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Huang S, Hu J, Hu M, Hou Y, Zhang B, Liu J, Liu X, Chen Z, Wang L. Cooperation between SIX1 and DHX9 transcriptionally regulates integrin-focal adhesion signaling mediated metastasis and sunitinib resistance in KIRC. Oncogene 2024; 43:2951-2969. [PMID: 39174859 DOI: 10.1038/s41388-024-03126-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 08/24/2024]
Abstract
High invasive capacity and acquired tyrosine kinase inhibitors (TKI) resistance of kidney renal clear cell carcinoma (KIRC) cells remain obstacles to prolonging the survival time of patients with advanced KIRC. In the present study, we reported that sine oculis homeobox 1 (SIX1) was upregulated in sunitinib-resistant KIRC cells and metastatic KIRC tissues. Subsequently, we found that SIX1 mediated metastasis and sunitinib resistance via Focal adhesion (FA) signaling, and knockdown of SIX1 enhanced the antitumor efficiency of sunitinib in KIRC. Mechanistically, Integrin subunit beta 1 (ITGB1), an upstream gene of FA signaling, was a direct transcriptional target of SIX1. In addition, we showed that DExH-box helicase 9 (DHX9) was an important mediator for SIX1-induced ITGB1 transcription, and silencing the subunits of SIX1/DHX9 complex significantly reduced transcription of ITGB1. Downregulation of SIX1 attenuated nuclear translocation of DHX9 and abrogated the binding of DHX9 to ITGB1 promoter. Collectively, our results unveiled a new signal axis SIX1/ITGB1/FAK in KIRC and identified a novel therapeutic strategy for metastatic KIRC patients.
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Affiliation(s)
- Shiyu Huang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
- Central Laboratory, Renmin Hospital of Wuhan University, 430060, Wuhan, Hubei, China
| | - Juncheng Hu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Min Hu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Yanguang Hou
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Banghua Zhang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
- Hubei Key Laboratory of Digestive System Disease, Wuhan, 430060, China
| | - Jiachen Liu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Xiuheng Liu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China.
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China.
| | - Zhiyuan Chen
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China.
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China.
| | - Lei Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China.
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China.
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2
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Gotur D, Case A, Liu J, Sickmier EA, Holt N, Knockenhauer KE, Yao S, Lee YT, Copeland RA, Buker SM, Boriack-Sjodin PA. Development of assays to support identification and characterization of modulators of DExH-box helicase DHX9. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:376-384. [PMID: 37625785 DOI: 10.1016/j.slasd.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/02/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
DHX9 is a DExH-box RNA helicase that utilizes hydrolysis of all four nucleotide triphosphates (NTPs) to power cycles of 3' to 5' directional movement to resolve and/or unwind double stranded RNA, DNA, and RNA/DNA hybrids, R-loops, triplex-DNA and G-quadraplexes. DHX9 activity is important for both viral amplification and maintaining genomic stability in cancer cells; therefore, it is a therapeutic target of interest for drug discovery efforts. Biochemical assays measuring ATP hydrolysis and oligonucleotide unwinding for DHX9 have been developed and characterized, and these assays can support high-throughput compound screening efforts under balanced conditions. Assay development efforts revealed DHX9 can use double stranded RNA with 18-mer poly(U) 3' overhangs and as well as significantly shorter overhangs at the 5' or 3' end as substrates. The enzymatic assays are augmented by a robust SPR assay for compound validation. A mechanism-derived inhibitor, GTPγS, was characterized as part of the validation of these assays and a crystal structure of GDP bound to cat DHX9 has been solved. In addition to enabling drug discovery efforts for DHX9, these assays may be extrapolated to other RNA helicases providing a valuable toolkit for this important target class.
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Affiliation(s)
- Deepali Gotur
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | - April Case
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | - Julie Liu
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | - E Allen Sickmier
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | - Nicholas Holt
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | | | - Shihua Yao
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | - Young-Tae Lee
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | | | - Shane M Buker
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
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3
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Yang S, Winstone L, Mondal S, Wu Y. Helicases in R-loop Formation and Resolution. J Biol Chem 2023; 299:105307. [PMID: 37778731 PMCID: PMC10641170 DOI: 10.1016/j.jbc.2023.105307] [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: 07/27/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023] Open
Abstract
With the development and wide usage of CRISPR technology, the presence of R-loop structures, which consist of an RNA-DNA hybrid and a displaced single-strand (ss) DNA, has become well accepted. R-loop structures have been implicated in a variety of circumstances and play critical roles in the metabolism of nucleic acid and relevant biological processes, including transcription, DNA repair, and telomere maintenance. Helicases are enzymes that use an ATP-driven motor force to unwind double-strand (ds) DNA, dsRNA, or RNA-DNA hybrids. Additionally, certain helicases have strand-annealing activity. Thus, helicases possess unique positions for R-loop biogenesis: they utilize their strand-annealing activity to promote the hybridization of RNA to DNA, leading to the formation of R-loops; conversely, they utilize their unwinding activity to separate RNA-DNA hybrids and resolve R-loops. Indeed, numerous helicases such as senataxin (SETX), Aquarius (AQR), WRN, BLM, RTEL1, PIF1, FANCM, ATRX (alpha-thalassemia/mental retardation, X-linked), CasDinG, and several DEAD/H-box proteins are reported to resolve R-loops; while other helicases, such as Cas3 and UPF1, are reported to stimulate R-loop formation. Moreover, helicases like DDX1, DDX17, and DHX9 have been identified in both R-loop formation and resolution. In this review, we will summarize the latest understandings regarding the roles of helicases in R-loop metabolism. Additionally, we will highlight challenges associated with drug discovery in the context of targeting these R-loop helicases.
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Affiliation(s)
- Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lacey Winstone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sohaumn Mondal
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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4
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Yamada M, Nitta Y, Uehara T, Suzuki H, Miya F, Takenouchi T, Tamura M, Ayabe S, Yoshiki A, Maeno A, Saga Y, Furuse T, Yamada I, Okamoto N, Kosaki K, Sugie A. Heterozygous loss-of-function DHX9 variants are associated with neurodevelopmental disorders: Human genetic and experimental evidences. Eur J Med Genet 2023:104804. [PMID: 37369308 DOI: 10.1016/j.ejmg.2023.104804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/14/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023]
Abstract
DExH-box helicases are involved in unwinding of RNA and DNA. Among the 16 DExH-box genes, monoallelic variants of DHX16, DHX30, DHX34, and DHX37 are known to be associated with neurodevelopmental disorders. In particular, DHX30 is well established as a causative gene for neurodevelopmental disorders. Germline variants of DHX9, the closest homolog of DHX30, have not been reported until now as being associated with congenital disorders in humans, except that one de novo heterozygous variant, p.(Arg1052Gln) of the gene was identified during comprehensive screening in a patient with autism; unfortunately, the phenotypic details of this individual are unknown. Herein, we report a patient with a heterozygous de novo missense variant, p.(Gly414Arg) of DHX9 who presented with a short stature, intellectual disability, and ventricular non-compaction cardiomyopathy. The variant was located in the glycine codon of the ATP-binding site, G-C-G-K-T. To assess the pathogenicity of this variants, we generated transgenic Drosophila lines expressing human wild-type and mutant DHX9 proteins: 1) the mutant proteins showed aberrant localization both in the nucleus and the cytoplasm; 2) ectopic expression of wild-type protein in the visual system led to the rough eye phenotype, whereas expression of the mutant proteins had minimal effect; 3) overexpression of the wild-type protein in the retina led to a reduction in axonal numbers, whereas expression of the mutant proteins had a less pronounced effect. Furthermore, in a gene-editing experiment of Dhx9 G416 to R416, corresponding to p.(Gly414Arg) in humans, heterozygous mice showed a reduced body size, reduced emotionality, and cardiac conduction abnormality. In conclusion, we established that heterozygosity for a loss-of-function variant of DHX9 can lead to a new neurodevelopmental disorder.
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Affiliation(s)
- Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Yohei Nitta
- Brain Research Institute, Niigata University, Niigata, Japan
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Fuyuki Miya
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Masaru Tamura
- Mouse Phenotype Analysis Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Shinya Ayabe
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Akiteru Maeno
- Cell Architecture Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yumiko Saga
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tamio Furuse
- Mouse Phenotype Analysis Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Ikuko Yamada
- Mouse Phenotype Analysis Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.
| | - Atsushi Sugie
- Brain Research Institute, Niigata University, Niigata, Japan.
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5
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Ren X, Wang D, Zhang G, Zhou T, Wei Z, Yang Y, Zheng Y, Lei X, Tao W, Wang A, Li M, Flavell RA, Zhu S. Nucleic DHX9 cooperates with STAT1 to transcribe interferon-stimulated genes. SCIENCE ADVANCES 2023; 9:eadd5005. [PMID: 36735791 PMCID: PMC9897671 DOI: 10.1126/sciadv.add5005] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 01/05/2023] [Indexed: 06/13/2023]
Abstract
RNA helicase DHX9 has been extensively characterized as a transcriptional regulator, which is consistent with its mostly nucleic localization. It is also involved in recognizing RNA viruses in the cytoplasm. However, there is no in vivo data to support the antiviral role of DHX9; meanwhile, as a nuclear protein, if and how nucleic DHX9 promotes antiviral immunity remains largely unknown. Here, we generated myeloid-specific and hepatocyte-specific DHX9 knockout mice and confirmed that DHX9 is crucial for host resistance to RNA virus infections in vivo. By additional knockout MAVS or STAT1 in DHX9-deficient mice, we demonstrated that nucleic DHX9 plays a positive role in regulating interferon-stimulated gene (ISG) expression downstream of type I interferon. Mechanistically, upon interferon stimulation, DHX9 is directly bound to STAT1 and recruits Pol II to the ISG promoter region to participate in STAT1-mediated transcription of ISGs. Collectively, these findings uncover an important role for nucleic DHX9 in antiviral immunity.
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Affiliation(s)
- Xingxing Ren
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, 230001 Hefei, China
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Department of Gastroenterology, Third Affiliated Hospital of Guangzhou Medical University, 510145 Guangzhou, China
| | - Decai Wang
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, 230001 Hefei, China
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Guorong Zhang
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, 230001 Hefei, China
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Tingyue Zhou
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, 230001 Hefei, China
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Zheng Wei
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Yi Yang
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Yunjiang Zheng
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Xuqiu Lei
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Wanyin Tao
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, 230001 Hefei, China
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Anmin Wang
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, 230001 Hefei, China
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Mingsong Li
- Department of Gastroenterology, Third Affiliated Hospital of Guangzhou Medical University, 510145 Guangzhou, China
| | - Richard A. Flavell
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Shu Zhu
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, 230001 Hefei, China
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- School of Data Science, University of Science and Technology of China, Hefei 230026, China
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China
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6
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Nikolenko JV, Georgieva SG, Kopytova DV. Diversity of MLE Helicase Functions in the Regulation of Gene Expression in Higher Eukaryotes. Mol Biol 2023. [DOI: 10.1134/s0026893323010107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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7
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Li J, Cheng C, Xu J, Zhang T, Tokat B, Dolios G, Ramakrishnan A, Shen L, Wang R, Xu PX. The transcriptional coactivator Eya1 exerts transcriptional repressive activity by interacting with REST corepressors and REST-binding sequences to maintain nephron progenitor identity. Nucleic Acids Res 2022; 50:10343-10359. [PMID: 36130284 PMCID: PMC9561260 DOI: 10.1093/nar/gkac760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/18/2022] [Accepted: 08/27/2022] [Indexed: 11/15/2022] Open
Abstract
Eya1 is critical for establishing and maintaining nephron progenitor cells (NPCs). It belongs to a family of proteins called phosphatase-transcriptional activators but without intrinsic DNA-binding activity. However, the spectrum of the Eya1-centered networks is underexplored. Here, we combined transcriptomic, genomic and proteomic approaches to characterize gene regulation by Eya1 in the NPCs. We identified Eya1 target genes, associated cis-regulatory elements and partner proteins. Eya1 preferentially occupies promoter sequences and interacts with general transcription factors (TFs), RNA polymerases, different types of TFs, chromatin-remodeling factors with ATPase or helicase activity, and DNA replication/repair proteins. Intriguingly, we identified REST-binding motifs in 76% of Eya1-occupied sites without H3K27ac-deposition, which were present in many Eya1 target genes upregulated in Eya1-deficient NPCs. Eya1 copurified REST-interacting chromatin-remodeling factors, histone deacetylase/lysine demethylase, and corepressors. Coimmunoprecipitation validated physical interaction between Eya1 and Rest/Hdac1/Cdyl/Hltf in the kidneys. Collectively, our results suggest that through interactions with chromatin-remodeling factors and specialized DNA-binding proteins, Eya1 may modify chromatin structure to facilitate the assembly of regulatory complexes that regulate transcription positively or negatively. These findings provide a mechanistic basis for how Eya1 exerts its activity by forming unique multiprotein complexes in various biological processes to maintain the cellular state of NPCs.
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Affiliation(s)
- Jun Li
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Chunming Cheng
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Jinshu Xu
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Ting Zhang
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Bengu Tokat
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Georgia Dolios
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | | | - Li Shen
- Department of Neurosciences, New York, NY 10029, USA
| | - Rong Wang
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Pin-Xian Xu
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA.,Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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8
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Tang S, Cao Y, Cai Z, Nie X, Ruan J, Zhou Z, Ruan G, Zhu Z, Han W, Ding C. The lncRNA PILA promotes NF-κB signaling in osteoarthritis by stimulating the activity of the protein arginine methyltransferase PRMT1. Sci Signal 2022; 15:eabm6265. [PMID: 35609127 DOI: 10.1126/scisignal.abm6265] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Inflammatory cytokine-induced activation of nuclear factor κB (NF-κB) signaling plays a critical role in the pathogenesis of osteoarthritis (OA). We identified PILA as a long noncoding RNA (lncRNA) that enhances NF-κB signaling and OA. The abundance of PILA was increased in damaged cartilage from patients with OA and in human articular chondrocytes stimulated with the proinflammatory cytokine tumor necrosis factor (TNF). Knockdown of PILA inhibited TNF-induced NF-κB signaling, extracellular matrix catabolism, and apoptosis in chondrocytes, whereas ectopic expression of PILA promoted NF-κB signaling and matrix degradation. PILA promoted PRMT1-mediated arginine methylation of DExH-box helicase 9 (DHX9), leading to an increase in the transcription of the gene encoding transforming growth factor β-activated kinase 1 (TAK1), an upstream activator of NF-κB signaling. Furthermore, intra-articular injection of an adenovirus vector encoding PILA triggered spontaneous cartilage loss and exacerbated posttraumatic OA in mice. This study provides insight into the regulation of NF-κB signaling in OA and identifies a potential therapeutic target for this disease.
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Affiliation(s)
- Su'an Tang
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, 510280 Guangzhou, Guangdong, China.,Centre of Orthopedics, Zhujiang Hospital, Southern Medical University, 510280 Guangzhou, Guangdong, China
| | - Yumei Cao
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, 510280 Guangzhou, Guangdong, China
| | - Zhaopeng Cai
- Department of Orthopedics, Eighth Affiliated Hospital, Sun Yat-sen University, 518033 Shenzhen, Guangdong, China
| | - Xiaoyu Nie
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, 510280 Guangzhou, Guangdong, China
| | - Jianzhao Ruan
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, 510280 Guangzhou, Guangdong, China
| | - Zuoqing Zhou
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, 510280 Guangzhou, Guangdong, China.,Department of Orthopedics, First Affiliated Hospital, Shaoyang University, 422099 Shaoyang, Hunan, China
| | - Guangfeng Ruan
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, 510280 Guangzhou, Guangdong, China
| | - Zhaohua Zhu
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, 510280 Guangzhou, Guangdong, China.,Centre of Orthopedics, Zhujiang Hospital, Southern Medical University, 510280 Guangzhou, Guangdong, China
| | - Weiyu Han
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, 510280 Guangzhou, Guangdong, China.,Centre of Orthopedics, Zhujiang Hospital, Southern Medical University, 510280 Guangzhou, Guangdong, China
| | - Changhai Ding
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, 510280 Guangzhou, Guangdong, China.,Menzies Institute for Medical Research, University of Tasmania, 7000 Hobart, Tasmania, Australia
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9
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Caterino M, Paeschke K. Action and function of helicases on RNA G-quadruplexes. Methods 2021; 204:110-125. [PMID: 34509630 PMCID: PMC9236196 DOI: 10.1016/j.ymeth.2021.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Methodological progresses and piling evidence prove the rG4 biology in vivo. rG4s step in virtually every aspect of RNA biology. Helicases unwinding of rG4s is a fine regulatory layer to the downstream processes and general cell homeostasis. The current knowledge is however limited to a few cell lines. The regulation of helicases themselves is delineating as a important question. Non-helicase rG4-processing proteins likely play a role.
The nucleic acid structure called G-quadruplex (G4) is currently discussed to function in nucleic acid-based mechanisms that influence several cellular processes. They can modulate the cellular machinery either positively or negatively, both at the DNA and RNA level. The majority of what we know about G4 biology comes from DNA G4 (dG4) research. RNA G4s (rG4), on the other hand, are gaining interest as researchers become more aware of their role in several aspects of cellular homeostasis. In either case, the correct regulation of G4 structures within cells is essential and demands specialized proteins able to resolve them. Small changes in the formation and unfolding of G4 structures can have severe consequences for the cells that could even stimulate genome instability, apoptosis or proliferation. Helicases are the most relevant negative G4 regulators, which prevent and unfold G4 formation within cells during different pathways. Yet, and despite their importance only a handful of rG4 unwinding helicases have been identified and characterized thus far. This review addresses the current knowledge on rG4s-processing helicases with a focus on methodological approaches. An example of a non-helicase rG4s-unwinding protein is also briefly described.
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Affiliation(s)
- Marco Caterino
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany.
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10
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Yuan W, Al-Hadid Q, Wang Z, Shen L, Cho H, Wu X, Yang Y. TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution. Nucleic Acids Res 2021; 49:8573-8591. [PMID: 34329467 PMCID: PMC8421139 DOI: 10.1093/nar/gkab642] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 06/14/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022] Open
Abstract
R-loops, which consist of a DNA/RNA hybrid and a displaced single-stranded DNA (ssDNA), are increasingly recognized as critical regulators of chromatin biology. R-loops are particularly enriched at gene promoters, where they play important roles in regulating gene expression. However, the molecular mechanisms that control promoter-associated R-loops remain unclear. The epigenetic ‘reader’ Tudor domain-containing protein 3 (TDRD3), which recognizes methylarginine marks on histones and on the C-terminal domain of RNA polymerase II, was previously shown to recruit DNA topoisomerase 3B (TOP3B) to relax negatively supercoiled DNA and prevent R-loop formation. Here, we further characterize the function of TDRD3 in R-loop metabolism and introduce the DExH-box helicase 9 (DHX9) as a novel interaction partner of the TDRD3/TOP3B complex. TDRD3 directly interacts with DHX9 via its Tudor domain. This interaction is important for recruiting DHX9 to target gene promoters, where it resolves R-loops in a helicase activity-dependent manner to facilitate gene expression. Additionally, TDRD3 also stimulates the helicase activity of DHX9. This stimulation relies on the OB-fold of TDRD3, which likely binds the ssDNA in the R-loop structure. Thus, DHX9 functions together with TOP3B to suppress promoter-associated R-loops. Collectively, these findings reveal new functions of TDRD3 and provide important mechanistic insights into the regulation of R-loop metabolism.
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Affiliation(s)
- Wei Yuan
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Qais Al-Hadid
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Zhihao Wang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Lei Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Hyejin Cho
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Xiwei Wu
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Yanzhong Yang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
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11
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Reunov A, Alexandrova Y, Komkova A, Reunova Y, Pimenova E, Vekhova E, Milani L. VASA-induced cytoplasmic localization of CYTB-positive mitochondrial substance occurs by destructive and nondestructive mitochondrial effusion, respectively, in early and late spermatogenic cells of the Manila clam. PROTOPLASMA 2021; 258:817-825. [PMID: 33580838 DOI: 10.1007/s00709-020-01601-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
To analyze the release of mitochondrial material, a process that is believed to be (i) induced by the VASA protein derived from germplasm granules, and (ii) which appears to play an important role during meiotic differentiation, the localization of the CYTB protein was studied in the process of spermatogenesis of the bivalve mollusk Ruditapes philippinarum (Manila clam). It was found that in early spermatogenic cells, such as spermatogonia and spermatocytes, the CYTB protein shows dispersion in the cytoplasm following the total disaggregation of VASA-invaded mitochondria, what is called here as "destructive mitochondrial effusion (DME)." It was found that the mitochondria of the maturing sperm cells also uptake VASA. It is accompanied by extramitochondrial transmembrane localization of CYTB assuming mitochondrial content release without mitochondrion demolishing. This phenomenon is called here as "nondestructive mitochondrial effusion (NDME)." Thus, in the spermatogenesis of the Manila clam, two patterns of mitochondrial release, DME and NDME, were found, which function, respectively, in early spermatogenic cells and in maturing spermatozoa. Despite the morphological difference, it is assumed that both DME and NDME have a similar functional nature. In both cases, the intramitochondrial localization of VASA coincides with the extramitochondrial localization of the mitochondrial matrix.
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Affiliation(s)
- Arkadiy Reunov
- Department of Biology, St. Francis Xavier University, Antigonish, NS, B2G 2W5, Canada.
- Far Eastern Branch of Russian Academy of Sciences, National Scientific Centre of Marine Biology, Vladivostok, 690041, Russia.
| | - Yana Alexandrova
- Far Eastern Branch of Russian Academy of Sciences, National Scientific Centre of Marine Biology, Vladivostok, 690041, Russia
| | - Alina Komkova
- Far Eastern Branch of Russian Academy of Sciences, National Scientific Centre of Marine Biology, Vladivostok, 690041, Russia
| | - Yulia Reunova
- Far Eastern Branch of Russian Academy of Sciences, National Scientific Centre of Marine Biology, Vladivostok, 690041, Russia
| | - Evgenia Pimenova
- Far Eastern Branch of Russian Academy of Sciences, National Scientific Centre of Marine Biology, Vladivostok, 690041, Russia
| | - Evgenia Vekhova
- Far Eastern Branch of Russian Academy of Sciences, National Scientific Centre of Marine Biology, Vladivostok, 690041, Russia
| | - Liliana Milani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi, 3, 40126, Bologna, Italy
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12
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Pan YQ, Xing L. The Current View on the Helicase Activity of RNA Helicase A and Its Role in Gene Expression. Curr Protein Pept Sci 2020; 22:29-40. [PMID: 33143622 DOI: 10.2174/1389203721666201103084122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/18/2020] [Accepted: 09/09/2020] [Indexed: 11/22/2022]
Abstract
RNA helicase A (RHA) is a DExH-box helicase that plays regulatory roles in a variety of cellular processes, including transcription, translation, RNA splicing, editing, transport, and processing, microRNA genesis and maintenance of genomic stability. It is involved in virus replication, oncogenesis, and innate immune response. RHA can unwind nucleic acid duplex by nucleoside triphosphate hydrolysis. The insight into the molecular mechanism of helicase activity is fundamental to understanding the role of RHA in the cell. Herein, we reviewed the current advances on the helicase activity of RHA and its relevance to gene expression, particularly, to the genesis of circular RNA.
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Affiliation(s)
- Yuan-Qing Pan
- Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, Shanxi province, China
| | - Li Xing
- Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, Shanxi province, China
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13
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Guo F, Xing L. RNA helicase A as co-factor for DNA viruses during replication. Virus Res 2020; 291:198206. [PMID: 33132162 DOI: 10.1016/j.virusres.2020.198206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 11/30/2022]
Abstract
RNA helicase A (RHA) is a ubiquitously expressed DExH-box helicase enzyme that is involved in a wide range of biological processes including transcription, translation, and RNA processing. A number of RNA viruses recruit RHA to the viral RNA to facilitate virus replication. DNA viruses contain a DNA genome and replicate using a DNA-dependent DNA polymerase. RHA has also been reported to associate with some DNA viruses during replication, in which the enzyme acts on the viral RNA or protein products. As shown for Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus, RHA has potential to allow the virus to control a switch in cellular gene expression to modulate the antiviral response. While the study of the interaction of RHA with DNA viruses is still at an early stage, preliminary evidence indicates that the underlying molecular mechanisms are diverse. We now review the current status of this emerging field.
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Affiliation(s)
- Fan Guo
- Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, Shanxi province, PR China
| | - Li Xing
- Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, Shanxi province, PR China.
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14
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Peng C, Hou ST, Deng CX, Zhang Y. Function of DHX33 in promoting Warburg effect via regulation of glycolytic genes. J Cell Physiol 2020; 236:981-996. [PMID: 32617965 DOI: 10.1002/jcp.29909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 06/15/2020] [Accepted: 06/15/2020] [Indexed: 01/21/2023]
Abstract
Cancer cells metabolize glucose through glycolysis to promote cell proliferation even with abundant oxygen. Multiple glycolysis genes are deregulated during cancer development. Despite intensive effort, the cause of their deregulation remains incompletely understood. Here in this study, we discovered that DHX33 plays a critical role in Warburg effect of cancer cells. DHX33 deficient cells have markedly reduced glycolysis activity. Through RNA-seq analysis, we found multiple critical genes involved in Warburg effect were downregulated after DHX33 deficiency. These genes include lactate dehydrogenase A (LDHA), pyruvate dehydrogenase kinase 1 (PDK1), pyruvate kinase muscle isoform 2 (PKM2), enolase 1 (ENO1), ENO2, hexokinase 1/2, among others. With LDHA, PDK1, and PKM2 as examples, we further revealed that DHX33 altered the epigenetic marks around the promoter of glycolytic genes. This is through DHX33 in complex with Gadd45a-a growth arrest and DNA damage protein. DHX33 is required for the loading of Gadd45a and DNA dioxygenase Tet1 at the promoter sites, which resulted in active DNA demethylation and enhanced histone H4 acetylation. We conclude that DHX33 changes local epigenetic marks in favor of the transcription of glycolysis genes to promote cancer cell proliferation. Our study highlights the significance of RNA helicase DHX33 in Warburg effect and cancer therapeutics.
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Affiliation(s)
- Cheng Peng
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Sheng-Tao Hou
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Chu-Xia Deng
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Yandong Zhang
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Shenzhen KeYe Life Technologies, Co., Ltd., Shenzhen, Guangdong, China
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15
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Palombo R, Verdile V, Paronetto MP. Poison-Exon Inclusion in DHX9 Reduces Its Expression and Sensitizes Ewing Sarcoma Cells to Chemotherapeutic Treatment. Cells 2020; 9:cells9020328. [PMID: 32023846 PMCID: PMC7072589 DOI: 10.3390/cells9020328] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing is a combinatorial mechanism by which exons are joined to produce multiple mRNA variants, thus expanding the coding potential and plasticity of eukaryotic genomes. Defects in alternative splicing regulation are associated with several human diseases, including cancer. Ewing sarcoma is an aggressive tumor of bone and soft tissue, mainly affecting adolescents and young adults. DHX9 is a key player in Ewing sarcoma malignancy, and its expression correlates with worse prognosis in patients. In this study, by screening a library of siRNAs, we have identified splicing factors that regulate the alternative inclusion of a poison exon in DHX9 mRNA, leading to its downregulation. In particular, we found that hnRNPM and SRSF3 bind in vivo to this poison exon and suppress its inclusion. Notably, DHX9 expression correlates with that of SRSF3 and hnRNPM in Ewing sarcoma patients. Furthermore, downregulation of SRSF3 or hnRNPM inhibited DHX9 expression and Ewing sarcoma cell proliferation, while sensitizing cells to chemotherapeutic treatment. Hence, our study suggests that inhibition of hnRNPM and SRSF3 expression or activity could be exploited as a therapeutic tool to enhance the efficacy of chemotherapy in Ewing sarcoma.
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Affiliation(s)
- Ramona Palombo
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy; (R.P.); (V.V.)
| | - Veronica Verdile
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy; (R.P.); (V.V.)
- Department of Movement, Human and Health Sciences, Università degli Studi di Roma “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
| | - Maria Paola Paronetto
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy; (R.P.); (V.V.)
- Department of Movement, Human and Health Sciences, Università degli Studi di Roma “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
- Correspondence: ; Tel.:+39-0636733576
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16
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Reunov A, Yakovlev K, Hu J, Reunova Y, Komkova A, Alexandrova Y, Pimenova E, Tiefenbach J, Krause H. Close association between vasa-positive germ plasm granules and mitochondria correlates with cytoplasmic localization of 12S and 16S mtrRNAs during zebrafish spermatogenesis. Differentiation 2019; 109:34-41. [PMID: 31494397 DOI: 10.1016/j.diff.2019.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 11/16/2022]
Abstract
The phenomenon of the cytoplasmic localisation of mitochondrial ribosomal subunits (12 S mitochondrial rRNA and 16 S mitochondrial rRNA) has been discovered by scientific teams working with spermatogenic cells of mice. Previous reports showed that the release of mitochondrial substance occurs during interaction of mitochondria with the germ plasm granules (GG). To determine if the interplay between the vasa-positive GG and the mitochondria is associated with cytoplasmic localisation of mtrRNAs, we studied the spermatogenic cells of zebrafish, Danio rerio. It was revealed that in type A undifferentiated spermatogonia the GG did not contact mitochondria, and the extra-mitochondrial localisation of the mtrRNAs was not found. In type A differentiated spermatogonia, the amount of GG in contact with mitochondria increased, but the extra-mitochondrial localisation of the mtrRNAs was not found either. In type B late spermatogonia, which are pre-meiotic cells, the GG/mitochondrion complexes were typically found in contact with the nucleus. This stage was associated with the intra-mitochondrial localisation of GG-originated vasa and extra-mitochondrial localisation of 12 S mtrRNA and 16 S mtrRNA. Until the onset of meiosis, which was determined by the observation of synaptonemal complexes in zygotene-pachytene spermatocytes I, the GG/mitochondrion complexes disappeared, but both types of mtrRNAs persisted in the cytoplasm of spermatids and spermatozoa.
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Affiliation(s)
- Arkadiy Reunov
- National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690041, Russia; St. Francis Xavier University, Antigonish, NS B2G 2W5, Canada.
| | - Konstantin Yakovlev
- National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690041, Russia
| | - Jack Hu
- Donnelly Ctr., 160 College St., University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Yulia Reunova
- National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690041, Russia
| | - Alina Komkova
- National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690041, Russia
| | - Yana Alexandrova
- National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690041, Russia
| | - Evgenia Pimenova
- National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690041, Russia
| | - Jens Tiefenbach
- Donnelly Ctr., 160 College St., University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Henry Krause
- Donnelly Ctr., 160 College St., University of Toronto, Toronto, ON M5S 3E1, Canada
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17
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Ng YC, Chung WC, Kang HR, Cho HJ, Park EB, Kang SJ, Song MJ. A DNA-sensing-independent role of a nuclear RNA helicase, DHX9, in stimulation of NF-κB-mediated innate immunity against DNA virus infection. Nucleic Acids Res 2019; 46:9011-9026. [PMID: 30137501 PMCID: PMC6158622 DOI: 10.1093/nar/gky742] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 08/11/2018] [Indexed: 01/12/2023] Open
Abstract
DExD/H-box helicase 9 (DHX9), or RNA helicase A (RHA), is an abundant multifunctional nuclear protein. Although it was previously reported to act as a cytosolic DNA sensor in plasmacytoid dendritic cells (pDCs), the role and molecular mechanisms of action of DHX9 in cells that are not pDCs during DNA virus infection are not clear. Here, a macrophage-specific knockout and a fibroblast-specific knockdown of DHX9 impaired antiviral innate immunity against DNA viruses, leading to increased virus replication. DHX9 enhanced NF-κB–mediated transactivation in the nucleus, which required its ATPase-dependent helicase (ATPase/helicase) domain, but not the cytosolic DNA-sensing domain. In addition, DNA virus infection did not induce cytoplasmic translocation of nuclear DHX9 in macrophages and fibroblasts. Nuclear DHX9 was associated with a multiprotein complex including both NF-κB p65 and RNA polymerase II (RNAPII) in chromatin containing NF-κB–binding sites. DHX9 was essential for the recruitment of RNAPII rather than NF-κB p65, to the corresponding promoters; this function also required its ATPase/helicase activity. Taken together, our results show a critical role of nuclear DHX9 (as a transcription coactivator) in the stimulation of NF-κB–mediated innate immunity against DNA virus infection, independently of DHX9’s DNA-sensing function.
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Affiliation(s)
- Yee Ching Ng
- Virus-Host Interactions Laboratory, Department of Biosystems and Biotechnology, Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Woo-Chang Chung
- Virus-Host Interactions Laboratory, Department of Biosystems and Biotechnology, Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Hye-Ri Kang
- Virus-Host Interactions Laboratory, Department of Biosystems and Biotechnology, Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Hye-Jeong Cho
- Virus-Host Interactions Laboratory, Department of Biosystems and Biotechnology, Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Eun-Byeol Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suk-Jo Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Moon Jung Song
- Virus-Host Interactions Laboratory, Department of Biosystems and Biotechnology, Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
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18
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Cellular RNA Helicase DHX9 Interacts with the Essential Epstein-Barr Virus (EBV) Protein SM and Restricts EBV Lytic Replication. J Virol 2019; 93:JVI.01244-18. [PMID: 30541834 DOI: 10.1128/jvi.01244-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/28/2018] [Indexed: 12/11/2022] Open
Abstract
Epstein-Barr virus (EBV) SM protein is an RNA-binding protein that has multiple posttranscriptional gene regulatory functions essential for EBV lytic replication. In this study, we identified an interaction between SM and DHX9, a DExH-box helicase family member, by mass spectrometry and coimmunoprecipitation. DHX9 participates in many cellular pathways involving RNA, including transcription, processing, transport, and translation. DHX9 enhances virus production or infectivity of a wide variety of DNA and RNA viruses. Surprisingly, an increase in EBV late gene expression and virion production occurred upon knockdown of DHX9. To further characterize the SM-DHX9 interaction, we performed immunofluorescence microscopy of EBV-infected cells and found that DHX9 partially colocalized with SM in nuclear foci during EBV lytic replication. However, the positive effect of DHX9 depletion on EBV lytic gene expression was not confined to SM-dependent genes, indicating that the antiviral effect of DHX9 was not mediated through its effects on SM. DHX9 enhanced activation of innate antiviral pathways comprised of several interferon-stimulated genes that are active against EBV. SM inhibited the transcription-activating function of DHX9, which acts through cAMP response elements (CREs), suggesting that SM may also act to counteract DHX9's antiviral functions during lytic replication.IMPORTANCE This study identifies an interaction between Epstein-Barr virus (EBV) SM protein and cellular helicase DHX9, exploring the roles that this interaction plays in viral infection and host defenses. Whereas most previous studies established DHX9 as a proviral factor, we demonstrate that DHX9 may act as an inhibitor of EBV virion production. DHX9 enhanced innate antiviral pathways active against EBV and was needed for maximal expression of several interferon-induced genes. We show that SM binds to and colocalizes DHX9 and may counteract the antiviral function of DHX9. These data indicate that DHX9 possesses antiviral activity and that SM may suppress the antiviral functions of DHX9 through this association. Our study presents a novel host-pathogen interaction between EBV and the host cell.
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19
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The Host DHX9 DExH-Box Helicase Is Recruited to Chikungunya Virus Replication Complexes for Optimal Genomic RNA Translation. J Virol 2019; 93:JVI.01764-18. [PMID: 30463980 DOI: 10.1128/jvi.01764-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/19/2018] [Indexed: 12/19/2022] Open
Abstract
Beyond their role in cellular RNA metabolism, DExD/H-box RNA helicases are hijacked by various RNA viruses in order to assist replication of the viral genome. Here, we identify the DExH-box RNA helicase 9 (DHX9) as a binding partner of chikungunya virus (CHIKV) nsP3 mainly interacting with the C-terminal hypervariable domain. We show that during early CHIKV infection, DHX9 is recruited to the plasma membrane, where it associates with replication complexes. At a later stage of infection, DHX9 is, however, degraded through a proteasome-dependent mechanism. Using silencing experiments, we demonstrate that while DHX9 negatively controls viral RNA synthesis, it is also required for optimal mature nonstructural protein translation. Altogether, this study identifies DHX9 as a novel cofactor for CHIKV replication in human cells that differently regulates the various steps of CHIKV life cycle and may therefore mediate a switch in RNA usage from translation to replication during the earliest steps of CHIKV replication.IMPORTANCE The reemergence of chikungunya virus (CHIKV), an alphavirus that is transmitted to humans by Aedes mosquitoes, is a serious global health threat. In the absence of effective antiviral drugs, CHIKV infection has a significant impact on human health, with chronic arthritis being one of the most serious complications. The molecular understanding of host-virus interactions is a prerequisite to the development of targeted therapeutics capable to interrupt viral replication and transmission. Here, we identify the host cell DHX9 DExH-Box helicase as an essential cofactor for early CHIKV genome translation. We demonstrate that CHIKV nsP3 protein acts as a key factor for DHX9 recruitment to replication complexes. Finally, we establish that DHX9 behaves as a switch that regulates the progression of the viral cycle from translation to genome replication. This study might therefore have a significant impact on the development of antiviral strategies.
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20
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Dempsey A, Keating SE, Carty M, Bowie AG. Poxviral protein E3-altered cytokine production reveals that DExD/H-box helicase 9 controls Toll-like receptor-stimulated immune responses. J Biol Chem 2018; 293:14989-15001. [PMID: 30111593 DOI: 10.1074/jbc.ra118.005089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Indexed: 11/06/2022] Open
Abstract
Host pattern recognition receptors (PRRs) such as Toll-like receptors (TLRs) detect viruses and other pathogens, inducing production of cytokines that cause inflammation and mobilize cells to control infection. Vaccinia virus (VACV) encodes proteins that antagonize these host innate immune responses, and elucidating the mechanisms of action of these viral proteins helped shed light on PRR signaling mechanisms. The VACV virulence factor E3 is one of the most intensely studied VACV proteins and has multiple effects on host cells, many of which cannot be explained by the currently known cellular targets of E3. Here, we report that E3 expression in human monocytes alters TLR2- and TLR8-dependent cytokine induction, and particularly inhibits interleukin (IL)-6. Using MS, we identified DExD/H-box helicase 9 (DHX9) as an E3 target. Although DHX9 has previously been implicated as a PRR for sensing nucleic acid in dendritic cells, we found no role for DHX9 as a nucleic acid-sensing PRR in monocytes. Rather, DHX9 suppression in these cells phenocopied the effects of E3 expression on TLR2- and TLR8-dependent cytokine induction, in that DHX9 was required for all TLR8-dependent cytokines measured, and for TLR2-dependent IL-6. Furthermore, DHX9 also had a cell- and stimulus-independent role in IL-6 promoter induction. DHX9 enhanced NF-κB-dependent IL-6 promoter activation, which was directly antagonized by E3. These results indicate new roles for DHX9 in regulating cytokines in innate immunity and reveal that VACV E3 disrupts innate immune responses by targeting of DHX9.
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Affiliation(s)
- Alan Dempsey
- From the School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Sinead E Keating
- From the School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Michael Carty
- From the School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Andrew G Bowie
- From the School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
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21
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Lee T, Pelletier J. The biology of DHX9 and its potential as a therapeutic target. Oncotarget 2018; 7:42716-42739. [PMID: 27034008 PMCID: PMC5173168 DOI: 10.18632/oncotarget.8446] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/16/2016] [Indexed: 12/25/2022] Open
Abstract
DHX9 is member of the DExD/H-box family of helicases with a “DEIH” sequence at its eponymous DExH-box motif. Initially purified from human and bovine cells and identified as a homologue of the Drosophila Maleless (MLE) protein, it is an NTP-dependent helicase consisting of a conserved helicase core domain, two double-stranded RNA-binding domains at the N-terminus, and a nuclear transport domain and a single-stranded DNA-binding RGG-box at the C-terminus. With an ability to unwind DNA and RNA duplexes, as well as more complex nucleic acid structures, DHX9 appears to play a central role in many cellular processes. Its functions include regulation of DNA replication, transcription, translation, microRNA biogenesis, RNA processing and transport, and maintenance of genomic stability. Because of its central role in gene regulation and RNA metabolism, there are growing implications for DHX9 in human diseases and their treatment. This review will provide an overview of the structure, biochemistry, and biology of DHX9, its role in cancer and other human diseases, and the possibility of targeting DHX9 in chemotherapy.
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Affiliation(s)
- Teresa Lee
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Department of Oncology, McGill University, Montreal, Quebec, Canada.,Department of Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada
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22
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Cellular RNA Helicases Support Early and Late Events in Retroviral Replication. RETROVIRUS-CELL INTERACTIONS 2018. [PMCID: PMC7149973 DOI: 10.1016/b978-0-12-811185-7.00007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Retroviruses commandeer cell RNA helicases (RHs). Cell RHs are necessary for early and late events in retrovirus replication. The provirus is adopted by the cell-endogenous nuclear and cytoplasmic gene expression types of machinery. Whereas retroviruses engender the supportive activity of cell RHs, other RNA viruses provoke theantiviral role of this superfamily of conserved proteins. In this chapter, we contrast retrovirus reliance on host RNA helicases to support their replication cycle, with the virus-encoded helicaseactivity utilized by RNA viruses in cytoplasmic factories. Ironically, RHs are agonists to retroviruses and antagonists to other RNA viruses.
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23
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Fidaleo M, De Paola E, Paronetto MP. The RNA helicase A in malignant transformation. Oncotarget 2017; 7:28711-23. [PMID: 26885691 PMCID: PMC5053757 DOI: 10.18632/oncotarget.7377] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/29/2016] [Indexed: 12/12/2022] Open
Abstract
The RNA helicase A (RHA) is involved in several steps of RNA metabolism, such as RNA processing, cellular transit of viral molecules, ribosome assembly, regulation of transcription and translation of specific mRNAs. RHA is a multifunctional protein whose roles depend on the specific interaction with different molecular partners, which have been extensively characterized in physiological situations. More recently, the functional implication of RHA in human cancer has emerged. Interestingly, RHA was shown to cooperate with both tumor suppressors and oncoproteins in different tumours, indicating that its specific role in cancer is strongly influenced by the cellular context. For instance, silencing of RHA and/or disruption of its interaction with the oncoprotein EWS-FLI1 rendered Ewing sarcoma cells more sensitive to genotoxic stresses and affected tumor growth and maintenance, suggesting possible therapeutic implications. Herein, we review the recent advances in the cellular functions of RHA and discuss its implication in oncogenesis, providing a perspective for future studies and potential translational opportunities in human cancer.
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Affiliation(s)
- Marco Fidaleo
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, CERC, Fondazione Santa Lucia, Rome, Italy
| | - Elisa De Paola
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, CERC, Fondazione Santa Lucia, Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, CERC, Fondazione Santa Lucia, Rome, Italy
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24
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Capitanio JS, Montpetit B, Wozniak RW. Nucleoplasmic Nup98 controls gene expression by regulating a DExH/D-box protein. Nucleus 2017; 9:1-8. [PMID: 28934014 PMCID: PMC5973140 DOI: 10.1080/19491034.2017.1364826] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The nucleoporin Nup98 has been linked to the regulation of transcription and RNA metabolism, 1-3 but the mechanisms by which Nup98 contributes to these processes remains largely undefined. Recently, we uncovered interactions between Nup98 and several DExH/D-box proteins (DBPs), a protein family well-known for modulating gene expression and RNA metabolism. 4-6 Analysis of Nup98 and one of these DBPs, DHX9, showed that they directly interact, their association is facilitated by RNA, and Nup98 binding stimulates DHX9 ATPase activity. 7 Furthermore, these proteins were dependent on one another for their proper association with a subset of gene loci to control transcription and modulate mRNA splicing. 7 On the basis of these observations, we proposed that Nup98 functions to regulate DHX9 activity within the nucleoplasm. 7 Since Nup98 is associated with several DBPs, regulation of DHX9 by Nup98 may represent a paradigm for understanding how Nup98, and possibly other FG-Nup proteins, could direct the diverse cellular activities of multiple DBPs.
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Affiliation(s)
| | - Ben Montpetit
- a Department of Cell Biology , University of Alberta , Edmonton , Canada.,b Department of Viticulture and Enology , University of California at Davis , Davis , CA , USA
| | - Richard W Wozniak
- a Department of Cell Biology , University of Alberta , Edmonton , Canada
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25
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Leone S, Bär D, Slabber CF, Dalcher D, Santoro R. The RNA helicase DHX9 establishes nucleolar heterochromatin, and this activity is required for embryonic stem cell differentiation. EMBO Rep 2017; 18:1248-1262. [PMID: 28588071 DOI: 10.15252/embr.201744330] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 04/22/2017] [Accepted: 04/25/2017] [Indexed: 02/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been implicated in the regulation of chromatin conformation and epigenetic patterns. lncRNA expression levels are widely taken as an indicator for functional properties. However, the role of RNA processing in modulating distinct features of the same lncRNA is less understood. The establishment of heterochromatin at rRNA genes depends on the processing of IGS-rRNA into pRNA, a reaction that is impaired in embryonic stem cells (ESCs) and activated only upon differentiation. The production of mature pRNA is essential since it guides the repressor TIP5 to rRNA genes, and IGS-rRNA abolishes this process. Through screening for IGS-rRNA-binding proteins, we here identify the RNA helicase DHX9 as a regulator of pRNA processing. DHX9 binds to rRNA genes only upon ESC differentiation and its activity guides TIP5 to rRNA genes and establishes heterochromatin. Remarkably, ESCs depleted of DHX9 are unable to differentiate and this phenotype is reverted by the addition of pRNA, whereas providing IGS-rRNA and pRNA mutants deficient for TIP5 binding are not sufficient. Our results reveal insights into lncRNA biogenesis during development and support a model in which the state of rRNA gene chromatin is part of the regulatory network that controls exit from pluripotency and initiation of differentiation pathways.
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Affiliation(s)
- Sergio Leone
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Dominik Bär
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | | | - Damian Dalcher
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
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26
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Capitanio JS, Montpetit B, Wozniak RW. Human Nup98 regulates the localization and activity of DExH/D-box helicase DHX9. eLife 2017; 6. [PMID: 28221134 PMCID: PMC5338925 DOI: 10.7554/elife.18825] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 02/16/2017] [Indexed: 12/17/2022] Open
Abstract
Beyond their role at nuclear pore complexes, some nucleoporins function in the nucleoplasm. One such nucleoporin, Nup98, binds chromatin and regulates gene expression. To gain insight into how Nup98 contributes to this process, we focused on identifying novel binding partners and understanding the significance of these interactions. Here we report on the identification of the DExH/D-box helicase DHX9 as an intranuclear Nup98 binding partner. Various results, including in vitro assays, show that the FG/GLFG region of Nup98 binds to N- and C-terminal regions of DHX9 in an RNA facilitated manner. Importantly, binding of Nup98 stimulates the ATPase activity of DHX9, and a transcriptional reporter assay suggests Nup98 supports DHX9-stimulated transcription. Consistent with these observations, our analysis revealed that Nup98 and DHX9 bind interdependently to similar gene loci and their transcripts. Based on our results, we propose that Nup98 functions as a co-factor that regulates DHX9 and, potentially, other RNA helicases.
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Affiliation(s)
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada.,Department of Viticulture and Enology, University of California, Davis, United states
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27
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Hu J, Khodadadi-Jamayran A, Mao M, Shah K, Yang Z, Nasim MT, Wang Z, Jiang H. AKAP95 regulates splicing through scaffolding RNAs and RNA processing factors. Nat Commun 2016; 7:13347. [PMID: 27824034 PMCID: PMC5105168 DOI: 10.1038/ncomms13347] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/22/2016] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing of pre-mRNAs significantly contributes to the complexity of gene expression in higher organisms, but the regulation of the splice site selection remains incompletely understood. We have previously demonstrated that a chromatin-associated protein, AKAP95, has a remarkable activity in enhancing chromatin transcription. In this study, we show that AKAP95 interacts with many factors involved in transcription and RNA processing, including selective groups of hnRNP proteins, through its N-terminal region, and directly regulates pre-mRNA splicing. AKAP95 binds preferentially to proximal intronic regions on pre-mRNAs in human transcriptome, and this binding requires its zinc-finger domains. By selectively coordinating with hnRNP H/F and U proteins, AKAP95 appears to mainly promote the inclusion of many exons in the genome. AKAP95 also directly interacts with itself. Taken together, our results establish AKAP95 as a mostly positive regulator of pre-mRNA splicing and a possible integrator of transcription and splicing regulation. The chromatin-associated protein AKAP95 is known for its chromatin-related functions including enhancing transcription. Here the authors show that AKAP95 interacts with the splicing regulatory factors as well as RNAs to regulate the inclusion of exons and pre-mRNA splicing.
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Affiliation(s)
- Jing Hu
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama 35294, USA
| | - Alireza Khodadadi-Jamayran
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama 35294, USA
| | - Miaowei Mao
- Lineberger Comprehensive Cancer Center, Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Kushani Shah
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama 35294, USA
| | - Zhenhua Yang
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama 35294, USA
| | - Md Talat Nasim
- University of Bradford School of Pharmacy, Bradford BD7 1DP, UK
| | - Zefeng Wang
- Lineberger Comprehensive Cancer Center, Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama 35294, USA
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28
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The DEAD-Box RNA Helicase DDX3 Interacts with NF-κB Subunit p65 and Suppresses p65-Mediated Transcription. PLoS One 2016; 11:e0164471. [PMID: 27736973 PMCID: PMC5063347 DOI: 10.1371/journal.pone.0164471] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 09/26/2016] [Indexed: 11/29/2022] Open
Abstract
RNA helicase family members exhibit diverse cellular functions, including in transcription, pre-mRNA processing, RNA decay, ribosome biogenesis, RNA export and translation. The RNA helicase DEAD-box family member DDX3 has been characterized as a tumour-associated factor and a transcriptional co-activator/regulator. Here, we demonstrate that DDX3 interacts with the nuclear factor (NF)-κB subunit p65 and suppresses NF-κB (p65/p50)-mediated transcriptional activity. The downregulation of DDX3 by RNA interference induces the upregulation of NF-κB (p65/p50)-mediated transcription. The regulation of NF-κB (p65/p50)-mediated transcriptional activity was further confirmed by the expression levels of its downstream cytokines, such as IL-6 and IL-8. Moreover, the binding of the ATP-dependent RNA helicase domain of DDX3 to the N-terminal Rel homology domain (RHD) of p65 is involved in the inhibition of NF-κB-regulated gene transcription. In summary, the results suggest that DDX3 functions to suppress the transcriptional activity of the NF-κB subunit p65.
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29
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Portnoy V, Lin SHS, Li KH, Burlingame A, Hu ZH, Li H, Li LC. saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription. Cell Res 2016; 26:320-35. [PMID: 26902284 PMCID: PMC4783471 DOI: 10.1038/cr.2016.22] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 10/22/2015] [Accepted: 01/12/2016] [Indexed: 12/21/2022] Open
Abstract
Small activating RNAs (saRNAs) targeting specific promoter regions are able to stimulate gene expression at the transcriptional level, a phenomenon known as RNA activation (RNAa). It is known that RNAa depends on Ago2 and is associated with epigenetic changes at the target promoters. However, the precise molecular mechanism of RNAa remains elusive. Using human CDKN1A (p21) as a model gene, we characterized the molecular nature of RNAa. We show that saRNAs guide Ago2 to and associate with target promoters. saRNA-loaded Ago2 facilitates the assembly of an RNA-induced transcriptional activation (RITA) complex, which, in addition to saRNA-Ago2 complex, includes RHA and CTR9, the latter being a component of the PAF1 complex. RITA interacts with RNA polymerase II to stimulate transcription initiation and productive elongation, accompanied by monoubiquitination of histone 2B. Our results establish the existence of a cellular RNA-guided genome-targeting and transcriptional activation mechanism and provide important new mechanistic insights into the RNAa process.
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Affiliation(s)
- Victoria Portnoy
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Szu Hua Sharon Lin
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alma Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Zheng-Hui Hu
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Hao Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Long-Cheng Li
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA.,Laboratory of Molecular Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
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30
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Lloyd RE. Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses. Virology 2015; 479-480:457-74. [PMID: 25818028 PMCID: PMC4426963 DOI: 10.1016/j.virol.2015.03.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/12/2015] [Accepted: 03/03/2015] [Indexed: 01/18/2023]
Abstract
Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. Nuclear shuttling host proteins are commonly hijacked by RNA viruses to support replication. A limited group of ubiquitous RNA binding proteins are commonly hijacked by a broad range of viruses. Key virus proteins alter roles of RNA binding proteins in different stages of virus replication.
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Affiliation(s)
- Richard E Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States.
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31
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Fujita H, Yagishita N, Aratani S, Saito-Fujita T, Morota S, Yamano Y, Hansson MJ, Inazu M, Kokuba H, Sudo K, Sato E, Kawahara KI, Nakajima F, Hasegawa D, Higuchi I, Sato T, Araya N, Usui C, Nishioka K, Nakatani Y, Maruyama I, Usui M, Hara N, Uchino H, Elmer E, Nishioka K, Nakajima T. The E3 ligase synoviolin controls body weight and mitochondrial biogenesis through negative regulation of PGC-1β. EMBO J 2015; 34:1042-55. [PMID: 25698262 DOI: 10.15252/embj.201489897] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/19/2015] [Indexed: 12/26/2022] Open
Abstract
Obesity is a major global public health problem, and understanding its pathogenesis is critical for identifying a cure. In this study, a gene knockout strategy was used in post-neonatal mice to delete synoviolin (Syvn)1/Hrd1/Der3, an ER-resident E3 ubiquitin ligase with known roles in homeostasis maintenance. Syvn1 deficiency resulted in weight loss and lower accumulation of white adipose tissue in otherwise wild-type animals as well as in genetically obese (ob/ob and db/db) and adipose tissue-specific knockout mice as compared to control animals. SYVN1 interacted with and ubiquitinated the thermogenic coactivator peroxisome proliferator-activated receptor coactivator (PGC)-1β, and Syvn1 mutants showed upregulation of PGC-1β target genes and increase in mitochondrion number, respiration, and basal energy expenditure in adipose tissue relative to control animals. Moreover, the selective SYVN1 inhibitor LS-102 abolished the negative regulation of PGC-1β by SYVN1 and prevented weight gain in mice. Thus, SYVN1 is a novel post-translational regulator of PGC-1β and a potential therapeutic target in obesity treatment.
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Affiliation(s)
- Hidetoshi Fujita
- Institute of Medical Science, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan Department of Future Medical Science, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - Naoko Yagishita
- Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Satoko Aratani
- Institute of Medical Science, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan Department of Future Medical Science, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - Tomoko Saito-Fujita
- Department of Obstetrics and Gynecology University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Saori Morota
- Department of Anesthesiology, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - Yoshihisa Yamano
- Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Magnus J Hansson
- Mitochondrial Pathophysiology Unit, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Masato Inazu
- Institute of Medical Science, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - Hiroko Kokuba
- Institute of Medical Science, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - Katsuko Sudo
- Animal Research Center, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - Eiichi Sato
- Institute of Medical Science, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan Medical Research Center, Tokyo Medical University Hospital, Shinjuku-ku, Tokyo, Japan
| | - Ko-Ichi Kawahara
- Department of Biomedical Engineering, Osaka Institute of Technology, Asahi-ku, 11Neurology and Geriatrics, Japan
| | - Fukami Nakajima
- Institute of Medical Science, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - Daisuke Hasegawa
- Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Itsuro Higuchi
- Neurology and Geriatrics, Faculty of Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Sakuragaoka, Kagoshima, Japan
| | - Tomoo Sato
- Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Natsumi Araya
- Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Chie Usui
- Department of Psychiatry, Juntendo University Nerima Hospital, Nerima-ku, Tokyo, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Yu Nakatani
- Department of Future Medical Science, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - Ikuro Maruyama
- Laboratory and Vascular Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Sakuragaoka, Kagoshima, Japan
| | - Masahiko Usui
- Institute of Medical Science, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - Naomi Hara
- Department of Anesthesiology, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - Hiroyuki Uchino
- Department of Anesthesiology, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - Eskil Elmer
- Mitochondrial Pathophysiology Unit, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Kusuki Nishioka
- Institute of Medical Science, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - Toshihiro Nakajima
- Institute of Medical Science, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan Department of Future Medical Science, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan Medical Research Center, Tokyo Medical University Hospital, Shinjuku-ku, Tokyo, Japan Department of Biomedical Engineering, Osaka Institute of Technology, Asahi-ku, 11Neurology and Geriatrics, Japan integrated Gene Editing Section (iGES), Tokyo Medical University Hospital, Shinjuku-ku, Tokyo, Japan Bayside Misato Medical Center, Niida, Kōchi, Japan
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32
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Erkizan HV, Schneider JA, Sajwan K, Graham GT, Griffin B, Chasovskikh S, Youbi SE, Kallarakal A, Chruszcz M, Padmanabhan R, Casey JL, Üren A, Toretsky JA. RNA helicase A activity is inhibited by oncogenic transcription factor EWS-FLI1. Nucleic Acids Res 2015; 43:1069-80. [PMID: 25564528 PMCID: PMC4333382 DOI: 10.1093/nar/gku1328] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
RNA helicases impact RNA structure and metabolism from transcription through translation, in part through protein interactions with transcription factors. However, there is limited knowledge on the role of transcription factor influence upon helicase activity. RNA helicase A (RHA) is a DExH-box RNA helicase that plays multiple roles in cellular biology, some functions requiring its activity as a helicase while others as a protein scaffold. The oncogenic transcription factor EWS-FLI1 requires RHA to enable Ewing sarcoma (ES) oncogenesis and growth; a small molecule, YK-4-279 disrupts this complex in cells. Our current study investigates the effect of EWS-FLI1 upon RHA helicase activity. We found that EWS-FLI1 reduces RHA helicase activity in a dose-dependent manner without affecting intrinsic ATPase activity; however, the RHA kinetics indicated a complex model. Using separated enantiomers, only (S)-YK-4-279 reverses the EWS-FLI1 inhibition of RHA helicase activity. We report a novel RNA binding property of EWS-FLI1 leading us to discover that YK-4-279 inhibition of RHA binding to EWS-FLI1 altered the RNA binding profile of both proteins. We conclude that EWS-FLI1 modulates RHA helicase activity causing changes in overall transcriptome processing. These findings could lead to both enhanced understanding of oncogenesis and provide targets for therapy.
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Affiliation(s)
- Hayriye Verda Erkizan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, 3970 Reservoir Road NW, New Research Building E316, Washington, DC 20007, USA
| | - Jeffrey A Schneider
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, 3970 Reservoir Road NW, New Research Building E316, Washington, DC 20007, USA
| | - Kamal Sajwan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, 3970 Reservoir Road NW, New Research Building E316, Washington, DC 20007, USA
| | - Garrett T Graham
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, 3970 Reservoir Road NW, New Research Building E316, Washington, DC 20007, USA
| | - Brittany Griffin
- Department of Microbiology and Immunology, Georgetown University Medical Center, SW 309 Med-Dent, Washington, DC 20007, USA
| | - Sergey Chasovskikh
- Department of Radiation Medicine, Georgetown University Medical Center, 3970 Reservoir Road NW, New Research Building E220, Washington, DC 20007, USA
| | - Sarah E Youbi
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, 3970 Reservoir Road NW, New Research Building E316, Washington, DC 20007, USA
| | - Abraham Kallarakal
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, 3970 Reservoir Road NW, New Research Building E316, Washington, DC 20007, USA
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Radhakrishnan Padmanabhan
- Department of Microbiology and Immunology, Georgetown University Medical Center, SW 309 Med-Dent, Washington, DC 20007, USA
| | - John L Casey
- Department of Microbiology and Immunology, Georgetown University Medical Center, SW 309 Med-Dent, Washington, DC 20007, USA
| | - Aykut Üren
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, 3970 Reservoir Road NW, New Research Building E316, Washington, DC 20007, USA
| | - Jeffrey A Toretsky
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, 3970 Reservoir Road NW, New Research Building E316, Washington, DC 20007, USA
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33
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Helicase associated 2 domain is essential for helicase activity of RNA helicase A. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1757-64. [DOI: 10.1016/j.bbapap.2014.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/30/2014] [Accepted: 07/02/2014] [Indexed: 02/04/2023]
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34
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Xing L, Niu M, Kleiman L. Role of the OB-fold of RNA helicase A in the synthesis of HIV-1 RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1069-78. [PMID: 25149208 DOI: 10.1016/j.bbagrm.2014.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 07/25/2014] [Accepted: 08/12/2014] [Indexed: 11/26/2022]
Abstract
RNA helicase A (RHA), a DExD/H protein, contains a stretch of repeated arginine and glycine-glycine (RGG) residues and an oligonucleotide/oligosaccharide-binding fold (OB-fold) at the C-terminus. RHA has been reported to function as a transcriptional cofactor. This study shows the role of RGG and OB-fold domains of RHA in the activation of transcription and splicing of HIV-1 RNA. RHA stimulates HIV-1 transcription by enhancing the occupancy of RNA polymerase II on the proviral DNA. Deletion of RGG or both RGG and OB-fold does not change the transcriptional activity of RHA, nor does the stability of viral RNA. However, deletion of both RGG and OB-fold rather than deletion of RGG only results in less production of multiply spliced 6D RNAs. The results suggest that the OB-fold is involved in modulating HIV-1 RNA splicing in the context of some HIV-1 strains while it is dispensable for the activation of HIV-1 transcription.
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Affiliation(s)
- Li Xing
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada.
| | - Meijuan Niu
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Lawrence Kleiman
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada.
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Koh HR, Xing L, Kleiman L, Myong S. Repetitive RNA unwinding by RNA helicase A facilitates RNA annealing. Nucleic Acids Res 2014; 42:8556-64. [PMID: 24914047 PMCID: PMC4117756 DOI: 10.1093/nar/gku523] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Helicases contribute to diverse biological processes including replication, transcription and translation. Recent reports suggest that unwinding of some helicases display repetitive activity, yet the functional role of the repetitiveness requires further investigation. Using single-molecule fluorescence assays, we elucidated a unique unwinding mechanism of RNA helicase A (RHA) that entails discrete substeps consisting of binding, activation, unwinding, stalling and reactivation stages. This multi-step process is repeated many times by a single RHA molecule without dissociation, resulting in repetitive unwinding/rewinding cycles. Our kinetic and mutational analysis indicates that the two double stand RNA binding domains at the N-terminus of RHA are responsible for such repetitive unwinding behavior in addition to providing an increased binding affinity to RNA. Further, the repetitive unwinding induces an efficient annealing of a complementary RNA by making the unwound strand more accessible. The complex and unusual mechanism displayed by RHA may help in explaining how the repetitive unwinding of helicases contributes to their biological functions.
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Affiliation(s)
- Hye Ran Koh
- Department of Physics, University of Illinois, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Li Xing
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada Department of Medicine, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Lawrence Kleiman
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada Department of Medicine, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Sua Myong
- Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA Physics Frontier Center (Center of Physics for Living Cells), University of Illinois, Urbana, IL 61801, USA Biophysics and Computational Biology, 1110 W. Green St., Urbana, IL 61801, USA
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36
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Xing L, Niu M, Zhao X, Kleiman L. Different activities of the conserved lysine residues in the double-stranded RNA binding domains of RNA helicase A in vitro and in the cell. Biochim Biophys Acta Gen Subj 2014; 1840:2234-43. [PMID: 24726449 DOI: 10.1016/j.bbagen.2014.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 04/02/2014] [Accepted: 04/03/2014] [Indexed: 12/25/2022]
Abstract
BACKGROUND RNA helicase A regulates a variety of RNA metabolism processes including HIV-1 replication and contains two double-stranded RNA binding domains (dsRBD1 and dsRBD2) at the N-terminus. Each dsRBD contains two invariant lysine residues critical for the binding of isolated dsRBDs to RNA. However, the role of these conserved lysine residues was not tested in the context of enzymatically active full-length RNA helicase A either in vitro or in the cells. METHODS The conserved lysine residues in each or both of dsRBDs were substituted by alanine in the context of full-length RNA helicase A. The mutant RNA helicase A was purified from mammalian cells. The effects of these mutations were assessed either in vitro upon RNA binding and unwinding or in the cell during HIV-1 production upon RNA helicase A-RNA interaction and RNA helicase A-stimulated viral RNA processes. RESULTS Unexpectedly, the substitution of the lysine residues by alanine in either or both of dsRBDs does not prevent purified full-length RNA helicase A from binding and unwinding duplex RNA in vitro. However, these mutations efficiently inhibit RNA helicase A-stimulated HIV-1 RNA metabolism including the accumulation of viral mRNA and tRNA(Lys3) annealing to viral RNA. Furthermore, these mutations do not prevent RNA helicase A from binding to HIV-1 RNA in vitro as well, but dramatically reduce RNA helicase A-HIV-1 RNA interaction in the cells. CONCLUSIONS The conserved lysine residues of dsRBDs play critical roles in the promotion of HIV-1 production by RNA helicase A. GENERAL SIGNIFICANCE The conserved lysine residues of dsRBDs are key to the interaction of RNA helicase A with substrate RNA in the cell, but not in vitro.
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Affiliation(s)
- Li Xing
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada.
| | - Meijuan Niu
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Xia Zhao
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Lawrence Kleiman
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada.
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Chen ZX, Wallis K, Fell SM, Sobrado VR, Hemmer MC, Ramsköld D, Hellman U, Sandberg R, Kenchappa RS, Martinson T, Johnsen JI, Kogner P, Schlisio S. RNA helicase A is a downstream mediator of KIF1Bβ tumor-suppressor function in neuroblastoma. Cancer Discov 2014; 4:434-51. [PMID: 24469107 DOI: 10.1158/2159-8290.cd-13-0362] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED Inherited KIF1B loss-of-function mutations in neuroblastomas and pheochromocytomas implicate the kinesin KIF1B as a 1p36.2 tumor suppressor. However, the mechanism of tumor suppression is unknown. We found that KIF1B isoform β (KIF1Bβ) interacts with RNA helicase A (DHX9), causing nuclear accumulation of DHX9, followed by subsequent induction of the proapoptotic XIAP-associated factor 1 (XAF1) and, consequently, apoptosis. Pheochromocytoma and neuroblastoma arise from neural crest progenitors that compete for growth factors such as nerve growth factor (NGF) during development. KIF1Bβ is required for developmental apoptosis induced by competition for NGF. We show that DHX9 is induced by and required for apoptosis stimulated by NGF deprivation. Moreover, neuroblastomas with chromosomal deletion of 1p36 exhibit loss of KIF1Bβ expression and impaired DHX9 nuclear localization, implicating the loss of DHX9 nuclear activity in neuroblastoma pathogenesis. SIGNIFICANCE KIF1Bβ has neuroblastoma tumor-suppressor properties and promotes and requires nuclear-localized DHX9 for its apoptotic function by activating XAF1 expression. Loss of KIF1Bβ alters subcellular localization of DHX9 and diminishes NGF dependence of sympathetic neurons, leading to reduced culling of neural progenitors, and, therefore, might predispose to tumor formation.
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Affiliation(s)
- Zhi Xiong Chen
- 1Ludwig Institute for Cancer Research Ltd.; 2Department of Cell and Molecular Biology, Karolinska Institutet; 3Department of Women's and Children's Health, Karolinska University Hospital, Stockholm; 4Ludwig Institute for Cancer Research Ltd., Biomedical Center, Uppsala; 5Department of Clinical Genetics, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, Göteborg, Sweden; and 6Moffitt Cancer Center, Neuro-Oncology Program, Tampa, Florida
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38
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Lawrence P, Conderino JS, Rieder E. Redistribution of demethylated RNA helicase A during foot-and-mouth disease virus infection: role of Jumonji C-domain containing protein 6 in RHA demethylation. Virology 2014; 452-453:1-11. [PMID: 24606677 DOI: 10.1016/j.virol.2013.12.040] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 12/20/2013] [Accepted: 12/28/2013] [Indexed: 11/20/2022]
Abstract
Previously, RNA helicase A (RHA) re-localization from the nucleus to the cytoplasm in foot-and-mouth disease virus (FMDV) infected cells was shown to coincide with loss of RHA methylated arginine residues at its C-terminus. The potential interaction between RHA and Jumonji C-domain (JmjC) protein 6 (JMJD6) arginine demethylase in infected cells was investigated. Treatment with N-oxalylglycine (NOG) inhibitor of JmjC demethylases prevented FMDV-induced RHA demethylation and re-localization, and also decreased viral protein synthesis and virus titers. Physical interaction between JMJD6 and RHA was demonstrated via reciprocal co-immunoprecipitation, where RHA preferentially bound JMJD6 monomers. Nuclear efflux of demethylated RHA (DM-RHA) coincided with nuclear influx of JMJD6, which was not observed using another picornavirus. A modified biochemical assay demonstrated JMJD6 induced dose-dependent demethylation of RHA and two RHA-derived isoforms, which could be inhibited by NOG. We propose a role for JMJD6 in RHA demethylation stimulated by FMDV, that appears to facilitate virus replication.
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Affiliation(s)
- Paul Lawrence
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, NAA, Plum Island Animal Disease Center, PO Box 848, Greenport, NY 11944-0848, USA
| | - Joseph S Conderino
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, NAA, Plum Island Animal Disease Center, PO Box 848, Greenport, NY 11944-0848, USA
| | - Elizabeth Rieder
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, NAA, Plum Island Animal Disease Center, PO Box 848, Greenport, NY 11944-0848, USA.
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39
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Nakajima T, Aratani S, Nakazawa M, Hirose T, Fujita H, Nishioka K. Implications of transcriptional coactivator CREB binding protein complexes in rheumatoid arthritis. Mod Rheumatol 2014. [DOI: 10.3109/s10165-003-0258-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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40
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Xing L, Niu M, Zhao X, Kleiman L. Roles of the linker region of RNA helicase A in HIV-1 RNA metabolism. PLoS One 2013; 8:e78596. [PMID: 24223160 PMCID: PMC3819368 DOI: 10.1371/journal.pone.0078596] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 09/20/2013] [Indexed: 12/21/2022] Open
Abstract
RNA helicase A (RHA) promotes multiple steps in HIV-1 production including transcription and translation of viral RNA, annealing of primer tRNALys3 to viral RNA, and elevating the ratio of unspliced to spliced viral RNA. At its amino terminus are two double-stranded RNA binding domains (dsRBDs) that are essential for RHA-viral RNA interaction. Linking the dsRBDs to the core helicase domain is a linker region containing 6 predicted helices. Working in vitro with purified mutant RHAs containing deletions of individual helices reveals that this region may regulate the enzyme's helicase activity, since deletion of helix 2 or 3 reduces the rate of unwinding RNA by RHA. The biological significance of this finding was then examined during HIV-1 production. Deletions in the linker region do not significantly affect either RHA-HIV-1 RNA interaction in vivo or the incorporation of mutant RHAs into progeny virions. While the partial reduction in helicase activity of mutant RHA containing a deletion of helices 2 or 3 does not reduce the ability of RHA to stimulate viral RNA synthesis, the promotion of tRNALys3 annealing to viral RNA is blocked. In contrast, deletion of helices 4 or 5 does not affect the ability of RHA to promote tRNALys3 annealing, but reduces its ability to stimulate viral RNA synthesis. Additionally, RHA stimulation of viral RNA synthesis results in an increased ratio of unspliced to spliced viral RNA, and this increase is not inhibited by deletions in the linker region, nor is the pattern of splicing changed within the ∼ 4.0 kb or ∼ 1.8 kb HIV-1 RNA classes, suggesting that RHA's effect on suppressing splicing is confined mainly to the first 5′-splice donor site. Overall, the differential responses to the mutations in the linker region of RHA reveal that RHA participates in HIV-1 RNA metabolism by multiple distinct mechanisms.
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Affiliation(s)
- Li Xing
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- * E-mail: (LX); (LK)
| | - Meijuan Niu
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Xia Zhao
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Lawrence Kleiman
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- * E-mail: (LX); (LK)
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41
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Maxwell SS, Pelka GJ, Tam PP, El-Osta A. Chromatin context and ncRNA highlight targets of MeCP2 in brain. RNA Biol 2013; 10:1741-57. [PMID: 24270455 DOI: 10.4161/rna.26921] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The discovery that Rett syndrome (RTT) is caused by mutation of the methyl-CpG-binding-protein MeCP2 provided a major breakthrough in understanding the neurodevelopmental disorder and accelerated MeCP2 research. However, gene regulation by MeCP2 is complicated. The current consensus for MeCP2 remains as a classical repressor complex, with major emphasis on its role in methylation-dependent binding and repression. However, recent evidence indicates additional regulatory roles, suggesting non-classical mechanisms in gene activation. This has opened the field of MeCP2 research and suggests that the gene targets may not be the usual suspects, that is, dependent only on DNA methylation. Here we examine how chromatin binding and sequence preference may confer MeCP2 functionality, and connect relevant pathways in an active genome. Finding both genomic and proteomic evidence to indicate MeCP2 spliceosome interaction, we consequently discovered broad MeCP2 enrichment of the transcriptome while our focus toward long non-coding RNA (lncRNA) revealed MeCP2 association with RNCR3. Our data may indicate an as-yet-unappreciated role between lncRNA and MeCP2. We hypothesize that ncRNA may mediate chromatin-remodeling events by interacting with MeCP2, thereby conferring changes in gene expression. We consider that these results may suggest new mechanisms of gene regulation conferred by MeCP2 and its interactions upon chromatin structure and gene function.
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Affiliation(s)
- Scott S Maxwell
- Epigenetics in Human Health and Disease Laboratory; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC, Australia
| | - Gregory J Pelka
- Embryology Unit; Children's Medical Research Institute; Sydney, NSW, Australia
| | - Patrick Pl Tam
- Embryology Unit; Children's Medical Research Institute; Sydney, NSW, Australia; Sydney Medical School; University of Sydney; Sydney, NSW, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC, Australia; Epigenomic Profiling Facility; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC, Australia; Department of Pathology; The University of Melbourne; Parkville, VIC, Australia; Faculty of Medicine, Nursing and Health Sciences; Monash University; VIC, Australia
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42
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Dridi S. Alu mobile elements: from junk DNA to genomic gems. SCIENTIFICA 2012; 2012:545328. [PMID: 24278713 PMCID: PMC3820591 DOI: 10.6064/2012/545328] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 11/06/2012] [Indexed: 06/02/2023]
Abstract
Alus, the short interspersed repeated sequences (SINEs), are retrotransposons that litter the human genomes and have long been considered junk DNA. However, recent findings that these mobile elements are transcribed, both as distinct RNA polymerase III transcripts and as a part of RNA polymerase II transcripts, suggest biological functions and refute the notion that Alus are biologically unimportant. Indeed, Alu RNAs have been shown to control mRNA processing at several levels, to have complex regulatory functions such as transcriptional repression and modulating alternative splicing and to cause a host of human genetic diseases. Alu RNAs embedded in Pol II transcripts can promote evolution and proteome diversity, which further indicates that these mobile retroelements are in fact genomic gems rather than genomic junks.
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Affiliation(s)
- Sami Dridi
- Nutrition Research Institute, The University of North Carolina at Chapel Hill, 500 Laureate Way, Kannapolis, NC 28081, USA
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43
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In vitro and in vivo analysis of the interaction between RNA helicase A and HIV-1 RNA. J Virol 2012; 86:13272-80. [PMID: 23015696 DOI: 10.1128/jvi.01993-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RNA helicase A (RHA) promotes multiple steps of HIV-1 RNA metabolism during viral replication, including transcription, translation, and the annealing of primer tRNA(3)(Lys) to the viral RNA. RHA is a member of the DExH subclass of RNA helicases that uniquely contains two double-stranded RNA binding domains (dsRBDs) at its N terminus. Here, we performed a genome-wide analysis of the interaction of RHA with HIV-1 RNA both in vitro, using fluorescence polarization, and during viral replication, using an RNA-protein coprecipitation assay. In vitro, RHA binds to all the isolated regions of the HIV-1 RNA genome tested, with K(d) (equilibrium dissociation constant) values ranging from 44 to 178 nM. In contrast, during viral replication, RNA-protein coprecipitation assays detected only a major interaction of RHA with the 5'-untranslated region (5'-UTR) and a minor interaction with the Rev response element (RRE) of HIV-1 RNA. Since RHA does not associate well with all the highly structured regions of HIV-1 RNA tested in vivo, the results suggest that other viral or cellular factors not present in vitro may modulate the direct interaction of RHA with HIV-1 RNA during virus replication. Nevertheless, a role for duplex RNA as a target for RHA binding in vivo is suggested by the fact that the deletion of either one or both dsRBDs eliminates the in vivo interaction of RHA with HIV-1 RNA. Furthermore, these mutant RHAs do not promote the in vivo annealing of tRNA(3)(Lys) to viral RNA, nor are they packaged into virions, demonstrating that the dsRBDs are essential for the role of RHA in HIV-1 replication.
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44
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Martin R, Straub AU, Doebele C, Bohnsack MT. DExD/H-box RNA helicases in ribosome biogenesis. RNA Biol 2012; 10:4-18. [PMID: 22922795 DOI: 10.4161/rna.21879] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Ribosome synthesis requires a multitude of cofactors, among them DExD/H-box RNA helicases. Bacterial RNA helicases involved in ribosome assembly are not essential, while eukaryotes strictly require multiple DExD/H-box proteins that are involved in the much more complex ribosome biogenesis pathway. Here, RNA helicases are thought to act in structural remodeling of the RNPs including the modulation of protein binding, and they are required for allowing access or the release of specific snoRNPs from pre-ribosomes. Interestingly, helicase action is modulated by specific cofactors that can regulate recruitment and enzymatic activity. This review summarizes the current knowledge and focuses on recent findings and open questions on RNA helicase function and regulation in ribosome synthesis.
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Affiliation(s)
- Roman Martin
- Centre for Biochemistry and Molecular Cell Biology, Göttingen University, Göttingen, Germany
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45
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Abstract
RNA helicases unwind their RNA substrates in an ATP-dependent reaction, and are central to all cellular processes involving RNA. They have important roles in viral life cycles, where RNA helicases are either virus-encoded or recruited from the host. Vertebrate RNA helicases sense viral infections, and trigger the innate antiviral immune response. RNA helicases have been implicated in protozoic, bacterial and fungal infections. They are also linked to neurological disorders, cancer, and aging processes. Genome-wide studies continue to identify helicase genes that change their expression patterns after infection or disease outbreak, but the mechanism of RNA helicase action has been defined for only a few diseases. RNA helicases are prognostic and diagnostic markers and suitable drug targets, predominantly for antiviral and anti-cancer therapies. This review summarizes the current knowledge on RNA helicases in infection and disease, and their growing potential as drug targets.
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Affiliation(s)
- Lenz Steimer
- University of Muenster, Institute for Physical Chemistry, Muenster, Germany
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46
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Manojlovic Z, Stefanovic B. A novel role of RNA helicase A in regulation of translation of type I collagen mRNAs. RNA (NEW YORK, N.Y.) 2012; 18:321-34. [PMID: 22190748 PMCID: PMC3264918 DOI: 10.1261/rna.030288.111] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 11/04/2011] [Indexed: 05/30/2023]
Abstract
Type I collagen is composed of two α1(I) polypeptides and one α2(I) polypeptide and is the most abundant protein in the human body. Expression of type I collagen is primarily controlled at the level of mRNA stability and translation. Coordinated translation of α(I) and α2(I) mRNAs is necessary for efficient folding of the corresponding peptides into the collagen heterotrimer. In the 5' untranslated region (5' UTR), collagen mRNAs have a unique 5' stem-loop structure (5' SL). La ribonucleoprotein domain family member 6 (LARP6) is the protein that binds 5' SL with high affinity and specificity and coordinates their translation. Here we show that RNA helicase A (RHA) is tethered to the 5' SL of collagen mRNAs by interaction with the C-terminal domain of LARP6. In vivo, collagen mRNAs immunoprecipitate with RHA in an LARP6-dependent manner. Knockdown of RHA prevents formation of polysomes on collagen mRNAs and dramatically reduces synthesis of collagen protein, without affecting the level of the mRNAs. A reporter mRNA with collagen 5' SL is translated three times more efficiently in the presence of RHA than the same reporter without the 5' SL, indicating that the 5' SL is the cis-acting element conferring the regulation. During activation of quiescent cells into collagen-producing cells, expression of RHA is highly up-regulated. We postulate that RHA is recruited to the 5' UTR of collagen mRNAs by LARP6 to facilitate their translation. Thus, RHA has been discovered as a critical factor for synthesis of the most abundant protein in the human body.
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Affiliation(s)
- Zarko Manojlovic
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, USA
| | - Branko Stefanovic
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, USA
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47
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Identification of RNA helicase A as a cellular factor that interacts with influenza A virus NS1 protein and its role in the virus life cycle. J Virol 2011; 86:1942-54. [PMID: 22171255 DOI: 10.1128/jvi.06362-11] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Influenza A virus NS1 protein has multiple functions in the infected cell during the virus life cycle. Identification of novel cellular factors that interact with NS1 and understanding their functions in virus infection are of great interest. Recombinant viruses carrying a tagged NS1 are valuable for investigation of interactions between NS1 and cellular factors in the context of virus infection. Here, we report the generation of replication-competent recombinant influenza A viruses bearing a Strep tag in the NS1 protein. Purification of a protein complex associated with Strep-tagged NS1 from virus-infected cells followed by mass spectrometry revealed a number of attractive host factors. Among them, we focused our study on RNA helicase A (RHA) in this report. Through biomedical and functional analyses, we demonstrated that RHA interacts with NS1 in an RNA-dependent manner. Knockdown of RHA resulted in a significant reduction on virus yield and polymerase activity in a minigenome assay. Our cell-free viral genome replication assay showed that viral RNA replication and transcription can be enhanced by addition of RHA, and the enhanced effect of RHA required its ATP-dependent helicase activity. In summary, we established a system to identify cellular factors that interact with NS1 protein during virus infection and furthermore demonstrated that RHA interacts with NS1 and enhances viral replication and transcription.
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48
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Salton M, Elkon R, Borodina T, Davydov A, Yaspo ML, Halperin E, Shiloh Y. Matrin 3 binds and stabilizes mRNA. PLoS One 2011; 6:e23882. [PMID: 21858232 PMCID: PMC3157474 DOI: 10.1371/journal.pone.0023882] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 07/30/2011] [Indexed: 12/26/2022] Open
Abstract
Matrin 3 (MATR3) is a highly conserved, inner nuclear matrix protein with two zinc finger domains and two RNA recognition motifs (RRM), whose function is largely unknown. Recently we found MATR3 to be phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Here, we show that MATR3 interacts in an RNA-dependent manner with several proteins with established roles in RNA processing, and maintains its interaction with RNA via its RRM2 domain. Deep sequencing of the bound RNA (RIP-seq) identified several small noncoding RNA species. Using microarray analysis to explore MATR3′s role in transcription, we identified 77 transcripts whose amounts depended on the presence of MATR3. We validated this finding with nine transcripts which were also bound to the MATR3 complex. Finally, we demonstrated the importance of MATR3 for maintaining the stability of several of these mRNA species and conclude that it has a role in mRNA stabilization. The data suggest that the cellular level of MATR3, known to be highly regulated, modulates the stability of a group of gene transcripts.
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Affiliation(s)
- Maayan Salton
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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49
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Gu Z, Zhou L, Gao S, Wang Z. Nuclear transport signals control cellular localization and function of androgen receptor cofactor p44/WDR77. PLoS One 2011; 6:e22395. [PMID: 21789256 PMCID: PMC3137635 DOI: 10.1371/journal.pone.0022395] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 06/20/2011] [Indexed: 12/26/2022] Open
Abstract
The androgen receptor (AR) cofactor p44/WDR77, which regulates expression of a set of androgen target genes, is required for differentiation of prostate epithelium. Aberrant localization of p44/WDR77 in the cytoplasm is associated with prostate tumorigenesis. Here, we describe studies that used the mouse prostate and human prostate cancer cells as model systems to investigate signals that control subcellular localization of p44/WDR77. We observed distinct subcellular location of p44/WDR77 during prostate development. p44/WDR77 localizes in the cytoplasm at the early stage of prostate development, when prostate epithelial cells are rapidly proliferating, and in the nucleus in adult prostate, when epithelial cells are fully differentiated. Subcellular localization assays designed to span the entire open-reading frame of p44/WDR77 protein revealed the presence of two nuclear exclusion signal (NES) and three nuclear localization signal (NLS) sequences in the p44/WDR77 protein. Site-directed mutagenesis of critical residues within an NLS led to loss of nuclear localization and transcriptional activity of p44/WDR77, suggesting that nuclear localization of p44/WDR77 is essential for its function as a transcriptional cofactor for AR. Three identified NLS were not functional in AR-positive prostate cancer (LNCaP and 22RV1) cells, which led to localization of p44/WDR77 in cytoplasm. The function of NLS in LNCaP cells could be restored by factor(s) from Cos 7 or PC3 cells. Mass spectrometric (MALDI-TOF/TOF) analysis identified proteins associated with an NLS and an NES in prostate cancer cells. These results provide a basis for understanding subcellular transport of p44/WDR77 during prostate development and tumorigenesis.
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Affiliation(s)
- Zhongping Gu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Liran Zhou
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Shen Gao
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Zhengxin Wang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
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Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes. DNA Repair (Amst) 2011; 10:654-65. [PMID: 21561811 DOI: 10.1016/j.dnarep.2011.04.013] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 04/08/2011] [Accepted: 04/11/2011] [Indexed: 02/02/2023]
Abstract
Human DHX9 helicase, also known as nuclear DNA helicase II (NDH II) and RNA helicase A (RHA), belongs to the SF2 superfamily of nucleic acid unwinding enzymes. DHX9 melts simple DNA-DNA, RNA-RNA, and DNA-RNA strands with a 3'-5' polarity; despite this little is known about its substrate specificity. Here, we used partial duplex DNA consisting of M13mp18 DNA and oligonucleotide-based replication and recombination intermediates. We show that DHX9 unwinds DNA- and RNA-containing forks, DNA- and RNA-containing displacement loops (D- and R-loops), and also G-quadruplexes. With these substrates, DHX9 behaved similarly as the RecQ helicase WRN. In contrast to WRN, DHX9 melted RNA-hybrids considerably faster than the corresponding DNA-DNA strands. DHX9 preferably unwound R-loops and DNA-based G-quadruplexes indicating that these structures may be biologically relevant. DHX9 also unwound RNA-based G-quadruplexes that have been reported to occur in human transcripts. It is believed that an improper dissolution of co-transcriptionally formed D-loops, R-loops, and DNA- or RNA-based G-quadruplexes represent potential roadblocks for transcription and thereby enhance transcription associated recombination events. By unwinding these structures, DHX9 may significantly contribute to transcriptional activation and also to the maintenance of genomic stability.
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