1
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Shang R, Kretov DA, Adamson SI, Treiber T, Treiber N, Vedanayagam J, Chuang J, Meister G, Cifuentes D, Lai E. Regulated dicing of pre-mir-144 via reshaping of its terminal loop. Nucleic Acids Res 2022; 50:7637-7654. [PMID: 35801921 PMCID: PMC9303283 DOI: 10.1093/nar/gkac568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/10/2022] [Accepted: 06/18/2022] [Indexed: 11/17/2022] Open
Abstract
Although the route to generate microRNAs (miRNAs) is often depicted as a linear series of sequential and constitutive cleavages, we now appreciate multiple alternative pathways as well as diverse strategies to modulate their processing and function. Here, we identify an unusually profound regulatory role of conserved loop sequences in vertebrate pre-mir-144, which are essential for its cleavage by the Dicer RNase III enzyme in human and zebrafish models. Our data indicate that pre-mir-144 dicing is positively regulated via its terminal loop, and involves the ILF3 complex (NF90 and its partner NF45/ILF2). We provide further evidence that this regulatory switch involves reshaping of the pre-mir-144 apical loop into a structure that is appropriate for Dicer cleavage. In light of our recent findings that mir-144 promotes the nuclear biogenesis of its neighbor mir-451, these data extend the complex hierarchy of nuclear and cytoplasmic regulatory events that can control the maturation of clustered miRNAs.
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Affiliation(s)
- Renfu Shang
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Dmitry A Kretov
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Scott I Adamson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Thomas Treiber
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Jeffrey Vedanayagam
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Eric C Lai
- To whom correspondence should be addressed. Tel: +1 212 639 5578; Fax: +1 212 717 3604;
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2
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Xu Z, Huang H, Li X, Ji C, Liu Y, Liu X, Zhu J, Wang Z, Zhang H, Shi J. High expression of interleukin-enhancer binding factor 3 predicts poor prognosis in patients with lung adenocarcinoma. Oncol Lett 2020; 19:2141-2152. [PMID: 32194712 PMCID: PMC7039148 DOI: 10.3892/ol.2020.11330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 11/11/2019] [Indexed: 12/28/2022] Open
Abstract
Interleukin-enhancer binding factor 3 (ILF3) is a double-stranded RNA-binding protein that has been reported to contribute to the occurrence and progression of various malignant tumors. The aim of the present study was to evaluate the prognostic value of ILF3 and to apply this knowledge to avoid excessive medical treatment in patients with lung adenocarcinoma (LUAD). ILF3 expression in a discovery set consisting of tumor and peri-tumor tissue microarrays was analyzed using immunohistochemical methods. The mRNA level of ILF3 was subsequently analyzed in a validation set downloaded from The Cancer Genome Atlas. The Kaplan-Meier method, univariate and multivariate Cox analyses, decision curve analysis and nomogram models were used to evaluate the prognostic value of ILF3. ILF3 expression was upregulated in tumor tissues compared with peri-tumor tissues and was negatively associated with the overall survival time of patients with LUAD in the discovery and validation sets. Moreover, ILF3 expression was used for risk stratification in patients with tumor-node-metastasis stages II-IV and poor-to-moderate tumor differentiation. ILF3 expression was identified as an independent predictor of adverse prognosis for patients with LUAD in the discovery and validation sets. Finally, nomogram models for the 3- and 5 year survival time of patients with LUAD revealed that ILF3 expression may be used to improve the predictive accuracy of the prognosis and to avoid excessive medical treatment for certain patients with the disease. Overall, the data obtained in the current study revealed that high ILF3 expression was associated with poor prognosis, and demonstrated that ILF3, as a potential independent risk factor, may improve the hierarchical postoperative management of patients with LUAD.
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Affiliation(s)
- Zhangyan Xu
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Hua Huang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Xing Li
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Cheng Ji
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Yifei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Xiaojuan Liu
- Department of Pathogen Biology, Medical College, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Jun Zhu
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Zhendong Wang
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Haijian Zhang
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Jiahai Shi
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
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3
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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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4
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Masuda K, Kuwano Y. Diverse roles of RNA-binding proteins in cancer traits and their implications in gastrointestinal cancers. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1520. [PMID: 30479000 DOI: 10.1002/wrna.1520] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 02/06/2023]
Abstract
Gene expression patterns in cancer cells are strongly influenced by posttranscriptional mechanisms. RNA-binding proteins (RBPs) play key roles in posttranscriptional gene regulation; they can interact with target mRNAs in a sequence- and structure-dependent manner, and determine cellular behavior by manipulating the processing of these mRNAs. Numerous RBPs are aberrantly deregulated in many human cancers and hence, affect the functioning of mRNAs that encode proteins, implicated in carcinogenesis. Here, we summarize the key roles of RBPs in posttranscriptional gene regulation, describe RBPs disrupted in cancer, and lastly focus on RBPs that are responsible for implementing cancer traits in the digestive tract. These evidences may reveal a potential link between changes in expression/function of RBPs and malignant transformation, and a framework for new insights and potential therapeutic applications. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Kiyoshi Masuda
- Kawasaki Medical School at Kurashiki-City, Okayama, Japan
| | - Yuki Kuwano
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School at Tokushima-City, Tokushima, Japan
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5
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Li W, Wang M, Sun J, Wang Y, Jiang R. Gene co-opening network deciphers gene functional relationships. MOLECULAR BIOSYSTEMS 2018; 13:2428-2439. [PMID: 28976510 DOI: 10.1039/c7mb00430c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Genome sequencing technology has generated a vast amount of genomic and epigenomic data, and has provided us a great opportunity to study gene functions on a global scale from an epigenomic view. In the last decade, network-based studies, such as those based on PPI networks and co-expression networks, have shown good performance in capturing functional relationships between genes. However, the functions of a gene and the mechanism of interaction of genes with each other to elucidate their functions are still not entirely clear. Here, we construct a gene co-opening network based on chromatin accessibility of genes. We show that genes related to a specific biological process or the same disease tend to be clustered in the co-opening network. This understanding allows us to detect functional clusters from the network and to predict new functions for genes. We further apply the network to prioritize disease genes for Psoriasis, and demonstrate the power of the joint analysis of the co-opening network and GWAS data in identifying disease genes. Taken together, the co-opening network provides a new viewpoint for the elucidation of gene associations and the interpretation of disease mechanisms.
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Affiliation(s)
- Wenran Li
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China.
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6
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Nakadai T, Fukuda A, Shimada M, Nishimura K, Hisatake K. The RNA binding complexes NF45-NF90 and NF45-NF110 associate dynamically with the c-fos gene and function as transcriptional coactivators. J Biol Chem 2015; 290:26832-45. [PMID: 26381409 DOI: 10.1074/jbc.m115.688317] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Indexed: 12/13/2022] Open
Abstract
The c-fos gene is rapidly induced to high levels by various extracellular stimuli. We used a defined in vitro transcription system that utilizes the c-fos promoter to purify a coactivator activity in an unbiased manner. We report here that NF45-NF90 and NF45-NF110, which possess archetypical double-stranded RNA binding motifs, have a direct function as transcriptional coactivators. The transcriptional activities of the nuclear factor (NF) complexes (NF45-NF90 and NF45-NF110) are mediated by both the upstream enhancer and core promoter regions of the c-fos gene and do not require their double-stranded RNA binding activities. The NF complexes cooperate with general coactivators, PC4 and Mediator, to elicit a high level of transcription and display multiple interactions with activators and the components of the general transcriptional machinery. Knockdown of the endogenous NF90/NF110 in mouse cells shows an important role for the NF complexes in inducing c-fos transcription. Chromatin immunoprecipitation assays demonstrate that the NF complexes occupy the c-fos enhancer/promoter region before and after serum induction and that their occupancies within the coding region of the c-fos gene increase in parallel to that of RNAPII upon serum induction. In light of their dynamic occupancy on the c-fos gene as well as direct functions in both transcription and posttranscriptional processes, the NF complexes appear to serve as multifunctional coactivators that coordinate different steps of gene expression to facilitate rapid response of inducible genes.
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Affiliation(s)
- Tomoyoshi Nakadai
- From the Department of Molecular Biology, Faculty of Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Iruma-gun, Saitama 350-0495, Japan and
| | - Aya Fukuda
- Department of Biochemistry, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Miho Shimada
- From the Department of Molecular Biology, Faculty of Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Iruma-gun, Saitama 350-0495, Japan and
| | - Ken Nishimura
- Department of Biochemistry, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Koji Hisatake
- Department of Biochemistry, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
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7
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NF90 isoforms, a new family of cellular proteins involved in viral replication? Biochimie 2015; 108:20-4. [DOI: 10.1016/j.biochi.2014.10.022] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 10/26/2014] [Indexed: 01/09/2023]
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8
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NF90 in posttranscriptional gene regulation and microRNA biogenesis. Int J Mol Sci 2013; 14:17111-21. [PMID: 23965975 PMCID: PMC3759954 DOI: 10.3390/ijms140817111] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 11/16/2022] Open
Abstract
Gene expression patterns are effectively regulated by turnover and translation regulatory (TTR) RNA-binding proteins (RBPs). The TTR-RBPs control gene expression at posttranscriptional levels, such as pre-mRNA splicing, mRNA cytoplasmic export, turnover, storage, and translation. Double-stranded RNA binding proteins (DSRBPs) are known to regulate many processes of cellular metabolism, including transcriptional control, translational control, mRNA processing and localization. Nuclear factor 90 (NF90), one of the DSRBPs, is abundantly expressed in vertebrate tissue and participates in many aspects of RNA metabolism. NF90 was originally purified as a component of a DNA binding complex which binds to the antigen recognition response element 2 in the interleukin 2 promoter. Recent studies have provided us with interesting insights into its possible physiological roles in RNA metabolism, including transcription, degradation, and translation. In addition, it was shown that NF90 regulates microRNA expression. In this review, we try to focus on the function of NF90 in posttranscriptional gene regulation and microRNA biogenesis.
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9
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Masuda K, Kuwano Y, Nishida K, Rokutan K. General RBP expression in human tissues as a function of age. Ageing Res Rev 2012; 11:423-31. [PMID: 22326651 DOI: 10.1016/j.arr.2012.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 01/09/2012] [Accepted: 01/19/2012] [Indexed: 10/14/2022]
Abstract
Gene expression patterns vary dramatically in a tissue-specific and age-dependent manner. RNA-binding proteins that regulate mRNA turnover and/or translation (TTR-RBPs) critically affect the subsets of expressed proteins. Although many proteins implicated in age-related processes are encoded by mRNAs that are targets of TTR-RBPs, very little is known regarding the tissue- and age-dependent expression of TTR-RBPs in humans. Recent analysis of TTR-RBPs expression using human tissue microarray has provided us interesting insight into their possibly physiologic roles as a function of age. This analysis has also revealed striking discrepancies between the levels of TTR-RBPs in senescent human diploid fibroblasts (HDFs), widely used as an in vitro model of aging, and the levels of TTR-RBPs in tissues from individuals of advancing age. In this article, we will review our knowledge of human TTR-RBP expression in different tissues as a function of age.
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10
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Yamauchi T, Nakamura N, Hiramoto M, Yuri M, Yokota H, Naitou M, Takeuchi M, Yamanaka K, Kita A, Nakahara T, Kinoyama I, Matsuhisa A, Kaneko N, Koutoku H, Sasamata M, Kobori M, Katou M, Tawara S, Kawabata S, Furuichi K. Sepantronium bromide (YM155) induces disruption of the ILF3/p54(nrb) complex, which is required for survivin expression. Biochem Biophys Res Commun 2012; 425:711-6. [PMID: 22842455 DOI: 10.1016/j.bbrc.2012.07.103] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 07/19/2012] [Indexed: 12/01/2022]
Abstract
YM155, a small-molecule survivin suppressant, specifically binds to the transcription factor ILF3, which regulates the expression of survivin[1]. In this experiment we have demonstrated that p54(nrb) binds to the survivin promoter and regulates survivin expression. p54(nrb) forms a complex with ILF3, which directly binds to YM155. YM155 induces disruption of the ILF3/p54(nrb) complex, which results in a different subcellular localization between ILF3 and p54(nrb). Thus, identification of molecular targets of YM155 in suppression of the survivin pathway, might lead to development of its use as a novel potential target in cancers.
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Affiliation(s)
- Tomohiro Yamauchi
- Drug Discovery Research, Astellas Pharma, Inc., Tsukuba-shi, Ibaraki, Japan.
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11
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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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12
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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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13
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Abdelmohsen K, Kuwano Y, Kim HH, Gorospe M. Posttranscriptional gene regulation by RNA-binding proteins during oxidative stress: implications for cellular senescence. Biol Chem 2008; 389:243-255. [PMID: 18177264 PMCID: PMC8481862 DOI: 10.1515/bc.2008.022] [Citation(s) in RCA: 215] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
To respond adequately to oxidative stress, mammalian cells elicit rapid and tightly controlled changes in gene expression patterns. Besides alterations in the subsets of transcribed genes, two posttranscriptional processes prominently influence the oxidant-triggered gene expression programs: mRNA turnover and translation. Here, we review recent progress in our knowledge of the turnover and translation regulatory (TTR) mRNA-binding proteins (RBPs) that influence gene expression in response to oxidative damage. Specifically, we identify oxidant damage-regulated mRNAs that are targets of TTR-RBPs, we review the oxidant-triggered signaling pathways that govern TTR-RBP function, and we examine emerging evidence that TTR-RBP activity is altered with senescence and aging. Given the potent influence of TTR-RBPs upon oxidant-regulated gene expression profiles, we propose that the senescence-associated changes in TTR-RBPs directly contribute to the impaired responses to oxidant damage that characterize cellular senescence and advancing age.
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Parrott AM, Mathews MB. Novel rapidly evolving hominid RNAs bind nuclear factor 90 and display tissue-restricted distribution. Nucleic Acids Res 2007; 35:6249-58. [PMID: 17855395 PMCID: PMC2094060 DOI: 10.1093/nar/gkm668] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Nuclear factor 90 (NF90) is a double-stranded RNA-binding protein implicated in multiple cellular functions, but with few identified RNA partners. Using in vivo cross-linking followed by immunoprecipitation, we discovered a family of small NF90-associated RNAs (snaR). These highly structured non-coding RNAs of ∼117 nucleotides are expressed in immortalized human cell lines of diverse lineages. In human tissues, they are abundant in testis, with minor distribution in brain, placenta and some other organs. Two snaR subsets were isolated from human 293 cells, and additional species were found by bioinformatic analysis. Their genes often occur in multiple copies arranged in two inverted regions of tandem repeats on chromosome 19. snaR-A is transcribed by RNA polymerase III from an intragenic promoter, turns over rapidly, and shares sequence identity with Alu RNA and two potential piRNAs. It interacts with NF90's double-stranded RNA-binding motifs. snaR orthologs are present in chimpanzee but not other mammals, and include genes located in the promoter of two chorionic gonadotropin hormone genes. snaRs appear to have undergone accelerated evolution and differential expansion in the great apes.
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15
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Parrott AM, Walsh MR, Mathews MB. Analysis of RNA:protein interactions in vivo: identification of RNA-binding partners of nuclear factor 90. Methods Enzymol 2007; 429:243-60. [PMID: 17913627 DOI: 10.1016/s0076-6879(07)29012-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ribonucleoprotein complexes (RNPs) perform a multitude of functions in the cell. Elucidating the composition of such complexes and unraveling their many interactions are current challenges in molecular biology. To stabilize complexes formed in cells and to preclude reassortment of their components during isolation, we employ chemical crosslinking of the RNA and protein moieties. Here we describe the identification of cellular RNAs bound to nuclear factor 90 (NF90), the founder member of a family of ubiquitous double-stranded RNA-binding proteins. Crosslinked RNA-NF90 complexes were immunoprecipitated from stable cell lines containing epitope-tagged NF90 protein isoforms. The bound RNA was released and identified through RNase H digestion and by various gene amplification techniques. We appraise the methods used by altering crosslinking conditions, and the binding profiles of different NF90 protein isoforms in synchronized and asynchronous cells are compared. This study discovers two novel RNA species and establishes NF90 as a multiclass RNA-binding protein, capable of binding representatives of all three classes of RNA.
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Affiliation(s)
- Andrew M Parrott
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey, USA
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Viranaicken W, Gasmi L, Chauvin C, Denoulet P, Larcher JC. Identification of a newly spliced exon in the mouse Ilf3 gene generating two long and short isoforms of Ilf3 and NF90. Genomics 2006; 88:622-32. [PMID: 16952437 DOI: 10.1016/j.ygeno.2006.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Revised: 04/14/2006] [Accepted: 08/09/2006] [Indexed: 11/24/2022]
Abstract
The mammalian IlF3 and NF90 proteins, involved in several cellular functions, have common N-terminal and central sequences and specific C-terminal regions. These proteins exhibit a large heterogeneity generated by posttranscriptional and posttranslational modifications. Part of their polymorphism is due to the alternative splicing of exon 3 located just downstream of the translation initiation codon. This 39-nucleotide-long exon, not described so far, codes for an N-terminal sequence of 13 residues (ALYHHHFITRRRR) also present in rat and human IlF3 or NF90. Four mRNAs are expressed in mouse brain, two for Ilf3 and two for NF90, differing in their 3' sequence to generate the specific Ilf3 and NF90 C-terminal domains and in the presence or the absence of exon 3 to generate long and short isoforms of both proteins. By RT-PCR, no other variants were found. Combining our results and GenBank sequences, we determined the exon-intron organization of the entire mouse Ilf3 gene divided into 22 exons.
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Affiliation(s)
- Wildriss Viranaicken
- Laboratoire de Biochimie Cellulaire, UMR 7098 CNRS, Université Pierre et Marie Curie, 9 Quai Saint-Bernard, Case 265, 75252 Paris Cedex 05, France
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Carinci F, Palmieri A, Perrotti V, Piattelli A, Cenzi R, Brunell G, Martinelli M, Arlotti M, Pezzetti F. Genetic Effects of Medpor® on Osteoblast-like Cells. J Craniofac Surg 2006; 17:1243-50. [PMID: 17119439 DOI: 10.1097/01.scs.0000248644.02718.28] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Porous polyethylene (PP or Medpor) is an alloplastic material used worldwide for craniofacial reconstruction. Although several clinical studies are available, there is a lack as regard the genetic effects. Because PP is always fixed on bone and the mechanism by which PP acts on osteoblasts is unknown, we therefore attempted to address this question by using microarray techniques to identify genes that are differently regulated in osteoblasts exposed to PP. By using DNA microarrays containing 19,200 genes, we identified in osteoblast-like cell lines (i.e. MG-63) cultured on PP several genes where expression was differentially regulated. The differentially expressed genes cover a broad range of functional activities: 1) signal transduction, 2) transcription, 3) translation, 4) cell cycle regulation, 5) vesicular transport, and 6) production of cytoskeletal elements, cell-adhesion molecules and extracellular matrix components. The data reported are, to our knowledge, the first genetic portrait of osteoblast-like cells cultured on PP. They are relevant to better understanding of the molecular mechanism of bone-PP interaction and as a model for comparing other materials used for bone reconstruction.
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Parrott AM, Walsh MR, Reichman TW, Mathews MB. RNA binding and phosphorylation determine the intracellular distribution of nuclear factors 90 and 110. J Mol Biol 2005; 348:281-93. [PMID: 15811368 DOI: 10.1016/j.jmb.2005.02.047] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 02/23/2005] [Accepted: 02/24/2005] [Indexed: 11/20/2022]
Abstract
Members of the nuclear factor 90 (NF90) family of human double-stranded RNA (dsRNA) binding proteins are phosphorylated and translocate into the cytoplasm with the onset of mitosis. We investigated the mechanism of translocation for NF90 and NF110, its larger splice variant. During interphase, NF90 is predominantly nuclear, NF110 is exclusively nuclear, and both are bound to RNA. About half of the NF90 is tethered in the nucleus by RNA bound to the protein's dsRNA-binding motifs. The nuclear localization of NF110 is also dependent on RNA binding but is independent of these motifs, and is governed by contacts made to the protein's unique C terminus. During mitosis, about half of the cytoplasmic NF90 becomes dissociated from RNA, but phosphorylation does not impair the binding affinity of either NF90 or NF110 for dsRNA. We conclude that NF90 and NF110 engage RNA differentially and translocate from the nucleus to the cytoplasm in mitosis because phosphorylation disturbs their interactions with other nuclear proteins.
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Affiliation(s)
- Andrew M Parrott
- Department of Biochemistry and Molecular Biology and New Jersey Medical School, UMDNJ, 185 South Orange Ave., P.O. Box 1709, Newark, NJ 07101-1709, USA
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Xu YH, Grabowski GA. Translation modulation of acid beta-glucosidase in HepG2 cells: participation of the PKC pathway. Mol Genet Metab 2005; 84:252-64. [PMID: 15694175 DOI: 10.1016/j.ymgme.2004.10.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2004] [Revised: 10/08/2004] [Accepted: 10/11/2004] [Indexed: 11/26/2022]
Abstract
Acid beta-glucosidase (GCase) is the enzyme deficient in Gaucher disease, a prototypical inherited metabolic error for enzyme and gene therapy. An 80 kDa mammalian cytoplasmic translational control protein (TCP80) modulates GCase translation in vitro and ex vivo by interacting with the 5' coding region of GCase RNA. Ten predicted PKC phosphorylation sites (Ser- or Thr-) are in the TCP80 protein. Phosphorylation of TCP80 in vitro by PKC greatly enhanced its translational inhibitory function using in vitro translation assays; binding of GCase mRNA to TCP80 was unaltered. Conversely, de-phosphorylation of TCP80 reduced its translational inhibitory function. Phosphorylation-related modulation of GCase mRNA translation also was studied in HepG2 cells. GCase expression (protein and activity levels) in HepG2 cells increased (>2-fold) in cells treated with bisindolylmaleimide (BIM), a highly selective PKC specific inhibitor. This correlated with a 90% reduction in TCP80 phosphorylation in the presence of BIM. The amount of TCP80 protein in cytoplasm and its RNA-binding activity were unchanged. These experiments indicate that GCase mRNA translation is modulated by PKC signaling pathways that are mediated through TCP80. These findings indicate potential broader impacts of the TCP/PKC system on expression of this and other genes of therapeutic interest.
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Affiliation(s)
- You-Hai Xu
- Division of Human Genetics, The Children's Hospital Research Foundation, Cincinnati, OH 45229-3039, USA
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