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Li P, Quan H, He W, Wu L, Chen Z, Yong B, Liu X, He C. Rice BARENTSZ genes are required to maintain floral developmental stability against temperature fluctuations. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39215633 DOI: 10.1111/tpj.17007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/09/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
BARENTSZ (BTZ), a core component of the exon junction complex, regulates diverse developmental processes in animals. However, its evolutionary and developmental roles in plants remain elusive. Here, we revealed that three groups of paralogous BTZ genes existed in Poaceae, and Group 2 underwent loss-of-function mutations during evolution. They showed surprisingly low (~33%) sequence identities, implying functional divergence. Two genes retained in rice, OsBTZ1 and OsBTZ3, were edited; however, the resultant osbtz1 and osbtz3 mutants showed similar floral morphological and functional defects at a low frequency. When growing under low-temperature conditions, developmental abnormalities became pronounced, and new floral variations were induced. In particular, stamen and carpel functionality was impaired in these rice btz mutants. The double-gene mutant osbtz1/3 shared these floral defects with an increased frequency, which was further induced under low-temperature conditions. OsBTZs interacted with OsMADS7 and OsMADS8, and the floral expressions of the OsTGA10 and MADS-box genes were correlatively altered in these osbtz mutants and responded to low-temperature treatment. These novel findings demonstrate that two highly diverged OsBTZs are required to maintain floral developmental stability under low-temperature conditions, and play an integral role in male and female fertility, thus providing new insights into the indispensable roles of BTZ genes in plant development and adaptive evolution.
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Affiliation(s)
- Peigang Li
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Quan
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenchao He
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lanfeng Wu
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhixiong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Bin Yong
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Chaoying He
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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2
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Roth JF, Braunschweig U, Wu M, Li JD, Lin ZY, Larsen B, Weatheritt RJ, Gingras AC, Blencowe BJ. Systematic analysis of alternative exon-dependent interactome remodeling reveals multitasking functions of gene regulatory factors. Mol Cell 2023; 83:4222-4238.e10. [PMID: 38065061 DOI: 10.1016/j.molcel.2023.10.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/09/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Alternative splicing significantly expands biological complexity, particularly in the vertebrate nervous system. Increasing evidence indicates that developmental and tissue-dependent alternative exons often control protein-protein interactions; yet, only a minor fraction of these events have been characterized. Using affinity purification-mass spectrometry (AP-MS), we show that approximately 60% of analyzed neural-differential exons in proteins previously implicated in transcriptional regulation result in the gain or loss of interaction partners, which in some cases form unexpected links with coupled processes. Notably, a neural exon in Chtop regulates its interaction with the Prmt1 methyltransferase and DExD-Box helicases Ddx39b/a, affecting its methylation and activity in promoting RNA export. Additionally, a neural exon in Sap30bp affects interactions with RNA processing factors, modulating a critical function of Sap30bp in promoting the splicing of <100 nt "mini-introns" that control nuclear RNA levels. AP-MS is thus a powerful approach for elucidating the multifaceted functions of proteins imparted by context-dependent alternative exons.
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Affiliation(s)
- Jonathan F Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Mingkun Wu
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jack Daiyang Li
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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3
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Rademacher DJ, Bello AI, May JP. CASC3 Biomolecular Condensates Restrict Turnip Crinkle Virus by Limiting Host Factor Availability. J Mol Biol 2023; 435:167956. [PMID: 36642157 PMCID: PMC10338645 DOI: 10.1016/j.jmb.2023.167956] [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: 09/07/2022] [Revised: 12/15/2022] [Accepted: 01/07/2023] [Indexed: 01/15/2023]
Abstract
The exon-junction complex (EJC) plays a role in post-transcriptional gene regulation and exerts antiviral activity towards several positive-strand RNA viruses. However, the spectrum of RNA viruses that are targeted by the EJC or the underlying mechanisms are not well understood. EJC components from Arabidopsis thaliana were screened for antiviral activity towards Turnip crinkle virus (TCV, Tombusviridae). Overexpression of the accessory EJC component CASC3 inhibited TCV accumulation > 10-fold in Nicotiana benthamiana while knock-down of endogenous CASC3 resulted in a > 4-fold increase in TCV accumulation. CASC3 forms cytoplasmic condensates and deletion of the conserved SELOR domain reduced condensate size 7-fold and significantly decreased antiviral activity towards TCV. Mass spectrometry of CASC3 complexes did not identify endogenous stress granule or P-body markers and CASC3 failed to co-localize with an aggresome-specific dye suggesting that CASC3 condensates are distinct from well-established membraneless compartments. Mass spectrometry and bimolecular fluorescence complementation assays revealed that CASC3 sequesters Heat shock protein 70 (Hsp70-1) and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), two host factors with roles in tombusvirus replication. Overexpression of Hsp70-1 or GAPDH reduced the antiviral activity of CASC3 2.1-fold and 2.8-fold, respectively, and suggests that CASC3 inhibits TCV by limiting host factor availability. Unrelated Tobacco mosaic virus (TMV) also depends on Hsp70-1 and CASC3 overexpression restricted TMV accumulation 4-fold and demonstrates that CASC3 antiviral activity is not TCV-specific. Like CASC3, Auxin response factor 19 (ARF19) forms poorly dynamic condensates but ARF19 overexpression failed to inhibit TCV accumulation and suggests that CASC3 has antiviral activities that are not ubiquitous among cytoplasmic condensates.
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Affiliation(s)
- Dana J Rademacher
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, 5009 Rockhill Road, Kansas City, MO 64110, USA
| | - Abudu I Bello
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, 5009 Rockhill Road, Kansas City, MO 64110, USA
| | - Jared P May
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, 5009 Rockhill Road, Kansas City, MO 64110, USA.
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4
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Yu CL, Chuang TW, Samuel SY, Lou YC, Tarn WY. Co-phase separation of Y14 and RNA in vitro and its implication for DNA repair. RNA (NEW YORK, N.Y.) 2023; 29:1007-1019. [PMID: 37001915 DOI: 10.1261/rna.079514.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
The multifunctional RNA recognition motif-containing protein Y14/RBM8A participates in mRNA metabolism and is essential for the efficient repair of DNA double-strand breaks (DSBs). Y14 contains highly charged, low-complexity sequences in both the amino- and carboxy-terminal domains. The feature of charge segregation suggests that Y14 may undergo liquid-liquid phase separation (LLPS). Recombinant Y14 formed phase-separated droplets, which were sensitive to pH and salt concentration. Domain mapping suggested that LLPS of Y14 involves multivalent electrostatic interactions and is partly determined by the net charge of its low-complexity regions. Phospho-mimicry of the carboxy-terminal arginine-serine dipeptides of Y14 suppressed phase separation. Moreover, RNA could phase separate into Y14 droplets and modulate Y14 LLPS in a concentration-dependent manner. Finally, the capacity of Y14 in LLPS and coacervation with RNA in vitro correlated with its activity in DSB repair. These results reveal a molecular rule for LLPS of Y14 in vitro and an implication for its co-condensation with RNA in genome stability.
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Affiliation(s)
- Chia-Lin Yu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Tzu-Wei Chuang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Sabrina Yeo Samuel
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Yuan-Chao Lou
- Biomedical Translation Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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5
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DEAD-box ATPases as regulators of biomolecular condensates and membrane-less organelles. Trends Biochem Sci 2023; 48:244-258. [PMID: 36344372 DOI: 10.1016/j.tibs.2022.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
RNA-dependent DEAD-box ATPases (DDXs) are emerging as major regulators of RNA-containing membrane-less organelles (MLOs). On the one hand, oligomerizing DDXs can promote condensate formation 'in cis', often using RNA as a scaffold. On the other hand, DDXs can disrupt RNA-RNA and RNA-protein interactions and thereby 'in trans' remodel the multivalent interactions underlying MLO formation. In this review, we discuss the best studied examples of DDXs modulating MLOs in cis and in trans. Further, we illustrate how this contributes to the dynamic assembly and turnover of MLOs which might help cells to modulate RNA sequestration and processing in a temporal and spatial manner.
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6
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Uzonyi A, Dierks D, Nir R, Kwon OS, Toth U, Barbosa I, Burel C, Brandis A, Rossmanith W, Le Hir H, Slobodin B, Schwartz S. Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability. Mol Cell 2023; 83:237-251.e7. [PMID: 36599352 DOI: 10.1016/j.molcel.2022.12.026] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/04/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023]
Abstract
N6-methyladenosine (m6A), a widespread destabilizing mark on mRNA, is non-uniformly distributed across the transcriptome, yet the basis for its selective deposition is unknown. Here, we propose that m6A deposition is not selective. Instead, it is exclusion based: m6A consensus motifs are methylated by default, unless they are within a window of ∼100 nt from a splice junction. A simple model which we extensively validate, relying exclusively on presence of m6A motifs and exon-intron architecture, allows in silico recapitulation of experimentally measured m6A profiles. We provide evidence that exclusion from splice junctions is mediated by the exon junction complex (EJC), potentially via physical occlusion, and that previously observed associations between exon-intron architecture and mRNA decay are mechanistically mediated via m6A. Our findings establish a mechanism coupling nuclear mRNA splicing and packaging with the covalent installation of m6A, in turn controlling cytoplasmic decay.
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Affiliation(s)
- Anna Uzonyi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - David Dierks
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - Oh Sung Kwon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Ursula Toth
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Isabelle Barbosa
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Cindy Burel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Boris Slobodin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel; Department of Biochemistry, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 31096, Israel.
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel.
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7
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Lee ES, Smith HW, Wolf EJ, Guvenek A, Wang YE, Emili A, Tian B, Palazzo AF. ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5' splice site motifs within nuclear speckles. RNA (NEW YORK, N.Y.) 2022; 28:878-894. [PMID: 35351812 PMCID: PMC9074902 DOI: 10.1261/rna.079104.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/12/2022] [Indexed: 05/22/2023]
Abstract
Quality control of mRNA represents an important regulatory mechanism for gene expression in eukaryotes. One component of this quality control is the nuclear retention and decay of misprocessed RNAs. Previously, we demonstrated that mature mRNAs containing a 5' splice site (5'SS) motif, which is typically found in misprocessed RNAs such as intronic polyadenylated (IPA) transcripts, are nuclear retained and degraded. Using high-throughput sequencing of cellular fractions, we now demonstrate that IPA transcripts require the zinc finger protein ZFC3H1 for their nuclear retention and degradation. Using reporter mRNAs, we demonstrate that ZFC3H1 promotes the nuclear retention of mRNAs with intact 5'SS motifs by sequestering them into nuclear speckles. Furthermore, we find that U1-70K, a component of the spliceosomal U1 snRNP, is also required for the nuclear retention of these reporter mRNAs and likely functions in the same pathway as ZFC3H1. Finally, we show that the disassembly of nuclear speckles impairs the nuclear retention of reporter mRNAs with 5'SS motifs. Our results highlight a splicing independent role of U1 snRNP and indicate that it works in conjunction with ZFC3H1 in preventing the nuclear export of misprocessed mRNAs by sequestering them into nuclear speckles.
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Affiliation(s)
- Eliza S Lee
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Harrison W Smith
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Eric J Wolf
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Aysegul Guvenek
- Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Yifan E Wang
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Andrew Emili
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Bin Tian
- Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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8
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The Physiological Roles of the Exon Junction Complex in Development and Diseases. Cells 2022; 11:cells11071192. [PMID: 35406756 PMCID: PMC8997533 DOI: 10.3390/cells11071192] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/19/2022] [Accepted: 03/24/2022] [Indexed: 01/12/2023] Open
Abstract
The exon junction complex (EJC) becomes an increasingly important regulator of early gene expression in the central nervous system (CNS) and other tissues. The EJC is comprised of three core proteins: RNA-binding motif 8A (RBM8A), Mago homolog (MAGOH), eukaryotic initiation factor 4A3 (EIF4A3), and a peripheral EJC factor, metastatic lymph node 51 (MLN51), together with various auxiliary factors. The EJC is assembled specifically at exon-exon junctions on mRNAs, hence the name of the complex. The EJC regulates multiple levels of gene expression, from splicing to translation and mRNA degradation. The functional roles of the EJC have been established as crucial to the normal progress of embryonic and neurological development, with wide ranging implications on molecular, cellular, and organism level function. Dysfunction of the EJC has been implicated in multiple developmental and neurological diseases. In this review, we discuss recent progress on the EJC’s physiological roles.
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9
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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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Rivera C, Verbel-Vergara D, Arancibia D, Lappala A, González M, Guzmán F, Merello G, Lee JT, Andrés ME. Revealing RCOR2 as a regulatory component of nuclear speckles. Epigenetics Chromatin 2021; 14:51. [PMID: 34819154 PMCID: PMC8611983 DOI: 10.1186/s13072-021-00425-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 10/31/2021] [Indexed: 12/26/2022] Open
Abstract
Background Nuclear processes such as transcription and RNA maturation can be impacted by subnuclear compartmentalization in condensates and nuclear bodies. Here, we characterize the nature of nuclear granules formed by REST corepressor 2 (RCOR2), a nuclear protein essential for pluripotency maintenance and central nervous system development. Results Using biochemical approaches and high-resolution microscopy, we reveal that RCOR2 is localized in nuclear speckles across multiple cell types, including neurons in the brain. RCOR2 forms complexes with nuclear speckle components such as SON, SRSF7, and SRRM2. When cells are exposed to chemical stress, RCOR2 behaves as a core component of the nuclear speckle and is stabilized by RNA. In turn, nuclear speckle morphology appears to depend on RCOR2. Specifically, RCOR2 knockdown results larger nuclear speckles, whereas overexpressing RCOR2 leads to smaller and rounder nuclear speckles. Conclusion Our study suggests that RCOR2 is a regulatory component of the nuclear speckle bodies, setting this co-repressor protein as a factor that controls nuclear speckles behavior. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00425-4.
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Affiliation(s)
- Carlos Rivera
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Del Libertador Bernardo O'Higgins 340, 8320000, Santiago, Chile.,Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, CPZN 6624, Boston, MA, 02114, USA.,Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, 02114, USA
| | - Daniel Verbel-Vergara
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Del Libertador Bernardo O'Higgins 340, 8320000, Santiago, Chile
| | - Duxan Arancibia
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Del Libertador Bernardo O'Higgins 340, 8320000, Santiago, Chile
| | - Anna Lappala
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, CPZN 6624, Boston, MA, 02114, USA.,Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, 02114, USA
| | - Marcela González
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Del Libertador Bernardo O'Higgins 340, 8320000, Santiago, Chile
| | - Fabián Guzmán
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Del Libertador Bernardo O'Higgins 340, 8320000, Santiago, Chile
| | - Gianluca Merello
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Del Libertador Bernardo O'Higgins 340, 8320000, Santiago, Chile
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, CPZN 6624, Boston, MA, 02114, USA. .,Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, 02114, USA.
| | - María Estela Andrés
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Del Libertador Bernardo O'Higgins 340, 8320000, Santiago, Chile.
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11
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Kanellis DC, Espinoza JA, Zisi A, Sakkas E, Bartkova J, Katsori AM, Boström J, Dyrskjøt L, Broholm H, Altun M, Elsässer SJ, Lindström MS, Bartek J. The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output. SCIENCE ADVANCES 2021; 7:eabf7561. [PMID: 34348895 PMCID: PMC8336962 DOI: 10.1126/sciadv.abf7561] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/14/2021] [Indexed: 05/22/2023]
Abstract
Eukaryotic initiation factor 4A-III (eIF4A3), a core helicase component of the exon junction complex, is essential for splicing, mRNA trafficking, and nonsense-mediated decay processes emerging as targets in cancer therapy. Here, we unravel eIF4A3's tumor-promoting function by demonstrating its role in ribosome biogenesis (RiBi) and p53 (de)regulation. Mechanistically, eIF4A3 resides in nucleoli within the small subunit processome and regulates rRNA processing via R-loop clearance. EIF4A3 depletion induces cell cycle arrest through impaired RiBi checkpoint-mediated p53 induction and reprogrammed translation of cell cycle regulators. Multilevel omics analysis following eIF4A3 depletion pinpoints pathways of cell death regulation and translation of alternative mouse double minute homolog 2 (MDM2) transcript isoforms that control p53. EIF4A3 expression and subnuclear localization among clinical cancer specimens correlate with the RiBi status rendering eIF4A3 an exploitable vulnerability in high-RiBi tumors. We propose a concept of eIF4A3's unexpected role in RiBi, with implications for cancer pathogenesis and treatment.
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Affiliation(s)
- Dimitris C Kanellis
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Jaime A Espinoza
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Asimina Zisi
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Elpidoforos Sakkas
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jirina Bartkova
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Anna-Maria Katsori
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm 17165, Sweden
| | - Johan Boström
- Science for Life Laboratory, Division of Clinical Physiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, SE-141 52 Huddinge, Sweden
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Helle Broholm
- Department of Pathology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mikael Altun
- Science for Life Laboratory, Division of Clinical Physiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, SE-141 52 Huddinge, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm 17165, Sweden
| | - Mikael S Lindström
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden.
| | - Jiri Bartek
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden.
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
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12
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The exon junction complex core factor eIF4A3 is a key regulator of HPV16 gene expression. Biosci Rep 2021; 41:228142. [PMID: 33760064 PMCID: PMC8026852 DOI: 10.1042/bsr20203488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/04/2021] [Accepted: 03/24/2021] [Indexed: 01/06/2023] Open
Abstract
High-risk human papillomavirus (hrHPVs), particularly HPV16 and HPV18, are the etiologic factors of ano-genital cancers and some head and neck squamous cell carcinomas (HNSCCs). Viral E6 and E7 oncoproteins, controlled at both transcriptional and post-transcriptional levels, drive hrHPVs-induced carcinogenesis. In the present study, we investigated the implication of the DEAD-box helicase eukaryotic translation initiation factor 4A3 (eIF4A3,) an Exon Junction Complex factor, in the regulation of HPV16 gene expression. Our data revealed that the depletion of the factor eIF4A3 up-regulated E7 oncoprotein levels. We also showed that the inhibition of the nonsense-mediated RNA decay (NMD) pathway, resulted in the up-regulation of E7 at both RNA and protein levels. We therefore proposed that HPV16 transcripts might present different susceptibilities to NMD and that this pathway could play a key role in the levels of expression of these viral oncoproteins during the development of HPV-related cancers.
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13
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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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14
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Hu J, Li P, Shi B, Tie J. Importin β1 mediates nuclear import of the factors associated with nonsense-mediated RNA decay. Biochem Biophys Res Commun 2021; 542:34-39. [PMID: 33486189 DOI: 10.1016/j.bbrc.2021.01.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/15/2022]
Abstract
In eukaryotic cells, nonsense-mediated RNA decay (NMD) is an essential physiological mechanism coupled to translation, regulating the stability of abnormal RNA containing premature termination codon (PTC) and a significant fraction of normal transcriptomes. So far, the molecular regulation mechanism of NMD pathway is far from fully elucidated. Previously, we observed the interaction between importin β1 (Impβ1) and UPF1, a core factor of NMD. Here, we demonstrated that Impβ1 knockdown stabilized NMD reporters, and Impβ1 and UPF1 interacted and co-regulated an extensive number of target transcripts. Furthermore, Impβ1 affected the interaction between UPF1 and SMG5 or MAGOH, and the nuclear distributions of UPF1, SMG1, SMG5 and MAGOH. Besides, Ran knockdown extremely promoted the dissociation of UPF1 from SMG5 or MAGOH. Our findings provide molecular insight into the potential function of Impβ1in nonsense-mediated RNA decay.
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Affiliation(s)
- Jianran Hu
- Department of Biological Science and Technology, Changzhi University, Changzhi, 046011, China.
| | - Ping Li
- Department of Biological Science and Technology, Changzhi University, Changzhi, 046011, China
| | - Baozhong Shi
- Department of Biological Science and Technology, Changzhi University, Changzhi, 046011, China
| | - Jun Tie
- Department of Biological Science and Technology, Changzhi University, Changzhi, 046011, China
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15
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Dou Y, Barbosa I, Jiang H, Iasillo C, Molloy KR, Schulze WM, Cusack S, Schmid M, Le Hir H, LaCava J, Jensen TH. NCBP3 positively impacts mRNA biogenesis. Nucleic Acids Res 2020; 48:10413-10427. [PMID: 32960271 PMCID: PMC7544205 DOI: 10.1093/nar/gkaa744] [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: 05/28/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/26/2022] Open
Abstract
The nuclear Cap-Binding Complex (CBC), consisting of Nuclear Cap-Binding Protein 1 (NCBP1) and 2 (NCBP2), associates with the nascent 5′cap of RNA polymerase II transcripts and impacts RNA fate decisions. Recently, the C17orf85 protein, also called NCBP3, was suggested to form an alternative CBC by replacing NCBP2. However, applying protein–protein interaction screening of NCBP1, 2 and 3, we find that the interaction profile of NCBP3 is distinct. Whereas NCBP1 and 2 identify known CBC interactors, NCBP3 primarily interacts with components of the Exon Junction Complex (EJC) and the TRanscription and EXport (TREX) complex. NCBP3-EJC association in vitro and in vivo requires EJC core integrity and the in vivo RNA binding profiles of EJC and NCBP3 overlap. We further show that NCBP3 competes with the RNA degradation factor ZC3H18 for binding CBC-bound transcripts, and that NCBP3 positively impacts the nuclear export of polyadenylated RNAs and the expression of large multi-exonic transcripts. Collectively, our results place NCBP3 with the EJC and TREX complexes in supporting mRNA expression.
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Affiliation(s)
- Yuhui Dou
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Isabelle Barbosa
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Claudia Iasillo
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Wiebke Manuela Schulze
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9 38042, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9 38042, France
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Hervé Le Hir
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen 9713 AV, Netherlands
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
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16
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Di Mattia T, Martinet A, Ikhlef S, McEwen AG, Nominé Y, Wendling C, Poussin-Courmontagne P, Voilquin L, Eberling P, Ruffenach F, Cavarelli J, Slee J, Levine TP, Drin G, Tomasetto C, Alpy F. FFAT motif phosphorylation controls formation and lipid transfer function of inter-organelle contacts. EMBO J 2020; 39:e104369. [PMID: 33124732 PMCID: PMC7705450 DOI: 10.15252/embj.2019104369] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 11/13/2022] Open
Abstract
Organelles are physically connected in membrane contact sites. The endoplasmic reticulum possesses three major receptors, VAP‐A, VAP‐B, and MOSPD2, which interact with proteins at the surface of other organelles to build contacts. VAP‐A, VAP‐B, and MOSPD2 contain an MSP domain, which binds a motif named FFAT (two phenylalanines in an acidic tract). In this study, we identified a non‐conventional FFAT motif where a conserved acidic residue is replaced by a serine/threonine. We show that phosphorylation of this serine/threonine is critical for non‐conventional FFAT motifs (named Phospho‐FFAT) to be recognized by the MSP domain. Moreover, structural analyses of the MSP domain alone or in complex with conventional and Phospho‐FFAT peptides revealed new mechanisms of interaction. Based on these new insights, we produced a novel prediction algorithm, which expands the repertoire of candidate proteins with a Phospho‐FFAT that are able to create membrane contact sites. Using a prototypical tethering complex made by STARD3 and VAP, we showed that phosphorylation is instrumental for the formation of ER‐endosome contacts, and their sterol transfer function. This study reveals that phosphorylation acts as a general switch for inter‐organelle contacts.
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Affiliation(s)
- Thomas Di Mattia
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Arthur Martinet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Souade Ikhlef
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, CNRS, Valbonne, France
| | - Alastair G McEwen
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Yves Nominé
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Corinne Wendling
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Pierre Poussin-Courmontagne
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Laetitia Voilquin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Pascal Eberling
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Frank Ruffenach
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Jean Cavarelli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - John Slee
- UCL Institute of Ophthalmology, London, UK
| | | | - Guillaume Drin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, CNRS, Valbonne, France
| | - Catherine Tomasetto
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Fabien Alpy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
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17
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Robinson-Thiewes S, McCloskey J, Kimble J. Two classes of active transcription sites and their roles in developmental regulation. Proc Natl Acad Sci U S A 2020; 117:26812-26821. [PMID: 33033228 PMCID: PMC7604424 DOI: 10.1073/pnas.2013163117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The expression of genes encoding powerful developmental regulators is exquisitely controlled, often at multiple levels. Here, we investigate developmental expression of three conserved genes, Caenorhabditis elegans mpk-1, lag-1, and lag-3/sel-8, which encode homologs of ERK/MAPK and core components of the Notch-dependent transcription complex, respectively. We use single-molecule FISH (smFISH) and MATLAB to visualize and quantify nuclear nascent transcripts and cytoplasmic mRNAs as a function of position along the germline developmental axis. Using differentially labeled probes, one spanning an exceptionally long first intron and the other spanning exons, we identify two classes of active transcription sites (ATS). The iATS class, for "incomplete" ATS, harbors only partial nascent transcripts; the cATS class, for "complete" ATS, harbors full-length nascent transcripts. Remarkably, the frequencies of iATS and cATS are patterned along the germline axis. For example, most mpk-1 ATS are iATS in hermaphrodite germline stem cells, but most are cATS in differentiating stem cell daughters. Thus, mpk-1 ATS class frequencies switch in a graded manner as stem cell daughters begin differentiation. Importantly, the patterns of ATS class frequency are gene-, stage-, and sex-specific, and cATS frequency strongly correlates with transcriptional output. Although the molecular mechanism underlying ATS classes is not understood, their primary difference is the extent of transcriptional progression. To generate only partial nascent transcripts in iATS, progression must be slowed, paused, or aborted midway through the gene. We propose that regulation of ATS class can be a critical mode of developmental gene regulation.
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Affiliation(s)
| | - John McCloskey
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
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18
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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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19
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Widespread remodeling of proteome solubility in response to different protein homeostasis stresses. Proc Natl Acad Sci U S A 2020; 117:2422-2431. [PMID: 31964829 DOI: 10.1073/pnas.1912897117] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The accumulation of protein deposits in neurodegenerative diseases has been hypothesized to depend on a metastable subproteome vulnerable to aggregation. To investigate this phenomenon and the mechanisms that regulate it, we measured the solubility of the proteome in the mouse Neuro2a cell line under six different protein homeostasis stresses: 1) Huntington's disease proteotoxicity, 2) Hsp70, 3) Hsp90, 4) proteasome, 5) endoplasmic reticulum (ER)-mediated folding inhibition, and 6) oxidative stress. Overall, we found that about one-fifth of the proteome changed solubility with almost all of the increases in insolubility were counteracted by increases in solubility of other proteins. Each stress directed a highly specific pattern of change, which reflected the remodeling of protein complexes involved in adaptation to perturbation, most notably, stress granule (SG) proteins, which responded differently to different stresses. These results indicate that the protein homeostasis system is organized in a modular manner and aggregation patterns were not correlated with protein folding stability (ΔG). Instead, distinct cellular mechanisms regulate assembly patterns of multiple classes of protein complexes under different stress conditions.
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20
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Ma Q, Tatsuno T, Nakamura Y, Ishigaki Y. The stability of Magoh and Y14 depends on their heterodimer formation and nuclear localization. Biochem Biophys Res Commun 2019; 511:631-636. [PMID: 30826064 DOI: 10.1016/j.bbrc.2019.02.097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 02/19/2019] [Indexed: 01/10/2023]
Abstract
Reduced expression of the Y14 gene is a cause of Thrombocytopenia-absent radius (TAR) syndrome. This gene contains a conserved RNA recognition motif (RRM) in the central region and nuclear localization/export sequences (NLS/NES) in the N-terminal. Y14 and Magoh proteins form tight heterodimers and are the core of exon junction complexes (EJCs), which mediate various processes of mRNA metabolism after transcription. In this report, we found that protein expression levels of exogenously expressed Magoh L136R and Y14 L118R (leucine-to-arginine substitution at amino acid residue 136 and 118 respectively, that results in the formation of the complex being lost) are lower than their wild-types. This reduction is likely caused by protein levels, as no difference in mRNA levels was detected. Meanwhile, a cycloheximide chase assay determined that the degradation rates of Magoh L136R and Y14 L118R were faster than their wild-types. Both Y14 L118R and Magoh L136R lost the ability to form heterodimers with corresponding wild-type proteins. However, Y14 L118R is able to still localize in the nucleus which causes the stability of Y14 L118R to be higher than Magoh L136R. These results reveal that the stability of Magoh and Y14 is not only dependent on the heterodimer structure, but also dependent on nuclear localization.
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Affiliation(s)
- Qingfeng Ma
- Medical Research Institute, Kanazawa Medical University, Uchinada, Kahoku, Japan; Department of Clinical Laboratory, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Takanori Tatsuno
- Medical Research Institute, Kanazawa Medical University, Uchinada, Kahoku, Japan
| | - Yuka Nakamura
- Medical Research Institute, Kanazawa Medical University, Uchinada, Kahoku, Japan
| | - Yasuhito Ishigaki
- Medical Research Institute, Kanazawa Medical University, Uchinada, Kahoku, Japan.
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21
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Ma Q, Tatsuno T, Nakamura Y, Izumi S, Tomosugi N, Ishigaki Y. Immuno‐detection of mRNA‐binding protein complex in human cells under transmission electron microscopy. Microsc Res Tech 2019; 82:680-688. [DOI: 10.1002/jemt.23214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 12/13/2018] [Accepted: 12/15/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Qingfeng Ma
- Medical Research InstituteKanazawa Medical University Uchinada Kahoku Japan
- Department of Clinical Laboratory, Liyuan Hospital, Tongji Medical CollegeHuazhong University of Science and Technology Wuhan China
| | - Takanori Tatsuno
- Medical Research InstituteKanazawa Medical University Uchinada Kahoku Japan
| | - Yuka Nakamura
- Medical Research InstituteKanazawa Medical University Uchinada Kahoku Japan
| | - Shin‐Ichi Izumi
- Department of Cell Biology, Unit of Biomedical SciencesNagasaki University Graduate School of Biomedical Sciences Sakamoto Nagasaki Japan
| | - Naohisa Tomosugi
- Medical Research InstituteKanazawa Medical University Uchinada Kahoku Japan
- Medical Care Proteomics Biotechnology Co., Ltd. Uchinada Kahoku Japan
| | - Yasuhito Ishigaki
- Medical Research InstituteKanazawa Medical University Uchinada Kahoku Japan
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22
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Mabin JW, Woodward LA, Patton RD, Yi Z, Jia M, Wysocki VH, Bundschuh R, Singh G. The Exon Junction Complex Undergoes a Compositional Switch that Alters mRNP Structure and Nonsense-Mediated mRNA Decay Activity. Cell Rep 2018; 25:2431-2446.e7. [PMID: 30466796 DOI: 10.1016/j.celrep.2018.11.046] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/22/2018] [Accepted: 11/12/2018] [Indexed: 01/08/2023] Open
Abstract
The exon junction complex (EJC) deposited upstream of mRNA exon junctions shapes structure, composition, and fate of spliced mRNA ribonucleoprotein particles (mRNPs). To achieve this, the EJC core nucleates assembly of a dynamic shell of peripheral proteins that function in diverse post-transcriptional processes. To illuminate consequences of EJC composition change, we purified EJCs from human cells via peripheral proteins RNPS1 and CASC3. We show that the EJC originates as an SR-rich mega-dalton-sized RNP that contains RNPS1 but lacks CASC3. Sometime before or during translation, the EJC undergoes compositional and structural remodeling into an SR-devoid monomeric complex that contains CASC3. Surprisingly, RNPS1 is important for nonsense-mediated mRNA decay (NMD) in general, whereas CASC3 is needed for NMD of only select mRNAs. The switch to CASC3-EJC slows down NMD. Overall, the EJC compositional switch dramatically alters mRNP structure and specifies two distinct phases of EJC-dependent NMD.
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Affiliation(s)
- Justin W Mabin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Lauren A Woodward
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Robert D Patton
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Zhongxia Yi
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Mengxuan Jia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Department of Physics, The Ohio State University, Columbus, OH 43210, USA; Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Guramrit Singh
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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23
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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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24
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Kiselev AM, Stepanova IS, Adonin LS, Batalova FM, Parfenov VN, Bogolyubov DS, Podgornaya OI. The exon junction complex factor Y14 is dynamic in the nucleus of the beetle Tribolium castaneum during late oogenesis. Mol Cytogenet 2017; 10:41. [PMID: 29151891 PMCID: PMC5679382 DOI: 10.1186/s13039-017-0342-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/27/2017] [Indexed: 12/02/2022] Open
Abstract
Background The oocyte chromosomes of the red flour beetle, Tribolium castaneum, are gathered into a knot, forming a karyosphere at the diplotene stage of meiotic prophase. Chromatin rearrangement, which is a characteristic feature of oocyte maturation, is well documented. The T. castaneum karyosphere is surrounded by a complex extrachromosomal structure termed the karyosphere capsule. The capsule contains the vast majority of oocyte RNA. We have previously shown using a BrUTP assay that oocyte chromosomes in T. castaneum maintain residual transcription up to the very end of oocyte maturation. Karyosphere transcription requires evidently not only transcription factors but also mRNA processing factors, including the components of the exon junction complex with its core component, the splicing factor Y14. We employed a gene engineering approach with injection of mRNA derived from the Myc-tagged Y14 plasmid-based construct in order to monitor the newly synthesized fusion protein in the oocyte nuclei. Results Our preliminary data have been presented as a brief correspondence elsewhere. Here, we provide a full-length article including immunoelectron-microscopy localization data on Y14–Myc distribution in the nucleus of previtellogenic and vitellogenic oocytes. The injections of the fusion protein Y14–Myc mRNA into the oocytes showed a dynamic pattern of the protein distribution. At the previtellogenic stage, there are two main locations for the protein: SC35 domains (the analogues of interchromatin granule clusters or nuclear speckles) and the karyosphere capsule. At the vitellogenic stage, SC35 domains were devoid of labels, and Y14–Myc was found in the perichromatin region of the karyosphere, presumably at the places of residual transcription. We show that karyosphere formation is accompanied by the movement of a nuclear protein while the residual transcription occurs during genome inactivation. Conclusions Our data indicate that the karyosphere capsule, being a destination site for a protein involved in mRNA splicing and export, is not only a specializes part of nuclear matrix separating the karyosphere from the products of chromosome activity, as believed previously, but represents a special nuclear compartment involved in the processes of gene expression in the case the karyosphere retains residual transcription activity. Electronic supplementary material The online version of this article (10.1186/s13039-017-0342-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Artem M Kiselev
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia.,Federal Almazov North-West Medical Research Centre, St. Petersburg, 197341 Russia.,ITMO University, Institute of Translational Medicine, St. Petersburg, 197101 Russia
| | - Irina S Stepanova
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Leonid S Adonin
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Florina M Batalova
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Vladimir N Parfenov
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Dmitry S Bogolyubov
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Olga I Podgornaya
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia.,Department of Cytology and Histology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034 Russia.,Far Eastern Federal University, School of Biomedicine, Vladivostok, 690950 Russia
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25
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Abstract
TRanscription and EXport (TREX) is a conserved multisubunit complex essential for embryogenesis, organogenesis and cellular differentiation throughout life. By linking transcription, mRNA processing and export together, it exerts a physiologically vital role in the gene expression pathway. In addition, this complex prevents DNA damage and regulates the cell cycle by ensuring optimal gene expression. As the extent of TREX activity in viral infections, amyotrophic lateral sclerosis and cancer emerges, the need for a greater understanding of TREX function becomes evident. A complete elucidation of the composition, function and interactions of the complex will provide the framework for understanding the molecular basis for a variety of diseases. This review details the known composition of TREX, how it is regulated and its cellular functions with an emphasis on mammalian systems.
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26
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Detection of RNA Polymerase II in Mouse Embryos During Zygotic Genome Activation Using Immunocytochemistry. Methods Mol Biol 2017. [PMID: 28456963 DOI: 10.1007/978-1-4939-6988-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Mammalian pre-implantation embryos represent a highly dynamic experimental model for comparative studies of nuclear structure and functions in the context of gradual reactivation of transcription. Here, we present details of the methods that allow localizing RNA polymerase II in mouse pre-implantation embryos with specific antibodies, using fluorescent/confocal and electron microscopy. We stress the special aspects of immunolabeling protocols in respect to the embryonic material. We made a special emphasis on the essential steps preceding the immunocytochemical experiments. In particular, we consider the procedures of female hormonal stimulation and embryo collection. The described approaches are also applicable to study other nuclear proteins.
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27
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Palazzo AF, Truong M. Single particle imaging of mRNAs crossing the nuclear pore: Surfing on the edge. Bioessays 2016; 38:744-50. [DOI: 10.1002/bies.201600038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - Mathew Truong
- Department of Biochemistry; University of Toronto; Toronto ON Canada
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28
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Hir HL, Saulière J, Wang Z. The exon junction complex as a node of post-transcriptional networks. Nat Rev Mol Cell Biol 2015; 17:41-54. [DOI: 10.1038/nrm.2015.7] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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29
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Zhang Q, Kota KP, Alam SG, Nickerson JA, Dickinson RB, Lele TP. Coordinated Dynamics of RNA Splicing Speckles in the Nucleus. J Cell Physiol 2015; 231:1269-75. [PMID: 26496460 DOI: 10.1002/jcp.25224] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 10/21/2015] [Indexed: 12/28/2022]
Abstract
Despite being densely packed with chromatin, nuclear bodies and a nucleoskeletal network, the nucleus is a remarkably dynamic organelle. Chromatin loops form and relax, RNA transcripts and transcription factors move diffusively, and nuclear bodies move. We show here that RNA splicing speckled domains (splicing speckles) fluctuate in constrained nuclear volumes and remodel their shapes. Small speckles move in a directed way toward larger speckles with which they fuse. This directed movement is reduced upon decreasing cellular ATP levels or inhibiting RNA polymerase II activity. The random movement of speckles is reduced upon decreasing cellular ATP levels, moderately reduced after inhibition of SWI/SNF chromatin remodeling and modestly increased upon inhibiting RNA polymerase II activity. To define the paths through which speckles can translocate in the nucleus, we generated a pressure gradient to create flows in the nucleus. In response to the pressure gradient, speckles moved along curvilinear paths in the nucleus. Collectively, our results demonstrate a new type of ATP-dependent motion in the nucleus. We present a model where recycling splicing factors return as part of small sub-speckles from distal sites of RNA processing to larger splicing speckles by a directed ATP-driven mechanism through interchromatin spaces.
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Affiliation(s)
- Qiao Zhang
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Krishna P Kota
- Department of Cellular and Tissue Imaging, Perkin Elmer Inc., Waltham, Massachusetts
| | - Samer G Alam
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Jeffrey A Nickerson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Richard B Dickinson
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Tanmay P Lele
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
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30
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Abstract
The cerebral cortex is built during embryonic neurogenesis, a period when excitatory neurons are generated from progenitors. Defects in neurogenesis can cause acute neurodevelopmental disorders, such as microcephaly (reduced brain size). Altered dosage of the 1q21.1 locus has been implicated in the etiology of neurodevelopmental phenotypes; however, the role of 1q21.1 genes in neurogenesis has remained elusive. Here, we show that haploinsufficiency for Rbm8a, an exon junction complex (EJC) component within 1q21.1, causes severe microcephaly and defective neurogenesis in the mouse. At the onset of neurogenesis, Rbm8a regulates radial glia proliferation and prevents premature neuronal differentiation. Reduced Rbm8a levels result in subsequent apoptosis of neurons, and to a lesser extent, radial glia. Hence, compared to control, Rbm8a-haploinsufficient brains have fewer progenitors and neurons, resulting in defective cortical lamination. To determine whether reciprocal dosage change of Rbm8a alters embryonic neurogenesis, we overexpressed human RBM8A in two animal models. Using in utero electroporation of mouse neocortices as well as zebrafish models, we find RBM8A overexpression does not significantly perturb progenitor number or head size. Our findings demonstrate that Rbm8a is an essential neurogenesis regulator, and add to a growing literature highlighting roles for EJC components in cortical development and neurodevelopmental pathology. Our results indicate that disruption of RBM8A may contribute to neurodevelopmental phenotypes associated with proximal 1q21.1 microdeletions.
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31
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Chuang TW, Lee KM, Tarn WY. Function and pathological implications of exon junction complex factor Y14. Biomolecules 2015; 5:343-55. [PMID: 25866920 PMCID: PMC4496676 DOI: 10.3390/biom5020343] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 01/01/2023] Open
Abstract
Eukaryotic mRNA biogenesis involves a series of interconnected steps, including nuclear pre-mRNA processing, mRNA export, and surveillance. The exon-junction complex (EJC) is deposited on newly spliced mRNAs and coordinates several downstream steps of mRNA biogenesis. The EJC core protein, Y14, functions with its partners in nonsense-mediated mRNA decay and translational enhancement. Y14 plays additional roles in mRNA metabolism, some of which are independent of the EJC, and it is also involved in other cellular processes. Genetic mutations or aberrant expression of Y14 results in physiological abnormality and may cause disease. Therefore, it is important to understand the various functions of Y14 and its physiological and pathological roles.
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Affiliation(s)
- Tzu-Wei Chuang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
| | - Kou-Ming Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
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32
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Khalouei S, Chow AM, Brown IR. Localization of heat shock protein HSPA6 (HSP70B') to sites of transcription in cultured differentiated human neuronal cells following thermal stress. J Neurochem 2014; 131:743-54. [DOI: 10.1111/jnc.12970] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/05/2014] [Accepted: 10/06/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Sam Khalouei
- Centre for the Neurobiology of Stress; Department of Biological Sciences; University of Toronto Scarborough; Toronto Ontario Canada
| | - Ari M. Chow
- Centre for the Neurobiology of Stress; Department of Biological Sciences; University of Toronto Scarborough; Toronto Ontario Canada
| | - Ian R. Brown
- Centre for the Neurobiology of Stress; Department of Biological Sciences; University of Toronto Scarborough; Toronto Ontario Canada
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33
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Cougot N, Daguenet E, Baguet A, Cavalier A, Thomas D, Bellaud P, Fautrel A, Godey F, Bertrand E, Tomasetto C, Gillet R. Overexpression of MLN51 triggers P-body disassembly and formation of a new type of RNA granules. J Cell Sci 2014; 127:4692-701. [PMID: 25205763 DOI: 10.1242/jcs.154500] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Metastatic lymph node 51 (MLN51, also known as CASC3) is a core component of the exon junction complex (EJC), which is loaded onto spliced mRNAs and plays an essential role in determining their fate. Unlike the three other EJC core components [eIF4AIII, Magoh and Y14 (also known as RBM8A)], MLN51 is mainly located in the cytoplasm, where it plays a key role in the assembly of stress granules. In this study, we further investigated the cytoplasmic role of MLN51. We show that MLN51 is a new component of processing bodies (P-bodies). When overexpressed, MLN51 localizes in novel small cytoplasmic foci. These contain RNA, show directed movements and are distinct from stress granules and P-bodies. The appearance of these foci correlates with the process of P-body disassembly. A similar reduction in P-body count is also observed in human HER2-positive (HER2(+)) breast cancer cells overexpressing MLN51. This suggests that P-body disassembly and subsequent mRNA deregulation might correlate with cancer progression.
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Affiliation(s)
- Nicolas Cougot
- Université de Rennes 1, UMR CNRS 6290 IGDR, «Translation and Folding Team», Campus de Beaulieu, 35042 Rennes cedex, France
| | - Elisabeth Daguenet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104, CNRS/U964 INSERM/Université de Strasbourg, 67404 Illkirch, France
| | - Aurélie Baguet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104, CNRS/U964 INSERM/Université de Strasbourg, 67404 Illkirch, France
| | - Annie Cavalier
- Université de Rennes 1, UMR CNRS 6290 IGDR, «Translation and Folding Team», Campus de Beaulieu, 35042 Rennes cedex, France
| | - Daniel Thomas
- Université de Rennes 1, UMR CNRS 6290 IGDR, «Translation and Folding Team», Campus de Beaulieu, 35042 Rennes cedex, France
| | - Pascale Bellaud
- Unité INSERM 991, Plateforme histopathologique, IFR 140 GFAS, Université de Rennes 1, 35043 Rennes, France
| | - Alain Fautrel
- Unité INSERM 991, Plateforme histopathologique, IFR 140 GFAS, Université de Rennes 1, 35043 Rennes, France
| | - Florence Godey
- Centre de Ressources Biologiques Santé de Rennes, Centre Eugène Marquis, Rue de la Bataille Flandres Dunkerque - 35042 Rennes cedex, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, CNRS, UMR 5535, 34293 Montpellier cedex 5, France
| | - Catherine Tomasetto
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104, CNRS/U964 INSERM/Université de Strasbourg, 67404 Illkirch, France
| | - Reynald Gillet
- Université de Rennes 1, UMR CNRS 6290 IGDR, «Translation and Folding Team», Campus de Beaulieu, 35042 Rennes cedex, France
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34
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Hett A, West S. Inhibition of U4 snRNA in human cells causes the stable retention of polyadenylated pre-mRNA in the nucleus. PLoS One 2014; 9:e96174. [PMID: 24796696 PMCID: PMC4010461 DOI: 10.1371/journal.pone.0096174] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 04/04/2014] [Indexed: 01/25/2023] Open
Abstract
Most human pre-mRNAs contain introns that are removed by splicing. Such a complex process needs strict control and regulation in order to prevent the expression of aberrant or unprocessed transcripts. To analyse the fate of pre-mRNAs that cannot be spliced, we inhibited splicing using an anti-sense morpholino (AMO) against U4 snRNA. As a consequence, splicing of several selected transcripts was strongly inhibited. This was accompanied by the formation of enlarged nuclear speckles containing polyadenylated RNA, splicing factors and the nuclear poly(A) binding protein. Consistently, more polyadenylated pre-mRNA could be isolated from nucleoplasmic as well as chromatin-associated RNA fractions following U4 inhibition. Further analysis demonstrated that accumulated pre-mRNAs were stable in the nucleus and that nuclear RNA degradation factors did not re-localise to nuclear speckles following splicing inhibition. The accumulation of pre-mRNA and the formation of enlarged speckles were sensitive to depletion of the 3′ end processing factor, CPSF73, suggesting a requirement for poly(A) site processing in this mechanism. Finally, we provide evidence that the pre-mRNAs produced following U4 snRNA inhibition remain competent for splicing, perhaps providing a biological explanation for their stability. These data further characterise processes ensuring the nuclear retention of pre-mRNA that cannot be spliced and suggest that, in some cases, unspliced transcripts can complete splicing sometime after their initial synthesis.
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Affiliation(s)
- Anne Hett
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Steven West
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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35
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Lu X, Ng HH, Bubulya PA. The role of SON in splicing, development, and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:637-46. [PMID: 24789761 DOI: 10.1002/wrna.1235] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/07/2014] [Accepted: 03/09/2014] [Indexed: 12/22/2022]
Abstract
SON is a nuclear protein involved in multiple cellular processes including transcription, pre-messenger RNA (mRNA) splicing, and cell cycle regulation. Although SON was discovered 25 years ago, the importance of SON's function was only realized recently when its roles in nuclear organization and pre-mRNA splicing as well as the influence of these activities in maintaining cellular health were unveiled. Furthermore, SON was implicated to have a key role in stem cells as well as during the onset of various diseases such as cancer, influenza, and hepatitis. Here we review the progress that has been made in studying this multifunctional protein and discuss questions that remain to be answered about SON.
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Affiliation(s)
- Xinyi Lu
- Gene Regulation Laboratory, Genome Institute of Singapore, Singapore, Singapore
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36
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Cau P, Navarro C, Harhouri K, Roll P, Sigaudy S, Kaspi E, Perrin S, De Sandre-Giovannoli A, Lévy N. WITHDRAWN: Nuclear matrix, nuclear envelope and premature aging syndromes in a translational research perspective. Semin Cell Dev Biol 2014:S1084-9521(14)00058-5. [PMID: 24685615 DOI: 10.1016/j.semcdb.2014.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/03/2014] [Accepted: 03/09/2014] [Indexed: 10/25/2022]
Abstract
The Publisher regrets that this article is an accidental duplication of an article that has already been published, http://dx.doi.org/10.1016/j.semcdb.2014.03.022. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Pierre Cau
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); AP-HM, Service de Biologie Cellulaire, Hôpital La Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France(2).
| | - Claire Navarro
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1)
| | - Karim Harhouri
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1)
| | - Patrice Roll
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); AP-HM, Service de Biologie Cellulaire, Hôpital La Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France(2)
| | - Sabine Sigaudy
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); AP-HM, Département de Génétique Médicale, Hôpital d'enfants Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France(3)
| | - Elise Kaspi
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); AP-HM, Service de Biologie Cellulaire, Hôpital La Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France(2)
| | - Sophie Perrin
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1)
| | - Annachiara De Sandre-Giovannoli
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); AP-HM, Département de Génétique Médicale, Hôpital d'enfants Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France(3)
| | - Nicolas Lévy
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); AP-HM, Département de Génétique Médicale, Hôpital d'enfants Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France(3).
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Cau P, Navarro C, Harhouri K, Roll P, Sigaudy S, Kaspi E, Perrin S, De Sandre-Giovannoli A, Lévy N. Nuclear matrix, nuclear envelope and premature aging syndromes in a translational research perspective. Semin Cell Dev Biol 2014; 29:125-47. [PMID: 24662892 DOI: 10.1016/j.semcdb.2014.03.021] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Lamin A-related progeroid syndromes are genetically determined, extremely rare and severe. In the past ten years, our knowledge and perspectives for these diseases has widely progressed, through the progressive dissection of their pathophysiological mechanisms leading to precocious and accelerated aging, from the genes mutations discovery until therapeutic trials in affected children. A-type lamins are major actors in several structural and functional activities at the nuclear periphery, as they are major components of the nuclear lamina. However, while this is usually poorly considered, they also play a key role within the rest of the nucleoplasm, whose defects are related to cell senescence. Although nuclear shape and nuclear envelope deformities are obvious and visible events, nuclear matrix disorganization and abnormal composition certainly represent the most important causes of cell defects with dramatic pathological consequences. Therefore, lamin-associated diseases should be better referred as laminopathies instead of envelopathies, this later being too restrictive, considering neither the key structural and functional roles of soluble lamins in the entire nucleoplasm, nor the nuclear matrix contribution to the pathophysiology of lamin-associated disorders and in particular in defective lamin A processing-associated aging diseases. Based on both our understanding of pathophysiological mechanisms and the biological and clinical consequences of progeria and related diseases, therapeutic trials have been conducted in patients and were terminated less than 10 years after the gene discovery, a quite fast issue for a genetic disease. Pharmacological drugs have been repurposed and used to decrease the toxicity of the accumulated, unprocessed and truncated prelaminA in progeria. To date, none of them may be considered as a cure for progeria and these clinical strategies were essentially designed toward reducing a subset of the most dramatic and morbid features associated to progeria. New therapeutic strategies under study, in particular targeting the protein expression pathway at the mRNA level, have shown a remarkable efficacy both in vitro in cells and in vivo in mice models. Strategies intending to clear the toxic accumulated proteins from the nucleus are also under evaluation. However, although exceedingly rare, improving our knowledge of genetic progeroid syndromes and searching for innovative and efficient therapies in these syndromes is of paramount importance as, even before they can be used to save lives, they may significantly (i) expand the affected childrens' lifespan and preserve their quality of life; (ii) improve our understanding of aging-related disorders and other more common diseases; and (iii) expand our fundamental knowledge of physiological aging and its links with major physiological processes such as those involved in oncogenesis.
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Affiliation(s)
- Pierre Cau
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; AP-HM, Service de Biologie Cellulaire, Hôpital La Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France.
| | - Claire Navarro
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
| | - Karim Harhouri
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
| | - Patrice Roll
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; AP-HM, Service de Biologie Cellulaire, Hôpital La Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France
| | - Sabine Sigaudy
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; AP-HM, Département de Génétique Médicale, Hôpital d'enfants Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France
| | - Elise Kaspi
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; AP-HM, Service de Biologie Cellulaire, Hôpital La Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France
| | - Sophie Perrin
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
| | - Annachiara De Sandre-Giovannoli
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; AP-HM, Département de Génétique Médicale, Hôpital d'enfants Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France
| | - Nicolas Lévy
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; AP-HM, Département de Génétique Médicale, Hôpital d'enfants Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France.
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Abstract
The eIF4A (eukaryotic initiation factor 4A) proteins belong to the extensive DEAD-box RNA helicase family, the members of which are involved in many aspects of RNA metabolism by virtue of their RNA-binding capacity and ATPase activity. Three eIF4A proteins have been characterized in vertebrates: eIF4A1 and eIF4A2 are cytoplasmic, whereas eIF4A3 is nuclear-localized. Although highly similar, they have been shown to possess rather diverse roles in the mRNA lifecycle. Their specific and diverse functions are often regulated and dictated by interacting partner proteins. The key differences between eIF4A family members are discussed in the present review.
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Correlative light and electron microscopy: from live cell dynamic to 3D ultrastructure. Methods Mol Biol 2014; 1117:485-501. [PMID: 24357376 DOI: 10.1007/978-1-62703-776-1_21] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Correlative light and electron microscopy (CLEM) aims at combining data acquired from the same sample through both imaging modalities. Many combinations can be found in the literature where almost any kind of light microscopy (LM) has been associated to different processing in electron microscopy (EM) and applied to a wide variety of specimen, from cultured cells to multicellular organisms. In this chapter, we focus on a technique that intends to combine LM acquisition on living cells with transmission EM (TEM) analysis. A specific attention is given to the description of a method to bring precise coordinates to the object of interest, to allow a straightforward correlation between LM and EM. Moreover, we describe how, by using high-pressure freezing as a fixation technique, dynamic events observed at the LM are captured and studied at the ultrastructural level.
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Burgute BD, Peche VS, Steckelberg AL, Glöckner G, Gaßen B, Gehring NH, Noegel AA. NKAP is a novel RS-related protein that interacts with RNA and RNA binding proteins. Nucleic Acids Res 2013; 42:3177-93. [PMID: 24353314 PMCID: PMC3950704 DOI: 10.1093/nar/gkt1311] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
NKAP is a highly conserved protein with roles in transcriptional repression, T-cell development, maturation and acquisition of functional competency and maintenance and survival of adult hematopoietic stem cells. Here we report the novel role of NKAP in splicing. With NKAP-specific antibodies we found that NKAP localizes to nuclear speckles. NKAP has an RS motif at the N-terminus followed by a highly basic domain and a DUF 926 domain at the C-terminal region. Deletion analysis showed that the basic domain is important for speckle localization. In pull-down experiments, we identified RNA-binding proteins, RNA helicases and splicing factors as interaction partners of NKAP, among them FUS/TLS. The FUS/TLS–NKAP interaction takes place through the RS domain of NKAP and the RGG1 and RGG3 domains of FUS/TLS. We analyzed the ability of NKAP to interact with RNA using in vitro splicing assays and found that NKAP bound both spliced messenger RNA (mRNA) and unspliced pre-mRNA. Genome-wide analysis using crosslinking and immunoprecipitation-seq revealed NKAP association with U1, U4 and U5 small nuclear RNA, and we also demonstrated that knockdown of NKAP led to an increase in pre-mRNA percentage. Our results reveal NKAP as nuclear speckle protein with roles in RNA splicing and processing.
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Affiliation(s)
- Bhagyashri D Burgute
- Institute of Biochemistry I, Medical Faculty, Center for Molecular Medicine Cologne (CMMC), 50931 Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany, Institute of Genetics, University of Cologne, 50931 Cologne, Germany and Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301, 12587 Berlin, Germany
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Akef A, Zhang H, Masuda S, Palazzo AF. Trafficking of mRNAs containing ALREX-promoting elements through nuclear speckles. Nucleus 2013; 4:326-40. [PMID: 23934081 PMCID: PMC3810340 DOI: 10.4161/nucl.26052] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
In vertebrates, the majority of mRNAs that encode secreted, membrane-bound or mitochondrial proteins contain RNA elements that activate an alternative mRNA nuclear export (ALREX) pathway. Here we demonstrate that mRNAs containing ALREX-promoting elements are trafficked through nuclear speckles. Although ALREX-promoting elements enhance nuclear speckle localization, additional features within the mRNA largely drive this process. Depletion of two TREX-associated RNA helicases, UAP56 and its paralog URH49, or inhibition of the TREX-associated nuclear transport factor, TAP, not only inhibits ALREX, but also appears to trap these mRNAs in nuclear speckles. mRNAs that contain ALREX-promoting elements associate with UAP56 in vivo. Finally, we demonstrate that mRNAs lacking a poly(A)-tail are not efficiently exported by the ALREX pathway and show enhanced association with nuclear speckles. Our data suggest that within the speckle, ALREX-promoting elements, in conjunction with the poly(A)-tail, likely stimulate UAP56/URH49 and TAP dependent steps that lead to the eventual egress of the export-competent mRNP from these structures.
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Affiliation(s)
- Abdalla Akef
- Department of Biochemistry; University of Toronto; Toronto, ON Canada; Division of Integrated Life Science; Graduate School of Biostudies; Kyoto University; Kyoto, Japan
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Teng IF, Wilson SA. Mapping interactions between mRNA export factors in living cells. PLoS One 2013; 8:e67676. [PMID: 23826332 PMCID: PMC3691119 DOI: 10.1371/journal.pone.0067676] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/20/2013] [Indexed: 11/18/2022] Open
Abstract
The TREX complex couples nuclear mRNA processing events with subsequent export to the cytoplasm. TREX also acts as a binding platform for the mRNA export receptor Nxf1. The sites of mRNA transcription and processing within the nucleus have been studied extensively. However, little is known about where TREX assembly takes place and where Nxf1 is recruited to TREX to form the export competent mRNP. Here we have used sensitized emission Förster resonance energy transfer (FRET) and fluorescence lifetime imaging (FLIM)-FRET, to produce a spatial map in living cells of the sites for the interaction of two TREX subunits, Alyref and Chtop, with Nxf1. Prominent assembly sites for export factors are found in the vicinity of nuclear speckles in regions known to be involved in transcription, splicing and exon junction complex formation highlighting the close coupling of mRNA export with mRNP biogenesis.
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Affiliation(s)
- I-Fang Teng
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
| | - Stuart A. Wilson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
- * E-mail:
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Bogolyubov DS, Batalova FM, Kiselyov AM, Stepanova IS. Nuclear structures in Tribolium castaneum oocytes. Cell Biol Int 2013; 37:1061-79. [PMID: 23686847 DOI: 10.1002/cbin.10135] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 04/21/2013] [Indexed: 12/12/2022]
Abstract
The first ultrastructural and immunomorphological characteristics of the karyosphere (karyosome) and extrachromosomal nuclear bodies in the red flour beetle, Tribolium castaneum, are presented. The karyosphere forms early in the diplotene stage of meiotic prophase by the gathering of all oocyte chromosomes in a limited nuclear volume. Using the BrUTP assay, T. castaneum oocyte chromosomes united in the karyosphere maintain their transcriptional activity until the end of oocyte growth. Hyperphosphorylated RNA polymerase II and basal transcription factors (TFIID and TFIIH) were detected in the perichromatin region of the karyosphere. The T. castaneum karyosphere has an extrachromosomal capsule that separates chromosomes from the rest of the nucleoplasm. Certain structural proteins (F-actin, lamin B) were found in the capsule. Unexpectedly, the karyosphere capsule in T. castaneum oocytes was found to be enriched in TMG-capped snRNAs, which suggests that the capsule is not only a structural support for the karyosphere, but may be involved in biogenesis of snRNPs. We also identified the counterparts of 'universal' extrachromosomal nuclear domains, Cajal bodies (CBs) and interchromatin granule clusters (IGCs). Nuclear bodies containing IGC marker protein SC35 display some features unusual for typical IGCs. SC35 domains in T. castaneum oocytes are predominantly fibrillar complex bodies that do not contain trimethyl guanosine (TMG)-capped small nuclear (sn) RNAs. Microinjections of 2'-O-methyl (U)22 probes into the oocytes allowed revealing poly(A)+ RNAs in these nuclear domains. Several proteins related to mRNA export (heterogeneous ribonucleoprotein core protein A1, export adapters Y14 and Aly and export receptor NXF1) were also detected there. We believe that unusual SC35 nuclear domains of T. castaneum oocytes are possibly involved in mRNP but not snRNP biogenesis.
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Affiliation(s)
- Dmitry S Bogolyubov
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia.
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Pandya-Jones A, Bhatt DM, Lin CH, Tong AJ, Smale ST, Black DL. Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression. RNA (NEW YORK, N.Y.) 2013; 19:811-27. [PMID: 23616639 PMCID: PMC3683915 DOI: 10.1261/rna.039081.113] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 03/13/2013] [Indexed: 05/26/2023]
Abstract
The expression of eukaryotic mRNAs is achieved though an intricate series of molecular processes that provide many steps for regulating the production of a final gene product. However, the relationships between individual steps in mRNA biosynthesis and the rates at which they occur are poorly understood. By applying RNA-seq to chromatin-associated and soluble nucleoplasmic fractions of RNA from Lipid A-stimulated macrophages, we examined the timing of exon ligation and transcript release from chromatin relative to the induction of transcription. We find that for a subset of genes in the Lipid A response, the ligation of certain exon pairs is delayed relative to the synthesis of the complete transcript. In contrast, 3' end cleavage and polyadenylation occur rapidly once transcription extends through the cleavage site. Our data indicate that these transcripts with delayed splicing are not released from the chromatin fraction until all the introns have been excised. These unusual kinetics result in a chromatin-associated pool of completely transcribed and 3'-processed transcripts that are not yet fully spliced. We also find that long introns containing repressed exons that will be excluded from the final mRNA are excised particularly slowly relative to other introns in a transcript. These results indicate that the kinetics of splicing and transcript release contribute to the timing of expression for multiple genes of the inflammatory response.
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Affiliation(s)
- Amy Pandya-Jones
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90025, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90025, USA
| | - Dev M. Bhatt
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90025, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90025, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90025, USA
| | - Ann-Jay Tong
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90025, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90025, USA
| | - Stephen T. Smale
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90025, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90025, USA
| | - Douglas L. Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90025, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90025, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, California 90025, USA
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Varia S, Potabathula D, Deng Z, Bubulya A, Bubulya PA. Btf and TRAP150 have distinct roles in regulating subcellular mRNA distribution. Nucleus 2013; 4:229-40. [PMID: 23778535 DOI: 10.4161/nucl.25187] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Transcription of protein-coding genes in mammalian cells is coordinated with pre-mRNA processing as well as the assembly and nuclear export of mRNPs. Btf (BCLAF1) and TRAP150 (THRAP3) were previously reported to associate with in vitro spliced mRNPs and also as a part of the spliceosome, suggesting they are involved in pre-mRNA processing. Btf and TRAP150 are serine-arginine-rich (SR) proteins with significant sequence similarity, but the extent of their functional overlap is not yet clear. We show that both Btf and TRAP150 localize at a constitutively active β-tropomyosin (BTM) reporter minigene locus in mammalian cells. Both proteins also localize at a U2OS 2-6-3 reporter gene locus in a RNA polymerase II (RNAPII) transcription-dependent manner. While Btf and TRAP150 showed some overlap with reporter RNA and other pre-mRNA processing factors at transcription loci, they showed the most precise overlap with the exon junction complex (EJC) protein Magoh. Since EJC components have roles in nuclear export, we examined nuclear/cytoplasmic mRNA distribution after Btf or TRAP150 knockdown. Btf depletion caused an increase of β-tropomyosin minigene reporter transcripts in the cytoplasm as well as global increase of endogenous polyadenylated RNA in the cytoplasm, while TRAP150 depletion did not. We provide evidence that Btf has functions distinct from TRAP150 in regulating the subcellular distribution of mRNAs in human cells.
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EJC core component MLN51 interacts with eIF3 and activates translation. Proc Natl Acad Sci U S A 2013; 110:5903-8. [PMID: 23530232 DOI: 10.1073/pnas.1218732110] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The multiprotein exon junction complex (EJC), deposited by the splicing machinery, is an important constituent of messenger ribonucleoprotein particles because it participates to numerous steps of the mRNA lifecycle from splicing to surveillance via nonsense-mediated mRNA decay pathway. By an unknown mechanism, the EJC also stimulates translation efficiency of newly synthesized mRNAs. Here, we show that among the four EJC core components, the RNA-binding protein metastatic lymph node 51 (MLN51) is a translation enhancer. Overexpression of MLN51 preferentially increased the translation of intron-containing reporters via the EJC, whereas silencing MLN51 decreased translation. In addition, modulation of the MLN51 level in cell-free translational extracts confirmed its direct role in protein synthesis. Immunoprecipitations indicated that MLN51 associates with translation-initiating factors and ribosomal subunits, and in vitro binding assays revealed that MLN51, alone or as part of the EJC, interacts directly with the pivotal eukaryotic translation initiation factor eIF3. Taken together, our data define MLN51 as a translation activator linking the EJC and the translation machinery.
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CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex. Nat Struct Mol Biol 2012; 19:1124-31. [PMID: 23085716 DOI: 10.1038/nsmb.2420] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 09/21/2012] [Indexed: 12/14/2022]
Abstract
The exon junction complex (EJC) is a central effector of the fate of mRNAs, linking nuclear processing to mRNA transport, translation and surveillance. However, little is known about its transcriptome-wide targets. We used cross-linking and immunoprecipitation methods coupled to high-throughput sequencing (CLIP-seq) in human cells to identify the binding sites of the DEAD-box helicase eIF4AIII, an EJC core component. CLIP reads form peaks that are located mainly in spliced mRNAs. Most expressed exons harbor peaks either in the canonical EJC region, located ~24 nucleotides upstream of exonic junctions, or in other noncanonical regions. Notably, both of these types of peaks are preferentially associated with unstructured and purine-rich sequences containing the motif GAAGA, which is a potential binding site for EJC-associated factors. Therefore, EJC positions vary spatially and quantitatively between exons. This transcriptome-wide mapping of human eIF4AIII reveals unanticipated aspects of the EJC and broadens its potential impact on post-transcriptional regulation.
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48
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Human CWC22 escorts the helicase eIF4AIII to spliceosomes and promotes exon junction complex assembly. Nat Struct Mol Biol 2012; 19:983-90. [DOI: 10.1038/nsmb.2380] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Accepted: 08/08/2012] [Indexed: 01/09/2023]
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