/2023] Open
Abstract
Y14 (RBM8A) is an RNA recognition motif-containing protein that forms heterodimers with MAGOH and serves as a core factor of the RNA surveillance machinery for the exon junction complex (EJC). The role of the Y14 C-terminal serine/arginine (RS) repeat-containing region, which has been reported to undergo modifications such as phosphorylation and methylation, has not been sufficiently investigated. Thus, we aimed to explore the functional significance of the Y14 C-terminal region. Deletion or dephosphorylation mimic mutants of the C-terminal region showed a shift in localization from the nucleoplasmic region; in addition, the C-terminal RS repeat-containing sequence itself exhibited the potential for nucleolar localization. Additionally, the regulation of Y14 localization by the C-terminal region was further found to be exquisitely controlled by MAGOH binding. Cumulatively, our findings, which demonstrated that Y14 localization is regulated not only by the previously reported N-terminal localization signal but also by the C-terminal RS repeat-containing region through phosphorylation and MAGOH binding to Y14, provide new insights for the mechanism of localization of short RS repeat-containing proteins.
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Kobayashi M, Chandrasekhar A, Cheng C, Martinez JA, Ng H, de la Hoz C, Zochodne DW. Diabetic polyneuropathy, sensory neurons, nuclear structure and spliceosome alterations: a role for CWC22. Dis Model Mech 2017; 10:215-224. [PMID: 28250049 PMCID: PMC5374325 DOI: 10.1242/dmm.028225] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 12/23/2016] [Indexed: 12/31/2022] Open
Abstract
Unique deficits in the function of adult sensory neurons as part of their early neurodegeneration might account for progressive polyneuropathy during chronic diabetes mellitus. Here, we provide structural and functional evidence for aberrant pre-mRNA splicing in a chronic type 1 model of experimental diabetic polyneuropathy (DPN). Cajal bodies (CBs), unique nuclear substructures involved in RNA splicing, increased in number in diabetic sensory neurons, but their expected colocalization with survival motor neuron (SMN) proteins was reduced - a mislocalization described in motor neurons of spinal muscular atrophy. Small nuclear ribonucleoprotein particles (snRNPs), also participants in the spliceosome, had abnormal multiple nuclear foci unassociated with CBs, and their associated snRNAs were reduced. CWC22, a key spliceosome protein, was aberrantly upregulated in diabetic dorsal root ganglia (DRG), and impaired neuronal function. CWC22 attenuated sensory neuron plasticity, with knockdown in vitro enhancing their neurite outgrowth. Further, axonal delivery of CWC22 siRNA unilaterally to locally knock down the aberrant protein in diabetic nerves improved aspects of sensory function in diabetic mice. Collectively, our findings identify subtle but significant alterations in spliceosome structure and function, including dysregulated CBs and CWC22 overexpression, in diabetic sensory neurons that offer new ideas regarding diabetic sensory neurodegeneration in polyneuropathy.
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Affiliation(s)
- Masaki Kobayashi
- Division of Neurology and Department of Medicine, Faculty of Medicine and Dentistry, and the Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada, T6G 2G3
| | - Ambika Chandrasekhar
- Division of Neurology and Department of Medicine, Faculty of Medicine and Dentistry, and the Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada, T6G 2G3
| | - Chu Cheng
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, Faculty of Medicine, University of Calgary, Canada, T2N 4N1
| | - Jose A Martinez
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, Faculty of Medicine, University of Calgary, Canada, T2N 4N1
| | - Hilarie Ng
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, Faculty of Medicine, University of Calgary, Canada, T2N 4N1
| | - Cristiane de la Hoz
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, Faculty of Medicine, University of Calgary, Canada, T2N 4N1
| | - Douglas W Zochodne
- Division of Neurology and Department of Medicine, Faculty of Medicine and Dentistry, and the Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada, T6G 2G3 .,Hotchkiss Brain Institute and Department of Clinical Neurosciences, Faculty of Medicine, University of Calgary, Canada, T2N 4N1
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40
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Zhang X, Yan C, Hang J, Finci LI, Lei J, Shi Y. An Atomic Structure of the Human Spliceosome. Cell 2017; 169:918-929.e14. [DOI: 10.1016/j.cell.2017.04.033] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 04/24/2017] [Accepted: 04/25/2017] [Indexed: 12/17/2022]
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41
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Carvalho T, Martins S, Rino J, Marinho S, Carmo-Fonseca M. Pharmacological inhibition of the spliceosome subunit SF3b triggers exon junction complex-independent nonsense-mediated decay. J Cell Sci 2017; 130:1519-1531. [PMID: 28302904 DOI: 10.1242/jcs.202200] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/06/2017] [Indexed: 12/12/2022] Open
Abstract
Spliceostatin A, meayamycin, and pladienolide B are small molecules that target the SF3b subunit of the spliceosomal U2 small nuclear ribonucleoprotein (snRNP). These compounds are attracting much attention as tools to manipulate splicing and for use as potential anti-cancer drugs. We investigated the effects of these inhibitors on mRNA transport and stability in human cells. Upon splicing inhibition, unspliced pre-mRNAs accumulated in the nucleus, particularly within enlarged nuclear speckles. However, a small fraction of the pre-mRNA molecules were exported to the cytoplasm. We identified the export adaptor ALYREF as being associated with intron-containing transcripts and show its requirement for the nucleo-cytoplasmic transport of unspliced pre-mRNA. In contrast, the exon junction complex (EJC) core protein eIF4AIII failed to form a stable complex with intron-containing transcripts. Despite the absence of EJC, unspliced transcripts in the cytoplasm were degraded by nonsense-mediated decay (NMD), suggesting that unspliced transcripts are degraded by an EJC-independent NMD pathway. Collectively, our results indicate that although blocking the function of SF3b elicits a massive accumulation of unspliced pre-mRNAs in the nucleus, intron-containing transcripts can still bind the ALYREF export factor and be transported to the cytoplasm, where they trigger an alternative NMD pathway.
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Affiliation(s)
- Teresa Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Sandra Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - José Rino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Sérgio Marinho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
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42
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Deciphering the mRNP Code: RNA-Bound Determinants of Post-Transcriptional Gene Regulation. Trends Biochem Sci 2017; 42:369-382. [PMID: 28268044 DOI: 10.1016/j.tibs.2017.02.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/27/2017] [Accepted: 02/10/2017] [Indexed: 12/16/2022]
Abstract
Eukaryotic cells determine the final protein output of their genetic program not only by controlling transcription but also by regulating the localization, translation and turnover rates of their mRNAs. Ultimately, the fate of any given mRNA is determined by the ensemble of all associated RNA-binding proteins (RBPs), non-coding RNAs and metabolites collectively known as the messenger ribonucleoprotein particle (mRNP). Although many mRNA-associated factors have been identified over the past years, little is known about the composition of individual mRNPs and the cooperation of their constituents. In this review we discuss recent progress that has been made on how this 'mRNP code' is established on individual transcripts and how it is interpreted during gene expression in eukaryotic cells.
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43
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Haberman N, Huppertz I, Attig J, König J, Wang Z, Hauer C, Hentze MW, Kulozik AE, Le Hir H, Curk T, Sibley CR, Zarnack K, Ule J. Insights into the design and interpretation of iCLIP experiments. Genome Biol 2017; 18:7. [PMID: 28093074 PMCID: PMC5240381 DOI: 10.1186/s13059-016-1130-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 12/08/2016] [Indexed: 01/16/2023] Open
Abstract
Background Ultraviolet (UV) crosslinking and immunoprecipitation (CLIP) identifies the sites on RNAs that are in direct contact with RNA-binding proteins (RBPs). Several variants of CLIP exist, which require different computational approaches for analysis. This variety of approaches can create challenges for a novice user and can hamper insights from multi-study comparisons. Here, we produce data with multiple variants of CLIP and evaluate the data with various computational methods to better understand their suitability. Results We perform experiments for PTBP1 and eIF4A3 using individual-nucleotide resolution CLIP (iCLIP), employing either UV-C or photoactivatable 4-thiouridine (4SU) combined with UV-A crosslinking and compare the results with published data. As previously noted, the positions of complementary DNA (cDNA)-starts depend on cDNA length in several iCLIP experiments and we now find that this is caused by constrained cDNA-ends, which can result from the sequence and structure constraints of RNA fragmentation. These constraints are overcome when fragmentation by RNase I is efficient and when a broad cDNA size range is obtained. Our study also shows that if RNase does not efficiently cut within the binding sites, the original CLIP method is less capable of identifying the longer binding sites of RBPs. In contrast, we show that a broad size range of cDNAs in iCLIP allows the cDNA-starts to efficiently delineate the complete RNA-binding sites. Conclusions We demonstrate the advantage of iCLIP and related methods that can amplify cDNAs that truncate at crosslink sites and we show that computational analyses based on cDNAs-starts are appropriate for such methods. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1130-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nejc Haberman
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.,The Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ina Huppertz
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.,MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.,European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Jan Attig
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.,The Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Julian König
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.,Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Zhen Wang
- Institut de Biologie de l'ENS (IBENS), 46 rue d'Ulm, Paris, F-75005, France.,CNRS UMR 8197, Paris Cedex 05, 75230, France
| | - Christian Hauer
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120, Heidelberg, Germany
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Hervé Le Hir
- Institut de Biologie de l'ENS (IBENS), 46 rue d'Ulm, Paris, F-75005, France.,CNRS UMR 8197, Paris Cedex 05, 75230, France
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška cesta 25, 1000, Ljubljana, Slovenia
| | - Christopher R Sibley
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.,Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany.
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK. .,The Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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44
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Alexandrov A, Shu MD, Steitz JA. Fluorescence Amplification Method for Forward Genetic Discovery of Factors in Human mRNA Degradation. Mol Cell 2017; 65:191-201. [PMID: 28017590 PMCID: PMC5301997 DOI: 10.1016/j.molcel.2016.11.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/05/2016] [Accepted: 11/18/2016] [Indexed: 12/21/2022]
Abstract
Nonsense-mediated decay (NMD) degrades mRNAs containing a premature termination codon (PTC). PTCs are a frequent cause of human genetic diseases, and the NMD pathway is known to modulate disease severity. Since partial NMD attenuation can potentially enhance nonsense suppression therapies, better definition of human-specific NMD is required. However, the majority of NMD factors were first discovered in model organisms and then subsequently identified by homology in human. Sensitivity and throughput limitations of existing approaches have hindered systematic forward genetic screening for NMD factors in human cells. We developed a method of in vivo amplification of NMD reporter fluorescence (Fireworks) that enables CRISPR-based forward genetic screening for NMD pathway defects in human cells. The Fireworks genetic screen identifies multiple known NMD factors and numerous human candidate genes, providing a platform for discovery of additional key factors in human mRNA degradation.
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Affiliation(s)
- Andrei Alexandrov
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.
| | - Mei-Di Shu
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
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45
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Woodward LA, Mabin JW, Gangras P, Singh G. The exon junction complex: a lifelong guardian of mRNA fate. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 28008720 DOI: 10.1002/wrna.1411] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/27/2016] [Accepted: 11/09/2016] [Indexed: 12/28/2022]
Abstract
During messenger RNA (mRNA) biogenesis and processing in the nucleus, many proteins are imprinted on mRNAs assembling them into messenger ribonucleoproteins (mRNPs). Some of these proteins remain stably bound within mRNPs and have a long-lasting impact on their fate. One of the best-studied examples is the exon junction complex (EJC), a multiprotein complex deposited primarily 24 nucleotides upstream of exon-exon junctions as a consequence of pre-mRNA splicing. The EJC maintains a stable, sequence-independent, hold on the mRNA until its removal during translation in the cytoplasm. Acting as a molecular shepherd, the EJC travels with mRNA across the cellular landscape coupling pre-mRNA splicing to downstream, posttranscriptional processes such as mRNA export, mRNA localization, translation, and nonsense-mediated mRNA decay (NMD). In this review, we discuss our current understanding of the EJC's functions during these processes, and expound its newly discovered functions (e.g., pre-mRNA splicing). Another focal point is the recently unveiled in vivo EJC interactome, which has shed new light on the EJC's location on the spliced RNAs and its intimate relationship with other mRNP components. We summarize new strides being made in connecting the EJC's molecular function with phenotypes, informed by studies of human disorders and model organisms. The progress toward understanding EJC functions has revealed, in its wake, even more questions, which are discussed throughout. WIREs RNA 2017, 8:e1411. doi: 10.1002/wrna.1411 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Lauren A Woodward
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Justin W Mabin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Pooja Gangras
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Guramrit Singh
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
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46
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Choudhury SR, Singh AK, McLeod T, Blanchette M, Jang B, Badenhorst P, Kanhere A, Brogna S. Exon junction complex proteins bind nascent transcripts independently of pre-mRNA splicing in Drosophila melanogaster. eLife 2016; 5. [PMID: 27879206 PMCID: PMC5158136 DOI: 10.7554/elife.19881] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/21/2016] [Indexed: 12/16/2022] Open
Abstract
Although it is currently understood that the exon junction complex (EJC) is recruited on spliced mRNA by a specific interaction between its central protein, eIF4AIII, and splicing factor CWC22, we found that eIF4AIII and the other EJC core proteins Y14 and MAGO bind the nascent transcripts of not only intron-containing but also intronless genes on Drosophila polytene chromosomes. Additionally, Y14 ChIP-seq demonstrates that association with transcribed genes is also splicing-independent in Drosophila S2 cells. The association of the EJC proteins with nascent transcripts does not require CWC22 and that of Y14 and MAGO is independent of eIF4AIII. We also show that eIF4AIII associates with both polysomal and monosomal RNA in S2 cell extracts, whereas Y14 and MAGO fractionate separately. Cumulatively, our data indicate a global role of eIF4AIII in gene expression, which would be independent of Y14 and MAGO, splicing, and of the EJC, as currently understood. DOI:http://dx.doi.org/10.7554/eLife.19881.001 Cells and organisms survive and thrive in large part due to the activities of thousands of proteins. The instructions for making these proteins are found in the DNA sequences of genes. However, these genes also tend to contain large sections called introns that do not encode protein. To make a protein, the gene’s full sequence is first copied to a temporary molecule called pre-messenger RNA (pre-mRNA for short). The introns are then removed from the pre-mRNA in a process known as splicing in the cell nucleus, during which the remaining regions of the molecule, called exons, are joined together to form a mature mRNA molecule. This mature mRNA can then move out of the cell nucleus and be used as a template to build proteins around the cell. Intriguingly, splicing of the pre-mRNAs in the nucleus affects how the mRNA is used to make proteins in the cytoplasm of the cell. This nucleus-cytoplasm connection is currently explained by the so-called exon junction complex, which is thought to attach to mature mRNAs at the junction between two exons and stay bound until the mRNA moves to the cytoplasm. Evidence suggests the exon junction complex affects how the mRNA is used to make protein, yet little is known about how it would do so. Choudhury, Singh et al. examined how exon junction complex proteins bind to newly made RNA in salivary gland cells of fruit flies and in cultured cells. Contrary to expectations, the three proteins thought to make the central part of the exon junction complex were found on different mRNAs and regardless of whether the mRNAs derived from genes with introns. Specifically, one of these proteins – eIF4AIII – can remain on the mRNA independently of the two other exon junction complex proteins or CWC22, a protein required for splicing. CWC22 is also thought to be required for the complex to be deposited precisely at exon junctions in human cells. Overall, it appears that our current understanding of the exon junction complex needs to be revised. The findings presented by Choudhury, Singh et al. predict alternative roles for these proteins, particularly eIF4AIII, which will be independent of any deposition of the exon junction complex. DOI:http://dx.doi.org/10.7554/eLife.19881.002
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Affiliation(s)
| | - Anand K Singh
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Tina McLeod
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Marco Blanchette
- Stowers Institute for Medical Research, Kansas city, United States
| | - Boyun Jang
- Institute of Biomedical Research, University of Birmingham, Birmingham, United Kingdom
| | - Paul Badenhorst
- Institute of Biomedical Research, University of Birmingham, Birmingham, United Kingdom
| | - Aditi Kanhere
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Saverio Brogna
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
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47
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Boehm V, Gehring NH. Exon Junction Complexes: Supervising the Gene Expression Assembly Line. Trends Genet 2016; 32:724-735. [PMID: 27667727 DOI: 10.1016/j.tig.2016.09.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/23/2016] [Accepted: 09/01/2016] [Indexed: 12/16/2022]
Abstract
The exon junction complex (EJC) is an RNA-binding protein complex that is assembled and deposited onto mRNAs during splicing. The EJC comprises four core components that bind to not only canonical sites upstream of exon-exon junctions, but also to noncanonical sites at other positions in exons. EJC-associated proteins are recruited by the EJC at different steps of gene expression to execute the multiple functions of the EJC. Recently, new insights have been obtained into how EJCs stimulate pre-mRNA splicing, and mRNA export, translation, and degradation. Furthermore, mutations in EJC core components were shown to result in severe disorders in humans, demonstrating the critical physiological role of the EJC. Hence, the EJC has been identified as an important player in post-transcriptional gene regulation in metazoans.
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Affiliation(s)
- Volker Boehm
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany.
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48
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Cryo-EM structure of the spliceosome immediately after branching. Nature 2016; 537:197-201. [PMID: 27459055 PMCID: PMC5156311 DOI: 10.1038/nature19316] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/19/2016] [Indexed: 12/11/2022]
Abstract
Precursor mRNA (pre-mRNA) splicing proceeds by two consecutive transesterification reactions via a lariat-intron intermediate. Here we present the 3.8 Å cryo-electron microscopy structure of the spliceosome immediately after lariat formation. The 5'-splice site is cleaved but remains close to the catalytic Mg2+ site in the U2/U6 small nuclear RNA (snRNA) triplex, and the 5'-phosphate of the intron nucleotide G(+1) is linked to the branch adenosine 2'OH. The 5'-exon is held between the Prp8 amino-terminal and linker domains, and base-pairs with U5 snRNA loop 1. Non-Watson-Crick interactions between the branch helix and 5'-splice site dock the branch adenosine into the active site, while intron nucleotides +3 to +6 base-pair with the U6 snRNA ACAGAGA sequence. Isy1 and the step-one factors Yju2 and Cwc25 stabilize docking of the branch helix. The intron downstream of the branch site emerges between the Prp8 reverse transcriptase and linker domains and extends towards the Prp16 helicase, suggesting a plausible mechanism of remodelling before exon ligation.
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The multiple functions of RNA helicases as drivers and regulators of gene expression. Nat Rev Mol Cell Biol 2016; 17:426-38. [PMID: 27251421 DOI: 10.1038/nrm.2016.50] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
RNA helicases comprise the largest family of enzymes involved in the metabolism of mRNAs, the processing and fate of which rely on their packaging into messenger ribonucleoprotein particles (mRNPs). In this Review, we describe how the capacity of some RNA helicases to either remodel or lock the composition of mRNP complexes underlies their pleiotropic functions at different steps of the gene expression process. We illustrate the roles of RNA helicases in coordinating gene expression steps and programmes, and propose that RNA helicases function as molecular drivers and guides of the progression of their mRNA substrates from one RNA-processing factory to another, to a productive mRNA pool that leads to protein synthesis or to unproductive mRNA pools that are stored or degraded.
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De I, Schmitzová J, Pena V. The organization and contribution of helicases to RNA splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:259-74. [PMID: 26874649 DOI: 10.1002/wrna.1331] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 12/08/2015] [Accepted: 12/09/2015] [Indexed: 12/27/2022]
Abstract
Splicing is an essential step of gene expression. It occurs in two consecutive chemical reactions catalyzed by a large protein-RNA complex named the spliceosome. Assembled on the pre-mRNA substrate from five small nuclear proteins, the spliceosome acts as a protein-controlled ribozyme to catalyze the two reactions and finally dissociates into its components, which are re-used for a new round of splicing. Upon following this cyclic pathway, the spliceosome undergoes numerous intermediate stages that differ in composition as well as in their internal RNA-RNA and RNA-protein contacts. The driving forces and control mechanisms of these remodeling processes are provided by specific molecular motors called RNA helicases. While eight spliceosomal helicases are present in all organisms, higher eukaryotes contain five additional ones potentially required to drive a more intricate splicing pathway and link it to an RNA metabolism of increasing complexity. Spliceosomal helicases exhibit a notable structural diversity in their accessory domains and overall architecture, in accordance with the diversity of their task-specific functions. This review summarizes structure-function knowledge about all spliceosomal helicases, including the latter five, which traditionally are treated separately from the conserved ones. The implications of the structural characteristics of helicases for their functions, as well as for their structural communication within the multi-subunits environment of the spliceosome, are pointed out.
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Affiliation(s)
- Inessa De
- Macromolecular Crystallography Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jana Schmitzová
- Macromolecular Crystallography Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vladimir Pena
- Macromolecular Crystallography Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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