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Izumikawa K, Yoshikawa H, Ishikawa H, Nobe Y, Yamauchi Y, Philipsen S, Simpson RJ, Isobe T, Takahashi N. Chtop (Chromatin target of Prmt1) auto-regulates its expression level via intron retention and nonsense-mediated decay of its own mRNA. Nucleic Acids Res 2016; 44:9847-9859. [PMID: 27683223 PMCID: PMC5175361 DOI: 10.1093/nar/gkw831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/05/2016] [Accepted: 09/06/2016] [Indexed: 12/25/2022] Open
Abstract
Chtop (chromatin target of Prmt1) regulates various aspects of gene expression including transcription and mRNA export. Despite these important functions, the regulatory mechanism underlying Chtop expression remains undetermined. Using Chtop-expressing human cell lines, we demonstrate that Chtop expression is controlled via an autoregulatory negative feedback loop whereby Chtop binds its own mRNA to retain intron 2 during splicing; a premature termination codon present at the 5′ end of intron 2 leads to nonsense-mediated decay of the mRNA. We also show that Chtop interacts with exon 2 of Chtop mRNA via its arginine-glycine-rich (RG) domain, and with intron 2 via its N-terminal (N1) domain; both are required for retention of intron 2. In addition, we show that hnRNP H accelerates intron 2 splicing of Chtop mRNA in a manner dependent on Chtop expression level, suggesting that Chtop and hnRNP H regulate intron 2 retention of Chtop mRNA antagonistically. Thus, the present study provides a novel molecular mechanism by which mRNA and protein levels are constitutively regulated by intron retention.
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Affiliation(s)
- Keiichi Izumikawa
- Department of Applied Biological Science, United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan.,Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Harunori Yoshikawa
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Hideaki Ishikawa
- Department of Applied Biological Science, United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Yuko Nobe
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan.,Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Yoshio Yamauchi
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan.,Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus MC, 3015 GE Rotterdam, The Netherlands
| | - Richard J Simpson
- Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.,La Trobe Institute for Molecular Science (LIMS) LIMS Building 1, Room 412 La Trobe University, Bundoora, Victoria 3086, Australia
| | - Toshiaki Isobe
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan.,Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Nobuhiro Takahashi
- Department of Applied Biological Science, United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan .,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan.,Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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Krishnaswamy S, Mohammed AK, Amer OE, Tripathi G, Alokail MS, Al-Daghri NM. Recepteur d'Origine nantais (RON) tyrosine kinase splicing variants lacking exons 18 and 19 occur ubiquitously in lung cancer. Int J Clin Exp Med 2015; 8:20778-20786. [PMID: 26885001 PMCID: PMC4723846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/01/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Aberrant expression of RON, a MET family receptor tyrosine kinase, has been correlated to tumor growth and metastasis. Intense research efforts are on to target RON using small molecule tyrosine kinase inhibitors or specific antibodies. However, progress towards specific targeting of RON is hampered by a lack of understanding of the nature and number of isoforms of RON expressed by tumors. We hypothesize that formation of different isoforms via alternative splicing may be fundamental to the tumor promoting functions associated with aberrantly expressed RON in cancers. METHODS In this study, we analyzed the transcript sequence variations caused by alternative splicing in the C-terminal region of RON cDNA by PCR amplification and sequencing of five small cell lung carcinoma (SCLC) and seven non-small cell lung carcinoma (NSCLC) cell lines. RESULTS Results revealed the presence of two alternatively spliced variants, each caused by unique exon(s) deletion: a previously known transcript variant lacking exon 19 and a novel one lacking exons 18+19. The two alternatively spliced variants together with the wild-type transcript were detected in each of the 12 lung cancer cell lines analyzed. Combined loss of exons 18+19 results in an in-frame deletion of 303 nucleotides corresponding to 101 amino acids of the tyrosine kinase domain. Translation products of transcript variants lacking exons 18 and 19 are expected to dominant negatively inhibit ligand stimulated RON signaling. CONCLUSIONS The ubiquitous presence of alternatively spliced transcripts and their translation products may affect quantitative expression analysis, either by immunological or PCR methods, by interfering with estimation of normal RON, leading to exaggerated values. Besides, RON isoforms with dominant negative activities may interfere with siRNA based functional analysis of wild-type RON.
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Affiliation(s)
- Soundararajan Krishnaswamy
- Biomarkers Research Program, Department of Riyadh Biochemistry, College of Science, King Saud University 11451Riyadh, Saudi Arabia
- Prince Mutaib Chair for Biomarkers of Osteoporosis, Department of Riyadh Biochemistry, College of Science, King Saud University 11451Riyadh, Saudi Arabia
| | - Abdul Khader Mohammed
- Biomarkers Research Program, Department of Riyadh Biochemistry, College of Science, King Saud University 11451Riyadh, Saudi Arabia
- Prince Mutaib Chair for Biomarkers of Osteoporosis, Department of Riyadh Biochemistry, College of Science, King Saud University 11451Riyadh, Saudi Arabia
| | - Osama E Amer
- Biomarkers Research Program, Department of Riyadh Biochemistry, College of Science, King Saud University 11451Riyadh, Saudi Arabia
- Prince Mutaib Chair for Biomarkers of Osteoporosis, Department of Riyadh Biochemistry, College of Science, King Saud University 11451Riyadh, Saudi Arabia
| | - Gyanendra Tripathi
- Division of Metabolic and Vascular Research, University of WarwickCoventry CV2 2DX, UK
| | - Majed S Alokail
- Biomarkers Research Program, Department of Riyadh Biochemistry, College of Science, King Saud University 11451Riyadh, Saudi Arabia
- Prince Mutaib Chair for Biomarkers of Osteoporosis, Department of Riyadh Biochemistry, College of Science, King Saud University 11451Riyadh, Saudi Arabia
| | - Nasser M Al-Daghri
- Biomarkers Research Program, Department of Riyadh Biochemistry, College of Science, King Saud University 11451Riyadh, Saudi Arabia
- Prince Mutaib Chair for Biomarkers of Osteoporosis, Department of Riyadh Biochemistry, College of Science, King Saud University 11451Riyadh, Saudi Arabia
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Nishida A, Minegishi M, Takeuchi A, Niba ETE, Awano H, Lee T, Iijima K, Takeshima Y, Matsuo M. Tissue- and case-specific retention of intron 40 in mature dystrophin mRNA. J Hum Genet 2015; 60:327-33. [PMID: 25833469 DOI: 10.1038/jhg.2015.24] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/10/2015] [Accepted: 02/12/2015] [Indexed: 11/09/2022]
Abstract
The dystrophin gene, which is mutated in Duchenne muscular dystrophy (DMD), comprises 79 exons that show multiple alternative splicing events. Intron retention, a type of alternative splicing, may control gene expression. We examined intron retention in dystrophin introns by reverse-transcription PCR from skeletal muscle, focusing on the nine shortest (all <1000 bp), because these are more likely to be retained. Only one, intron 40, was retained in mRNA; sequencing revealed insertion of a complete intron 40 (851 nt) between exons 40 and 41. The intron 40 retention product accounted for 1.2% of the total product but had a premature stop codon at the fifth intronic codon. Intron 40 retention was most strongly observed in the kidney (36.6%) and was not obtained from the fetal liver, lung, spleen or placenta. This indicated that intron retention is a tissue-specific event whose level varies among tissues. In two DMD patients, intron 40 retention was observed in one patient but not in the other. Examination of splicing regulatory factors revealed that intron 40 had the highest guanine-cytosine content of all examined introns in a 30-nt segment at its 3' end. Further studies are needed to clarify the biological role of intron 40-retained dystrophin mRNA.
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Affiliation(s)
- Atsushi Nishida
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Kobe, Japan
| | - Maki Minegishi
- Department of Clinical Pharmacy, Kobe Pharmaceutical University, Kobe, Japan
| | - Atsuko Takeuchi
- Department of Clinical Pharmacy, Kobe Pharmaceutical University, Kobe, Japan
| | - Emma Tabe Eko Niba
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Kobe, Japan
| | - Hiroyuki Awano
- Department of Pediatrics, Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Tomoko Lee
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Graduate School of Medicine, Kobe University, Kobe, Japan
| | | | - Masafumi Matsuo
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Kobe, Japan
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O’Connor BP, Danhorn T, De Arras L, Flatley BR, Marcus RA, Farias-Hesson E, Leach SM, Alper S. Regulation of toll-like receptor signaling by the SF3a mRNA splicing complex. PLoS Genet 2015; 11:e1004932. [PMID: 25658809 PMCID: PMC4450051 DOI: 10.1371/journal.pgen.1004932] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 12/02/2014] [Indexed: 12/31/2022] Open
Abstract
The innate immune response plays a key role in fighting infection by activating inflammation and stimulating the adaptive immune response. However, chronic activation of innate immunity can contribute to the pathogenesis of many diseases with an inflammatory component. Thus, various negatively acting factors turn off innate immunity subsequent to its activation to ensure that inflammation is self-limiting and to prevent inflammatory disease. These negatively acting pathways include the production of inhibitory acting alternate proteins encoded by alternative mRNA splice forms of genes in Toll-like receptor (TLR) signaling pathways. We previously found that the SF3a mRNA splicing complex was required for a robust innate immune response; SF3a acts to promote inflammation in part by inhibiting the production of a negatively acting splice form of the TLR signaling adaptor MyD88. Here we inhibit SF3a1 using RNAi and subsequently perform an RNAseq study to identify the full complement of genes and splicing events regulated by SF3a in murine macrophages. Surprisingly, in macrophages, SF3a has significant preference for mRNA splicing events within innate immune signaling pathways compared with other biological pathways, thereby affecting the splicing of specific genes in the TLR signaling pathway to modulate the innate immune response. Within minutes after we are exposed to pathogens, our bodies react with a rapid response known as the “innate immune response.” This arm of the immune response regulates the process of inflammation, in which various immune cells are recruited to sites of infection and are activated to produce a host of antimicrobial compounds. This response is critical to fight infection. However, this response, if it is activated too strongly or if it becomes chronic, can do damage and can contribute to numerous very common diseases ranging from atherosclerosis to asthma to cancer. Thus it is essential that this response be tightly regulated, turned on when we have an infection, and turned off when not needed. We are investigating a mechanism that helps turn off this response, to ensure that inflammation is limited to prevent inflammatory disease. This mechanism involves the production of alternate forms of RNAs and proteins that control inflammation. We have discovered that a protein known as SF3a1 can regulate the expression of these alternate inhibitory RNA forms and are investigating how to use this knowledge to better control inflammation.
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Affiliation(s)
- Brian P. O’Connor
- Department of Pediatrics, National Jewish Health, Denver, Colorado, United States of America
- Integrated Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, United States of America
- Department of Biomedical Research, National Jewish Health, Denver, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Aurora, Colorado, United States of America
| | - Thomas Danhorn
- Integrated Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Lesly De Arras
- Integrated Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Brenna R. Flatley
- Integrated Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, United States of America
- Department of Biomedical Research, National Jewish Health, Denver, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Aurora, Colorado, United States of America
| | - Roland A. Marcus
- Department of Pediatrics, National Jewish Health, Denver, Colorado, United States of America
- Integrated Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Eveline Farias-Hesson
- Integrated Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Sonia M. Leach
- Integrated Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Scott Alper
- Integrated Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, United States of America
- Department of Biomedical Research, National Jewish Health, Denver, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Aurora, Colorado, United States of America
- * E-mail:
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