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Gu J, Li Y, Tian Y, Zhang Y, Cheng Y, Tang Y. Noncanonical functions of microRNAs in the nucleus. Acta Biochim Biophys Sin (Shanghai) 2024; 56:151-161. [PMID: 38167929 PMCID: PMC10984876 DOI: 10.3724/abbs.2023268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 11/03/2023] [Indexed: 01/05/2024] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs (ncRNAs) that play their roles in the regulation of physiological and pathological processes. Originally, it was assumed that miRNAs only modulate gene expression posttranscriptionally in the cytoplasm by inducing target mRNA degradation. However, with further research, evidence shows that mature miRNAs also exist in the cell nucleus, where they can impact gene transcription and ncRNA maturation in several ways. This review provides an overview of novel models of nuclear miRNA functions. Some of the models remain to be verified by experimental evidence, and more details of the miRNA regulation network remain to be discovered in the future.
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Affiliation(s)
- Jiayi Gu
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Yuanan Li
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Youtong Tian
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Yehao Zhang
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Yongjun Cheng
- Department of Rheumatologythe First People’s Hospital of WenlingWenling317500China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology/Department of RheumatologyRenji HospitalShanghai Jiao Tong University School of MedicineShanghai200001China
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteRenji HospitalShanghai200031China
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2
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Hao LY, Zhang M, Tao Y, Xu H, Liu Q, Yang K, Wei R, Zhou H, Jin T, Liu XD, Xue Z, Shen W, Cao JL, Pan Z. miRNA-22 Upregulates Mtf1 in Dorsal Horn Neurons and Is Essential for Inflammatory Pain. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8622388. [PMID: 35242280 PMCID: PMC8886789 DOI: 10.1155/2022/8622388] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/05/2021] [Accepted: 12/14/2021] [Indexed: 11/27/2022]
Abstract
Chronic inflammatory pain seriously affects patients' quality of life because of a paucity of effective clinical treatments caused, at least in part, by lack of full understanding of the underlying mechanisms. miRNAs are known to be involved in inflammatory pain via silencing or degrading of target mRNA in the cytoplasm. The present study provides a novel mechanism by which miRNA-22 positively regulates metal-regulatory transcription factor 1 (Mtf1) in the nuclei of neurons in the dorsal horn of the spinal cord. We found that miRNA-22 was significantly increased in the dorsal horn of mice with either inflammatory pain induced by plantar injection of complete Freund's adjuvant (CFA) or neuropathic pain induced by unilateral sciatic nerve chronic constrictive injury (CCI). Knocking down or blocking miRNA-22 alleviated CFA-induced mechanical allodynia and heat hyperalgesia, whereas overexpressing miRNA-22 produced pain-like behaviors. Mechanistically, the increased miRNA-22 binds directly to the Mtf1 promoter to recruit RNA polymerase II and elevate Mtf1 expression. The increased Mtf1 subsequently enhances spinal central sensitization, as evidenced by increased expression of p-ERK1/2, GFAP, and c-Fos in the dorsal horn. Our findings suggest that the miRNA-22-Mtf1 signaling axis in the dorsal horn plays a critical role in the induction and maintenance of inflammatory pain. This signaling pathway may be a promising therapeutic target in inflammatory pain.
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Affiliation(s)
- Ling-Yun Hao
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou 221004, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou 221004, China
| | - Ming Zhang
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou 221004, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou 221004, China
| | - Yang Tao
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou 221004, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou 221004, China
| | - Hengjun Xu
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou 221004, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou 221004, China
| | - Qiaoqiao Liu
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou 221004, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou 221004, China
| | - Kehui Yang
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou 221004, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou 221004, China
| | - Runa Wei
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou 221004, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou 221004, China
| | - Huimin Zhou
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou 221004, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou 221004, China
| | - Tong Jin
- Department of Pain, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Xiao-Dan Liu
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou 221004, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou 221004, China
| | - Zhouya Xue
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou 221004, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou 221004, China
| | - Wen Shen
- Department of Pain, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China
| | - Jun-Li Cao
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou 221004, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou 221004, China
- Department of Anesthesiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China
| | - Zhiqiang Pan
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou 221004, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou 221004, China
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3
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Dvorak P, Hlavac V, Soucek P. 5' Untranslated Region Elements Show High Abundance and Great Variability in Homologous ABCA Subfamily Genes. Int J Mol Sci 2020; 21:ijms21228878. [PMID: 33238634 PMCID: PMC7700387 DOI: 10.3390/ijms21228878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 11/16/2022] Open
Abstract
The 12 members of the ABCA subfamily in humans are known for their ability to transport cholesterol and its derivatives, vitamins, and xenobiotics across biomembranes. Several ABCA genes are causatively linked to inborn diseases, and the role in cancer progression and metastasis is studied intensively. The regulation of translation initiation is implicated as the major mechanism in the processes of post-transcriptional modifications determining final protein levels. In the current bioinformatics study, we mapped the features of the 5' untranslated regions (5'UTR) known to have the potential to regulate translation, such as the length of 5'UTRs, upstream ATG codons, upstream open-reading frames, introns, RNA G-quadruplex-forming sequences, stem loops, and Kozak consensus motifs, in the DNA sequences of all members of the subfamily. Subsequently, the conservation of the features, correlations among them, ribosome profiling data as well as protein levels in normal human tissues were examined. The 5'UTRs of ABCA genes contain above-average numbers of upstream ATGs, open-reading frames and introns, as well as conserved ones, and these elements probably play important biological roles in this subfamily, unlike RG4s. Although we found significant correlations among the features, we did not find any correlation between the numbers of 5'UTR features and protein tissue distribution and expression scores. We showed the existence of single nucleotide variants in relation to the 5'UTR features experimentally in a cohort of 105 breast cancer patients. 5'UTR features presumably prepare a complex playground, in which the other elements such as RNA binding proteins and non-coding RNAs play the major role in the fine-tuning of protein expression.
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Affiliation(s)
- Pavel Dvorak
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (V.H.); (P.S.)
- Correspondence: ; Tel.: +420-377593263
| | - Viktor Hlavac
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (V.H.); (P.S.)
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (V.H.); (P.S.)
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
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Avgeris M, Panoutsopoulou K, Papadimitriou MA, Scorilas A. Circulating exosomal miRNAs: clinical significance in human cancers. Expert Rev Mol Diagn 2019; 19:979-995. [PMID: 31594418 DOI: 10.1080/14737159.2019.1673732] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Introduction: The identification of novel noninvasive biomarkers to ameliorate early-diagnosis, and disease prognosis, as well as to support personalized treatment and monitoring decisions is of first clinical priority for cancer patients' care. Exosomes are natural endosome-derived extracellular vesicles that have emerged as crucial mediators of intercellular communication and tumor progression. Considering that deregulated miRNA levels have been described in numerous human malignancies and that tumor-derived exosomes reflect miRNA expression of donor tumor cells, the evaluation of exosome-derived circulating miRNAs (exomiRs) may offer a new promising class of noninvasive molecular markers to improve patients' management and quality-of-life. Areas covered: In the current review we have summarized the existing knowledge on the clinical relevance of circulating exosomal miRNAs in improving cancer diagnosis and prognosis, and thus supporting personalized patients' management Expert commentary: Cancer research has highlighted the abundance of exomiRs in patients' plasma and serum samples, as well as their biomarker capabilities in the vast majority of human malignancies studied so far. Their analytical stability constitutes exomiRs ideal molecular markers to overcome numerous limitations of cancer clinical management, while future large-scale studies should unveil exomiRs translational utility in modern cancer molecular diagnostics.
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Affiliation(s)
- Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens , Athens , Greece
| | - Konstantina Panoutsopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens , Athens , Greece
| | - Maria-Alexandra Papadimitriou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens , Athens , Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens , Athens , Greece
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5
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Liu H, Lei C, He Q, Pan Z, Xiao D, Tao Y. Nuclear functions of mammalian MicroRNAs in gene regulation, immunity and cancer. Mol Cancer 2018; 17:64. [PMID: 29471827 PMCID: PMC5822656 DOI: 10.1186/s12943-018-0765-5] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/12/2018] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous non-coding RNAs that contain approximately 22 nucleotides. They serve as key regulators in various biological processes and their dysregulation is implicated in many diseases including cancer and autoimmune disorders. It has been well established that the maturation of miRNAs occurs in the cytoplasm and miRNAs exert post-transcriptional gene silencing (PTGS) via RNA-induced silencing complex (RISC) pathway in the cytoplasm. However, numerous studies reaffirm the existence of mature miRNA in the nucleus, and nucleus-cytoplasm transport mechanism has also been illustrated. Moreover, active regulatory functions of nuclear miRNAs were found including PTGS, transcriptional gene silencing (TGS), and transcriptional gene activation (TGA), in which miRNAs bind nascent RNA transcripts, gene promoter regions or enhancer regions and exert further effects via epigenetic pathways. Based on existing interaction rules, some miRNA binding sites prediction software tools are developed, which are evaluated in this article. In addition, we attempt to explore and review the nuclear functions of miRNA in immunity, tumorigenesis and invasiveness of tumor. As a non-canonical aspect of miRNA action, nuclear miRNAs supplement miRNA regulatory networks and could be applied in miRNA based therapies.
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Affiliation(s)
- Hongyu Liu
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
- Key Laboratory of Carcinogenesis, Ministry of Education, Cancer Research Institute, School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Cheng Lei
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
- Key Laboratory of Carcinogenesis, Ministry of Education, Cancer Research Institute, School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Qin He
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
- Key Laboratory of Carcinogenesis, Ministry of Education, Cancer Research Institute, School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Zou Pan
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
- Key Laboratory of Carcinogenesis, Ministry of Education, Cancer Research Institute, School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
| | - Yongguang Tao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China.
- Key Laboratory of Carcinogenesis, Ministry of Education, Cancer Research Institute, School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China.
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, China.
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6
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Sourour SK, Aboelenein HR, Elemam NM, Abdelhamid AK, Salah S, Abdelaziz AI. Unraveling the expression of microRNA-27a* & NKG2D in peripheral blood mononuclear cells and natural killer cells of pediatric systemic lupus erythematosus patients. Int J Rheum Dis 2017; 20:1237-1246. [PMID: 28523761 DOI: 10.1111/1756-185x.13099] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND AIM The activity of natural killer (NK) cells is known to be decreased in systemic lupus erythematosus (SLE) patients. Nevertheless, the exact contribution of NK cells in the pathogenesis of SLE is still inconclusive. MicroRNAs (miRNAs), are small noncoding RNA molecules that play a fundamental role in regulating NK cell function. The objective of this study was to investigate the expression of miRNAs that might potentially target an essential activating receptor, NKG2D in peripheral blood mononuclear cells (PBMCs) and NK cells of SLE patients. METHODS In silico analysis revealed miR-27a* to potentially target NKG2D messenger RNA (mRNA), hence PBMCs and NK cells were isolated from blood samples of SLE patients and healthy controls. Next, the cells were transfected using mimics and antagomirs, after which miRNA/mRNA were quantified using real time quantitative reverse transcription polymerase chain reaction. RESULTS The results of this study showed that miR-27a* is overexpressed in the PBMCs and NK cells of SLE patients. In contrast, NKG2D was found to be downregulated in PBMCs and NK cells of SLE patients. Forcing the expression of miR-27a* in PBMCs and NK cells enhances the expression of NKG2D in SLE patients. Furthermore, the ligand of NKG2D, ULBP2, was found to be downregulated in the PBMCs of SLE patients. CONCLUSION The altered expression of the triad, miR-27a* as well as NKG2D and ULBP2, is thought to be characteristic for NK cells in SLE patients. Hence, the ability of miR-27a* to alter the expression of NKG2D may provide a new groundwork for understanding the role of miRNAs in NK cells of SLE patients.
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Affiliation(s)
- Shady K Sourour
- Department of Pharmacology and Toxicology, German University in Cairo, Cairo, Egypt
| | - Heba R Aboelenein
- Department of Pharmacology and Toxicology, German University in Cairo, Cairo, Egypt
| | - Noha M Elemam
- Department of Pharmacology and Toxicology, German University in Cairo, Cairo, Egypt.,Sharjah Institute for Medical Research (SIMR), College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Amira K Abdelhamid
- Department of Pharmaceutical Biology, German University in Cairo, Cairo, Egypt
| | - Samia Salah
- Department of Pediatrics, Kasr AlAiny Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Ahmed I Abdelaziz
- Department of Pharmacology and Toxicology, German University in Cairo, Cairo, Egypt.,School of Medicine, NewGiza University (NGU), Cairo, Egypt
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7
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Shi J, Pabon K, Scotto KW. Methylxanthines Increase Expression of the Splicing Factor SRSF2 by Regulating Multiple Post-transcriptional Mechanisms. J Biol Chem 2015; 290:14986-5003. [PMID: 25818199 DOI: 10.1074/jbc.m114.624254] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Indexed: 01/20/2023] Open
Abstract
We have previously reported that the methylxanthine caffeine increases expression of the splicing factor SRSF2, the levels of which are normally controlled by a negative autoregulatory loop. In the present study we have investigated the mechanisms by which methylxanthines induce this aberrant overexpression. RT-PCR analyses suggested little impact of caffeine on SRSF2 total mRNA levels. Instead, caffeine induced changes in the levels of SRSF2 3' UTR splice variants. Although some of these variants were substrates for nonsense-medicated decay (NMD), and could potentially have been stabilized by caffeine-mediated inhibition of NMD, down-regulation of NMD by a genetic approach was not sufficient to reproduce the phenotype. Furthermore, cell-based assays demonstrated that some of the caffeine-induced variants were intrinsically more efficiently translated than others; the addition of caffeine increased the translational efficiency of most SRSF2 transcripts. MicroRNA array analyses revealed a significant caffeine-mediated decrease in the expression of two SRSF2-targeting miRs, both of which were shown to repress translation of specific SRSF2 splice variants. These data support a complex model whereby caffeine down-regulates SRSF2-targeting microRNAs, leading to an increase in SRSF2 translation, which in turn induces SRSF2 splicing. SRSF2 splice variants are then stabilized by caffeine-mediated NMD inhibition, breaking the normal negative feedback loop and allowing the aberrant increase in SRSF2 protein levels. These findings highlight the complexity of SRSF2 gene regulation, and suggest ways in which SRSF2 expression may be dysregulated in disease.
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Affiliation(s)
- Jia Shi
- From the Rutgers Cancer Institute of New Jersey, the Robert Wood Johnson Medical School, and the Graduate School of Biomedical Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903
| | - Kirk Pabon
- From the Rutgers Cancer Institute of New Jersey, the Robert Wood Johnson Medical School, and the Graduate School of Biomedical Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903
| | - Kathleen W Scotto
- From the Rutgers Cancer Institute of New Jersey, the Robert Wood Johnson Medical School, and the Graduate School of Biomedical Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903
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8
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Tsotakos N, Silveyra P, Lin Z, Thomas N, Vaid M, Floros J. Regulation of translation by upstream translation initiation codons of surfactant protein A1 splice variants. Am J Physiol Lung Cell Mol Physiol 2014; 308:L58-75. [PMID: 25326576 DOI: 10.1152/ajplung.00058.2014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Surfactant protein A (SP-A), a molecule with roles in lung innate immunity and surfactant-related functions, is encoded by two genes in humans: SFTPA1 (SP-A1) and SFTPA2 (SP-A2). The mRNAs from these genes differ in their 5'-untranslated regions (5'-UTR) due to differential splicing. The 5'-UTR variant ACD' is exclusively found in transcripts of SP-A1, but not in those of SP-A2. Its unique exon C contains two upstream AUG codons (uAUGs) that may affect SP-A1 translation efficiency. The first uAUG (u1) is in frame with the primary start codon (p), but the second one (u2) is not. The purpose of this study was to assess the impact of uAUGs on SP-A1 expression. We employed RT-qPCR to determine the presence of exon C-containing SP-A1 transcripts in human RNA samples. We also used in vitro techniques including mutagenesis, reporter assays, and toeprinting analysis, as well as in silico analyses to determine the role of uAUGs. Exon C-containing mRNA is present in most human lung tissue samples and its expression can, under certain conditions, be regulated by factors such as dexamethasone or endotoxin. Mutating uAUGs resulted in increased luciferase activity. The mature protein size was not affected by the uAUGs, as shown by a combination of toeprint and in silico analysis for Kozak sequence, secondary structure, and signal peptide and in vitro translation in the presence of microsomes. In conclusion, alternative splicing may introduce uAUGs in SP-A1 transcripts, which in turn negatively affect SP-A1 translation, possibly affecting SP-A1/SP-A2 ratio, with potential for clinical implication.
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Affiliation(s)
- Nikolaos Tsotakos
- Center for Host Defense, Inflammation and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Patricia Silveyra
- Center for Host Defense, Inflammation and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Zhenwu Lin
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Neal Thomas
- Center for Host Defense, Inflammation and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania; Department of Public Health Sciences, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania; and
| | - Mudit Vaid
- Center for Host Defense, Inflammation and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Joanna Floros
- Center for Host Defense, Inflammation and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania; Department of Obstetrics and Gynecology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania
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9
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Schiller C, Nowak C, Diakopoulos KN, Weidle UH, Weiss EH. An upstream open reading frame regulates LST1 expression during monocyte differentiation. PLoS One 2014; 9:e96245. [PMID: 24816991 PMCID: PMC4015914 DOI: 10.1371/journal.pone.0096245] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 04/04/2014] [Indexed: 01/23/2023] Open
Abstract
The regulation of gene expression depends on the interplay of multiple factors at the transcriptional and translational level. Upstream open reading frames (uORFs) play an important role as translational repressors of main ORFs and their presence or usage in transcripts can be regulated by different mechanisms. The main objective of the present study was to assess whether uORFs regulate the expression of the MHC class III gene LST1. We report that expression of LST1 is tightly regulated by alternative transcription initiation and the presence of an uORF in the 5′-UTR of transcripts. Specifically, using EGFP reporter constructs in human HeLa and HEK-293T cells and flow cytometry as well as western blot analysis we found the uORF to reduce the expression of the main ORF by roughly two-thirds. Furthermore, we were able to correlate a previously detected increase in LST1 protein expression during monocyte differentiation with an increase of transcription initiation at an alternative exon that does not contain an uORF.
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Affiliation(s)
- Christian Schiller
- Department of Biology II, Ludwig-Maximilians-Universität München, Germany
| | - Carina Nowak
- Department of Biology II, Ludwig-Maximilians-Universität München, Germany
| | | | | | - Elisabeth H. Weiss
- Department of Biology II, Ludwig-Maximilians-Universität München, Germany
- * E-mail:
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10
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Comincini S, Allavena G, Palumbo S, Morini M, Durando F, Angeletti F, Pirtoli L, Miracco C. microRNA-17 regulates the expression of ATG7 and modulates the autophagy process, improving the sensitivity to temozolomide and low-dose ionizing radiation treatments in human glioblastoma cells. Cancer Biol Ther 2013; 14:574-86. [PMID: 23792642 PMCID: PMC3742487 DOI: 10.4161/cbt.24597] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/18/2013] [Accepted: 04/07/2013] [Indexed: 12/19/2022] Open
Abstract
ATG7 is a key autophagy-promoting gene that plays a critical role in the regulation of cell death and survival of various cell types. We report here that microRNAs (miRNAs), a class of endogenous 22-24 nucleotide noncoding RNA molecules able to affect stability and translation of mRNA, may represent a novel mechanism for regulating ATG7 expression and therefore autophagy. We demonstrated that ATG7 is a potential target for miR-17, and this miRNA could negatively regulate ATG7 expression, resulting in a modulation of the autophagic status in T98G glioblastoma cells. Treatment of these tumor cells with the miR-17 mimic decreased, and with the antagomir increased, the expression of ATG7 protein. Dual luciferase reporter assay confirmed that a specific miR-17 binding sequence in the 3'-UTR of ATG7 contributed to the modulation of the expression of the gene by miR-17. Interestingly, our results showed that anti-miR-17 administration activated autophagy through autophagosome formation, as resulted by LC3B and ATG7 protein expression increase, and by the analysis of GFP-LC3 positive autophagosome vesicles in living cells. Furthermore, the autophagy activation by anti-miR-17 resulted in a decrease of the threshold resistance at temozolomide doses in T98G cells, while miR-17 modulation in U373-MG glioblastoma cells resulted in a sensitization to low ionizing radiation doses. Our study of the role of miR-17 in regulating ATG7 expression and autophagy reveals a novel function for this miRNA sequence in a critical cellular event with significant impacts in cancer development, progression and treatment.
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Affiliation(s)
- Sergio Comincini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy.
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Tan Gana NH, Onuki T, Victoriano AFB, Okamoto T. MicroRNAs in HIV-1 infection: an integration of viral and cellular interaction at the genomic level. Front Microbiol 2012; 3:306. [PMID: 22936931 PMCID: PMC3426883 DOI: 10.3389/fmicb.2012.00306] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/01/2012] [Indexed: 12/15/2022] Open
Abstract
The microRNA pathways govern complex interactions of the host and virus at the transcripts level that regulate cellular responses, viral replication and viral pathogenesis. As a group of single-stranded short non-coding ribonucleotides (ncRNAs), the microRNAs complement their messenger RNA (mRNA) targets to effect post-transcriptional or translational gene silencing. Previous studies showed the ability of human immunodeficiency virus 1 (HIV-1) to encode microRNAs which modify cellular defence mechanisms thus creating an environment favorable for viral invasion and replication. In corollary, cellular microRNAs were linked to the alteration of HIV-1 infection at different stages of replication and latency. As evidences further establish the regulatory involvement of both cellular and viral microRNA in HIV-1-host interactions, there is a necessity to organize this information. This paper would present current and emerging knowledge on these multi-dimensional interactions that may facilitate the design of microRNAs as effective antiretroviral reagents.
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Affiliation(s)
- Neil H Tan Gana
- Department of Molecular and Cell Biology, Nagoya City University Graduate School of Medical Sciences Nagoya, Japan
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MicroRNAs in inner ear biology and pathogenesis. Hear Res 2012; 287:6-14. [PMID: 22484222 DOI: 10.1016/j.heares.2012.03.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 03/19/2012] [Accepted: 03/20/2012] [Indexed: 11/23/2022]
Abstract
MicroRNAs (miRNA) are a group of small noncoding RNAs that regulate gene expression. The discovery of these small RNAs has added a new layer of complexity to molecular biology. Every day, new advances are being made in understanding the biochemistry and genetics of miRNAs and their roles in cellular function and homeostasis. Studies indicate diverse roles for miRNAs in inner ear biology and pathogenesis. This article reviews recent developments in miRNA research in the field of inner ear biology. A brief history of miRNA discovery is discussed, and their genomics and functional roles are described. Advances in the understanding of miRNA involvement in inner ear development in the zebrafish and the mouse are presented. Finally, this review highlights the potential roles of miRNAs in genetic hearing loss, hair cell regeneration, and inner ear pathogenesis resulting from various pathological insults.
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Jakobson M, Lintulahti A, Arumäe U. mRNA for N-Bak, a neuron-specific BH3-only splice isoform of Bak, escapes nonsense-mediated decay and is translationally repressed in the neurons. Cell Death Dis 2012; 3:e269. [PMID: 22297299 PMCID: PMC3288346 DOI: 10.1038/cddis.2012.4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
mRNA for neuronal Bak (N-Bak), a splice variant of pro-apoptotic Bcl-2 family member Bak is expressed in the neurons. Surprisingly the endogeneous N-Bak protein cannot be demonstrated in the neurons, although the antibodies recognize N-Bak protein from in vitro translation or transiently transfected cells. As N-Bak mRNA contains premature termination codon (PTC) at 89 nucleotides upstream from the last exon–exon junction, it could be degraded by nonsense-mediated decay (NMD) during the pioneer round of translation thus explaining the absence of the protein. We show here that the endogeneous neuronal N-Bak mRNA is not the NMD substrate, as it is not accumulating by cycloheximide treatment, it has a long lifetime, and even prevention of PTC by interfering with the alternative splicing did not lead to translation of the Bak mRNA. N-Bak protein is also not revealed by proteasome inhibitors. Our data suggest strong translational arrest of N-Bak mRNA in the neurons. We show that this arrest is partially mediated by 5′-untranslated region of Bak mRNA and it is not released during mitochondrial apoptosis.
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Affiliation(s)
- M Jakobson
- Institute of Biotechnology, University of Helsinki, FIN-00014 Helsinki, Finland
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Abstract
PURPOSE OF REVIEW This review aims to describe the recent findings obtained on the regulation of ion transport by microRNAs in physiological and pathological situations in different organs and organisms. RECENT FINDINGS The number of ion channels or transporters can be regulated by increasing or decreasing the transcription and/or translation of the corresponding genes. In this context, a new class of regulators of gene expression has emerged as an important modulator of ion transport. microRNAs are short noncoding RNAs which inhibit gene expression by enhancing the degradation or inhibiting the translation of their targets. Most of the studies published so far describe their roles during embryonic development and tumorigenesis. However, recent studies have started to unravel how microRNA-mediated modulation of ion transport could contribute not only to the development of pathological states, such as heart disease, but also to the osmotic regulation of various organisms. SUMMARY The contribution of microRNAs to the regulation of ion transport has only begun to be unraveled, mostly in cardiomyocytes. Only a few studies have focused on the kidney but they strongly suggest that microRNAs could play an important role in the regulation of renal ion transport in response to variation in daily food intake.
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Tan Gana NH, Victoriano AFB, Okamoto T. Evaluation of online miRNA resources for biomedical applications. Genes Cells 2011; 17:11-27. [PMID: 22077698 DOI: 10.1111/j.1365-2443.2011.01564.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
MicroRNAs (miRNAs) are endogenous single-stranded, 22-nt (nucleotide) RNAs which complement mRNA to initiate post-transcriptional regulation. This review presents updates and evaluations of the public domain resources available for miRNA identification and target prediction toward their utilization in the biomedical research approach. This study discusses the basic principles of miRNA computational studies based on the nature and mechanism of action of miRNAs. Furthermore, we have explored fifty-nine current online miRNA tools that can be categorized into three classes in this paper: (i) miRNA identification; (ii) miRNA target prediction; and (iii) specialized miRNA tools.
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Affiliation(s)
- Neil H Tan Gana
- Department of Molecular and Cell Biology, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya City 467-8601, Japan
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Nelson PT, Wang WX, Mao G, Wilfred BR, Xie K, Jennings MH, Gao Z, Wang X. Specific sequence determinants of miR-15/107 microRNA gene group targets. Nucleic Acids Res 2011; 39:8163-72. [PMID: 21724616 PMCID: PMC3185429 DOI: 10.1093/nar/gkr532] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) target mRNAs in human cells via complex mechanisms that are still incompletely understood. Using anti-Argonaute (anti-AGO) antibody co-immunoprecipitation, followed by microarray analyses and downstream bioinformatics, 'RIP-Chip' experiments enable direct analyses of miRNA targets. RIP-Chip studies (and parallel assessments of total input mRNA) were performed in cultured H4 cells after transfection with miRNAs corresponding to the miR-15/107 gene group (miR-103, miR-107, miR-16 and miR-195), and five control miRNAs. Three biological replicates were run for each condition with a total of 54 separate human Affymetrix Human Gene 1.0 ST array replicates. Computational analyses queried for determinants of miRNA:mRNA binding. The analyses support four major findings: (i) RIP-Chip studies correlated with total input mRNA profiling provides more comprehensive information than using either RIP-Chip or total mRNA profiling alone after miRNA transfections; (ii) new data confirm that miR-107 paralogs target coding sequence (CDS) of mRNA; (iii) biochemical and computational studies indicate that the 3' portion of miRNAs plays a role in guiding miR-103/7 to the CDS of targets; and (iv) there are major sequence-specific targeting differences between miRNAs in terms of CDS versus 3'-untranslated region targeting, and stable AGO association versus mRNA knockdown. Future studies should take this important miRNA-to-miRNA variability into account.
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Affiliation(s)
- Peter T Nelson
- Department of Pathology and Division of Neuropathology, University of Kentucky Medical Center, Lexington, KY 40536, USA.
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Kubokawa I, Takeshima Y, Ota M, Enomoto M, Okizuka Y, Mori T, Nishimura N, Awano H, Yagi M, Matsuo M. Molecular characterization of the 5'-UTR of retinal dystrophin reveals a cryptic intron that regulates translational activity. Mol Vis 2010; 16:2590-7. [PMID: 21151598 PMCID: PMC3000234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 12/02/2010] [Indexed: 10/25/2022] Open
Abstract
PURPOSE Mutations in the dystrophin (DMD) gene cause Duchenne or Becker muscular dystrophy (DMD/BMD). DMD contains a retina-specific promoter in intron 29. The short R-dystrophin transcript from this promoter has a retina-specific exon 1 (R1) joined to exon 30 of the DMD gene. It has been claimed that this is responsible for the ophthalmological problems observed in DMD/BMD. This research characterizes the structure of the 5'-untranslated region (5'-UTR) of human R-dystrophin. METHODS The 5'-UTR of the human R-dystrophin transcript was amplified from human retina and 20 other human tissue RNAs by reverse transcription polymerase chain reaction (RT-PCR). Amplified products were identified by sequencing. The translational activities of transcripts bearing differing 5'-UTRs were measured using a dual luciferase assay system. RESULTS RT-PCR amplification of the R-dystrophin transcript from the retina using a conventional primer set revealed one product comprising exon R1 and exons 30 to 32 (R-dys α). In contrast, three amplified products were obtained when a forward primer at the far 5'-end of exon R1 was employed for RT-PCR. R-dys α, and a shorter form in which 98 bp was deleted from exon R1 (R-dys β), were the two major products. A minor, short form was also identified, in which 143 bp was deleted from exon R1 (R-dys γ). The two primary retinal products (R-dys α and β) encoded an identical open reading frame. The 98 bp deleted in R-dys β was identified as a cryptic intron that was evolutionarily acquired in higher mammals. The shorter R-dys β was expressed in several tissues with a wide range in expression level, while R-dys α was retina specific. The 5'-UTRs of R-dys α and β were examined for translational activity using a dual luciferase assay system. Unexpectedly, the 5'-UTR of R-dys β showed lower translational activity than that of R-dys α. This lower activity was presumed to be due to the removal of internal ribosome entry sites by activation of cryptic intron splicing. CONCLUSIONS An evolutionarily-acquired cryptic intron was identified in the 5'-UTR of the human R-dystrophin transcript. The two abundant R-dystrophin transcripts in the retina showed different translational activities in vitro owing to their differential splicing of the cryptic intron. This evolutionarily-acquired alternative splicing may act as a molecular switch that regulates translation of the R-dystrophin transcript.
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