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Jia R, Ajiro M, Yu L, McCoy P, Zheng ZM. Oncogenic splicing factor SRSF3 regulates ILF3 alternative splicing to promote cancer cell proliferation and transformation. RNA (NEW YORK, N.Y.) 2019; 25:630-644. [PMID: 30796096 PMCID: PMC6467003 DOI: 10.1261/rna.068619.118] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 02/21/2019] [Indexed: 05/28/2023]
Abstract
Alternative RNA splicing is an important focus in molecular and clinical oncology. We report here that SRSF3 regulates alternative RNA splicing of interleukin enhancer binding factor 3 (ILF3) and production of this double-strand RNA-binding protein. An increased coexpression of ILF3 isoforms and SRSF3 was found in various types of cancers. ILF3 isoform-1 and isoform-2 promote cell proliferation and transformation. Tumor cells with reduced SRSF3 expression produce aberrant isoform-5 and -7 of ILF3. By binding to RNA sequence motifs, SRSF3 regulates the production of various ILF3 isoforms by exclusion/inclusion of ILF3 exon 18 or by selection of an alternative 3' splice site within exon 18. ILF3 isoform-5 and isoform-7 suppress tumor cell proliferation and the isoform-7 induces cell apoptosis. Our data indicate that ILF3 isoform-1 and isoform-2 are two critical factors for cell proliferation and transformation. The increased SRSF3 expression in cancer cells plays an important role in maintaining the steady status of ILF3 isoform-1 and isoform-2.
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Affiliation(s)
- Rong Jia
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Ke Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Masahiko Ajiro
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Lulu Yu
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Philip McCoy
- Flow Cytometry Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
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Nativel B, Figuester A, Andries J, Planesse C, Couprie J, Gasque P, Viranaicken W, Iwema T. Soluble expression of disulfide-bonded C-type lectin like domain of human CD93 in the cytoplasm of Escherichia coli. J Immunol Methods 2016; 439:67-73. [PMID: 27742562 DOI: 10.1016/j.jim.2016.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 10/07/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
CD93 belongs to the group XIV C-type lectin like domain (CTLD) and is closely related to thrombomodulin (CD141). Although CD93 is known to be involved in the regulation of cell adhesion and phagocytosis, its role in innate immunity remains to be fully investigated. Critically, published data about CD141 suggest that CD93 CTLD could be involved in the control of inflammation. In order to address further functional and structural analyses, we expressed human CD93 CTLD with several disulfide bonds in an E. coli expression system. As the E. coli cytoplasm is a reducing compartment, production of disulfide-bond proteins remains a challenge. Hence, we decided to over express CD93 CTLD in commercially available strains of E. coli and co-expressed a sulfhydryl oxidase (Erv1p) and a disulfide isomerase (DsbC). This strategy led to high yield expression of a native form of CD93 CTLD. NMR studies revealed that Ca2+ was not able to bind to CD93 CTLD. We also showed that the recombinant protein could alter LPS pro-inflammatory activity on THP1. This work provides new tool for further functional and structural studies to decipher the functions associated to the CTLD of CD93. This approach may also be used for others members of the group XIV C-type lectin like domain (CD141, CD248 and CLec14A).
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Affiliation(s)
- Brice Nativel
- Inserm, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Université de La Réunion, Plateforme CYROI, Sainte-Clotilde, F-97490, France; GRI, EA4517, Université de la Réunion, Saint-Denis F-97400, France
| | - Audrey Figuester
- GRI, EA4517, Université de la Réunion, Saint-Denis F-97400, France; Inserm, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Université de La Réunion, Plateforme CYROI, Sainte-Clotilde, F-97490, France
| | - Jessica Andries
- GRI, EA4517, Université de la Réunion, Saint-Denis F-97400, France
| | - Cynthia Planesse
- Inserm, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Université de La Réunion, Plateforme CYROI, Sainte-Clotilde, F-97490, France
| | - Joël Couprie
- Inserm, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Université de La Réunion, Plateforme CYROI, Sainte-Clotilde, F-97490, France
| | - Philippe Gasque
- GRI, EA4517, Université de la Réunion, Saint-Denis F-97400, France; UM134, Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Université de La Réunion, INSERM1187, CNRS 9192, IRD 249, Plateforme CYROI, Sainte-Clotilde F-97490, France; Laboratoire de Biologie, LICE-OI, CHU de la Réunion, 1 allée des Topazes, 97400, France
| | - Wildriss Viranaicken
- GRI, EA4517, Université de la Réunion, Saint-Denis F-97400, France; UM134, Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Université de La Réunion, INSERM1187, CNRS 9192, IRD 249, Plateforme CYROI, Sainte-Clotilde F-97490, France.
| | - Thomas Iwema
- GRI, EA4517, Université de la Réunion, Saint-Denis F-97400, France; CALIXAR, 60 Avenue Rockefeller, 69008 Lyon, France
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Castella S, Bernard R, Corno M, Fradin A, Larcher JC. Ilf3 and NF90 functions in RNA biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:243-56. [PMID: 25327818 DOI: 10.1002/wrna.1270] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/09/2014] [Accepted: 09/17/2014] [Indexed: 12/24/2022]
Abstract
Double-stranded RNA-binding proteins (DRBPs) are known to regulate many processes of RNA metabolism due, among others, to the presence of double-stranded RNA (dsRNA)-binding motifs (dsRBMs). Among these DRBPs, Interleukin enhancer-binding factor 3 (Ilf3) and Nuclear Factor 90 (NF90) are two ubiquitous proteins generated by mutually exclusive and alternative splicings of the Ilf3 gene. They share common N-terminal and central sequences but display specific C-terminal regions. They present a large heterogeneity generated by several post-transcriptional and post-translational modifications involved in their subcellular localization and biological functions. While Ilf3 and NF90 were first identified as activators of gene expression, they are also implicated in cellular processes unrelated to RNA metabolism such as regulation of the cell cycle or of enzymatic activites. The implication of Ilf3 and NF90 in RNA biology will be discussed with a focus on eukaryote transcription and translation regulation, on viral replication and translation as well as on noncoding RNA field.
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Affiliation(s)
- Sandrine Castella
- Laboratoire de Biologie du développement, Institut de Biologie Paris-Seine, Sorbonne Universités, UPMC Univ Paris 06, Paris, France; Laboratoire de Biologie du développement, Institut de Biologie Paris-Seine, CNRS, UMR 7622, Paris, France
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Chaumet A, Castella S, Gasmi L, Fradin A, Clodic G, Bolbach G, Poulhe R, Denoulet P, Larcher JC. Proteomic analysis of interleukin enhancer binding factor 3 (Ilf3) and nuclear factor 90 (NF90) interactome. Biochimie 2013; 95:1146-57. [PMID: 23321469 DOI: 10.1016/j.biochi.2013.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 01/04/2013] [Indexed: 11/17/2022]
Abstract
Interleukin enhancer binding factor 3 (Ilf3) and Nuclear Factor 90 (NF90) are two ubiquitous proteins generated by alternative splicing from the ILF3 gene that provides each protein with a long and identical N-terminal domain of 701 amino acids and a specific C-terminal domain of 210 and 15 amino acids, respectively. They exhibit a high polymorphism due to their posttranscriptional and posttranslational modifications. Ilf3 and NF90 functions remain unclear although they have been described as RNA binding proteins but have been implicated in a large scale of cellular phenomena depending on the nature of their interacting partners, the composition of their protein complexes and their subcellular localization. In order to better understand the functions of Ilf3 and NF90, we have investigated their protein partners by an affinity chromatography approach. In this report, we have identified six partners of Ilf3 and NF90 that interact with their double-stranded RNA binding motifs: hnRNP A/B, hnRNP A2/B1, hnRNP A3, hnRNP D, hnRNP Q and PSF. These hnRNP are known to be implicated in mRNA stabilization, transport and/or translation regulation whereas PSF is a splicing factor. Furthermore, Ilf3, NF90 and most of their identified partners have been shown to be present in large complexes. Altogether, these data suggest an implication of Ilf3 and NF90 in mRNA metabolism. This work allows to establish a link between Ilf3 and NF90 functions, as RNA binding proteins, and their interacting partners implicated in these functions.
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Affiliation(s)
- Alexandre Chaumet
- Laboratoire de Biologie du Développement, UMR 7622 CNRS, UPMC Univ Paris 06, 9 quai Saint Bernard, 75252 Paris Cedex 05, France
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Viranaicken W, Gasmi L, Chaumet A, Durieux C, Georget V, Denoulet P, Larcher JC. L-Ilf3 and L-NF90 traffic to the nucleolus granular component: alternatively-spliced exon 3 encodes a nucleolar localization motif. PLoS One 2011; 6:e22296. [PMID: 21811582 PMCID: PMC3139624 DOI: 10.1371/journal.pone.0022296] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 06/23/2011] [Indexed: 11/18/2022] Open
Abstract
Ilf3 and NF90, two proteins containing double-stranded RNA-binding domains, are generated by alternative splicing and involved in several functions. Their heterogeneity results from posttranscriptional and posttranslational modifications. Alternative splicing of exon 3, coding for a 13 aa N-terminal motif, generates for each protein a long and short isoforms. Subcellular fractionation and localization of recombinant proteins showed that this motif acts as a nucleolar localization signal. Deletion and substitution mutants identified four arginines, essential for nucleolar targeting, and three histidines to stabilize the proteins within the nucleolus. The short isoforms are never found in the nucleoli, whereas the long isoforms are present in the nucleoplasm and the nucleoli. For Ilf3, only the posttranslationally-unmodified long isoform is nucleolar, suggesting that this nucleolar targeting is abrogated by posttranslational modifications. Confocal microscopy and FRAP experiments have shown that the long Ilf3 isoform localizes to the granular component of the nucleolus, and that L-Ilf3 and L-NF90 exchange rapidly between nucleoli. The presence of this 13 aminoacid motif, combined with posttranslational modifications, is responsible for the differences in Ilf3 and NF90 isoforms subcellular localizations. The protein polymorphism of Ilf3/NF90 and the various subcellular localizations of their isoforms may partially explain the various functions previously reported for these proteins.
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Affiliation(s)
- Wildriss Viranaicken
- UPMC Univ Paris 06, UMR 7622, Laboratoire de Biologie du Développement, Paris, France
- CNRS, UMR 7622, Laboratoire de Biologie du Développement, Paris, France
| | - Laila Gasmi
- UPMC Univ Paris 06, UMR 7622, Laboratoire de Biologie du Développement, Paris, France
- CNRS, UMR 7622, Laboratoire de Biologie du Développement, Paris, France
| | - Alexandre Chaumet
- UPMC Univ Paris 06, UMR 7622, Laboratoire de Biologie du Développement, Paris, France
- CNRS, UMR 7622, Laboratoire de Biologie du Développement, Paris, France
| | - Christiane Durieux
- Institut Jacques Monod, UMR7592 CNRS - Université Denis Diderot, Paris, France
| | - Virginie Georget
- UPMC Université Paris 06, IFR 83, Institut de Biologie Intégrative, Paris, France
| | - Philippe Denoulet
- UPMC Univ Paris 06, UMR 7622, Laboratoire de Biologie du Développement, Paris, France
- CNRS, UMR 7622, Laboratoire de Biologie du Développement, Paris, France
| | - Jean-Christophe Larcher
- UPMC Univ Paris 06, UMR 7622, Laboratoire de Biologie du Développement, Paris, France
- CNRS, UMR 7622, Laboratoire de Biologie du Développement, Paris, France
- * E-mail:
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Neplioueva V, Dobrikova EY, Mukherjee N, Keene JD, Gromeier M. Tissue type-specific expression of the dsRNA-binding protein 76 and genome-wide elucidation of its target mRNAs. PLoS One 2010; 5:e11710. [PMID: 20668518 PMCID: PMC2909144 DOI: 10.1371/journal.pone.0011710] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 06/29/2010] [Indexed: 11/29/2022] Open
Abstract
Background RNA-binding proteins accompany all steps in the life of mRNAs and provide dynamic gene regulatory functions for rapid adjustment to changing extra- or intracellular conditions. The association of RNA-binding proteins with their targets is regulated through changing subcellular distribution, post-translational modification or association with other proteins. Methodology We demonstrate that the dsRNA binding protein 76 (DRBP76), synonymous with nuclear factor 90, displays inherently distinct tissue type-specific subcellular distribution in the normal human central nervous system and in malignant brain tumors of glial origin. Altered subcellular localization and isoform distribution in malignant glioma indicate that tumor-specific changes in DRBP76-related gene products and their regulatory functions may contribute to the formation and/or maintenance of these tumors. To identify endogenous mRNA targets of DRBP76, we performed RNA-immunoprecipitation and genome-wide microarray analyses in HEK293 cells, and identified specific classes of transcripts encoding critical functions in cellular metabolism. Significance Our data suggest that physiologic DRBP76 expression, isoform distribution and subcellular localization are profoundly altered upon malignant transformation. Thus, the functional role of DRBP76 in co- or post-transcriptional gene regulation may contribute to the neoplastic phenotype.
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Affiliation(s)
- Valentina Neplioueva
- Division of Neurosurgery, Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
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Nuclear factor 45 (NF45) is a regulatory subunit of complexes with NF90/110 involved in mitotic control. Mol Cell Biol 2008; 28:4629-41. [PMID: 18458058 DOI: 10.1128/mcb.00120-08] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nuclear factor 90 (NF90) and its C-terminally extended isoform, NF110, have been isolated as DNA- and RNA-binding proteins together with the less-studied protein NF45. These complexes have been implicated in gene regulation, but little is known about their cellular roles and whether they are redundant or functionally distinct. We show that heterodimeric core complexes, NF90-NF45 and NF110-NF45, exist within larger complexes that are more labile and contain multiple NF90/110 isoforms and additional proteins. Depletion of the NF45 subunit by RNA interference is accompanied by a dramatic decrease in the levels of NF90 and NF110. Reciprocally, depletion of NF90 but not of NF110 greatly reduces the level of NF45. Coregulation of NF90 and NF45 is a posttranscriptional phenomenon, resulting from protein destabilization in the absence of partners. Depletion of NF90-NF45 complexes retards cell growth by inhibition of DNA synthesis. Giant multinucleated cells containing nuclei attached by constrictions accumulate when either NF45 or NF90, but not NF110, is depleted. This study identified NF45 as an unstable regulatory subunit of NF90-NF45 complexes and uncovered their critical role in normal cell division. Furthermore, the study revealed that NF90 is functionally distinct from NF110 and is more important for cell growth.
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