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Ravegnini E, Trabocchi A, Lenci E. Small-molecule RNA ligands: a patent review (2018-2024). Expert Opin Ther Pat 2025:1-19. [PMID: 40219716 DOI: 10.1080/13543776.2025.2492759] [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: 01/04/2025] [Revised: 03/17/2025] [Accepted: 04/09/2025] [Indexed: 04/14/2025]
Abstract
INTRODUCTION Targeting three-dimensional RNA structures with traditional drug-like small molecules is gaining wide attention in both the academia and the pharmaceutical industries, due to their good oral bioavailability, cheap production cost, and the possibility of fine-tuning ADMET properties, which represent a powerful alternative to the current RNA-targeted therapies, including ASO and siRNA. As RNAs are involved in nearly all the physiological and pathological processes, small molecules RNA ligands can have a plethora of different therapeutic applications, spanning from cancer to infectious and neurological diseases. AREAS COVERED This review describes patents concerning small molecules RNA ligands published within January 2018 and October 2024, searched through Espacenet, Patentscope, and Google Patents databases. EXPERT OPINION The number of patents that has been released in the last few years demonstrates the relevance of targeting RNA structures for the development of next generation chemotherapeutic agents and antiviral/antibacterial drugs, even though this field is still in its infancy and many issues still need to be resolved, in particular related to selectivity. An emerging approach to considerably limiting side effects is presented by RIBOTAC derivatives, as promoting a selective RNase-L mediated RNA degradation allows to significantly reduce the dose of the compound.
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Affiliation(s)
- Elia Ravegnini
- Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy
| | - Andrea Trabocchi
- Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy
| | - Elena Lenci
- Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy
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2
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Li Y, Xu Y, Yu X, Su S, Wu B, Su Y, Guo L. Long non-coding RNA NEAT1 promotes colorectal cancer progression via interacting with SIRT1. Sci Rep 2025; 15:5673. [PMID: 39955367 PMCID: PMC11830096 DOI: 10.1038/s41598-025-90416-2] [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: 08/13/2024] [Accepted: 02/12/2025] [Indexed: 02/17/2025] Open
Abstract
Nuclear-enriched abundant transcript 1 (NEAT1), a long noncoding RNA, is found to be significantly dysregulated in different types of cancer, including colorectal cancer (CRC). Nevertheless, there is still much to learn about the precise functions and processes of NEAT1 in the progression of CRC. Using The Cancer Genome Atlas (TCGA) database and 50 CRC specimens from the First Affiliated Hospital of Dali University, we assessed the expression of NEAT1 to determine its clinical impact. Through gene set enrichment analysis (GSEA), Cancer Single-cell State Atlas (CancerSEA), and immune infiltration studies, we elucidated key functions of NEAT1. We utilized Cell Counting Kit-8 (CCK8), wound healing, and Transwell assays to investigate the role of NEAT1 in the progression of CRC. Through the use of GSEA and immunohistochemistry, additional investigations were conducted to unveil the downstream targets of NEAT1 and gain insights into their regulatory dynamics. Our in vitro studies confirmed the regulatory role of NEAT1 in CRC. Findings indicate that increased NEAT1 expression correlates with adverse outcomes in colorectal tissues. In the CRC model, reduced levels of NEAT1 lead to reduced cell proliferation, invasion, and migration. Additionally, NEAT1 influenced immune cell infiltration in CRC and functioned as an oncogene by upregulating Sirtuin 1 (SIRT1) expression. This study demonstrates that NEAT1 promotes CRC progression and metastasis through a SIRT1-mediated mechanism, suggesting its potential as a prognostic biomarker and therapeutic target for CRC.
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Affiliation(s)
- Yuwei Li
- Department of Medical Microbiology and Immunology, School of Basic Medical Sciences, Dali University, Dali, Yunnan, P.R. China
| | - Yunchun Xu
- Department of Medical Microbiology and Immunology, School of Basic Medical Sciences, Dali University, Dali, Yunnan, P.R. China
| | - Xinya Yu
- Department of Medical Microbiology and Immunology, School of Basic Medical Sciences, Dali University, Dali, Yunnan, P.R. China
| | - Shuangyan Su
- Department of Medical Microbiology and Immunology, School of Basic Medical Sciences, Dali University, Dali, Yunnan, P.R. China
| | - Bihua Wu
- Department of Medical Microbiology and Immunology, School of Basic Medical Sciences, Dali University, Dali, Yunnan, P.R. China
| | - Yunpeng Su
- Department of Medical Microbiology and Immunology, School of Basic Medical Sciences, Dali University, Dali, Yunnan, P.R. China
| | - Le Guo
- Department of Medical Microbiology and Immunology, School of Basic Medical Sciences, Dali University, Dali, Yunnan, P.R. China.
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3
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Wu R, Sun C, Chen X, Yang R, Luan Y, Zhao X, Yu P, Luo R, Hou Y, Tian R, Bian S, Li Y, Dong Y, Liu Q, Dai W, Fan Z, Yan R, Pan B, Feng S, Wu J, Chen F, Yang C, Wang H, Dai H, Shu M. NSUN5/TET2-directed chromatin-associated RNA modification of 5-methylcytosine to 5-hydroxymethylcytosine governs glioma immune evasion. Proc Natl Acad Sci U S A 2024; 121:e2321611121. [PMID: 38547058 PMCID: PMC10998593 DOI: 10.1073/pnas.2321611121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/28/2024] [Indexed: 04/02/2024] Open
Abstract
Malignant glioma exhibits immune evasion characterized by highly expressing the immune checkpoint CD47. RNA 5-methylcytosine(m5C) modification plays a pivotal role in tumor pathogenesis. However, the mechanism underlying m5C-modified RNA metabolism remains unclear, as does the contribution of m5C-modified RNA to the glioma immune microenvironment. In this study, we demonstrate that the canonical 28SrRNA methyltransferase NSUN5 down-regulates β-catenin by promoting the degradation of its mRNA, leading to enhanced phagocytosis of tumor-associated macrophages (TAMs). Specifically, the NSUN5-induced suppression of β-catenin relies on its methyltransferase activity mediated by cysteine 359 (C359) and is not influenced by its localization in the nucleolus. Intriguingly, NSUN5 directly interacts with and deposits m5C on CTNNB1 caRNA (chromatin-associated RNA). NSUN5-induced recruitment of TET2 to chromatin is independent of its methyltransferase activity. The m5C modification on caRNA is subsequently oxidized into 5-hydroxymethylcytosine (5hmC) by TET2, which is dependent on its binding affinity for Fe2+ and α-KG. Furthermore, NSUN5 enhances the chromatin recruitment of RBFOX2 which acts as a 5hmC-specific reader to recognize and facilitate the degradation of 5hmC caRNA. Notably, hmeRIP-seq analysis reveals numerous mRNA substrates of NSUN5 that potentially undergo this mode of metabolism. In addition, NSUN5 is epigenetically suppressed by DNA methylation and is negatively correlated with IDH1-R132H mutation in glioma patients. Importantly, pharmacological blockage of DNA methylation or IDH1-R132H mutant and CD47/SIRPα signaling synergistically enhances TAM-based phagocytosis and glioma elimination in vivo. Our findings unveil a general mechanism by which NSUN5/TET2/RBFOX2 signaling regulates RNA metabolism and highlight NSUN5 targeting as a potential strategy for glioma immune therapy.
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Affiliation(s)
- Ruixin Wu
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai200040, China
| | - Chunming Sun
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Neurology, Huashan hospital, Fudan University, Shanghai200040, China
| | - Xi Chen
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Runyue Yang
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai200032, China
| | - Yuxuan Luan
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Microbiology, Key Laboratory of Medical Molecular Virology (Ministry of Education/ National Health Commission/ Chinese Academy of Medical Sciences), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Xiang Zhao
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Panpan Yu
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Rongkui Luo
- Department of Pathology, Zhongshan hospital, Fudan University, Shanghai200032, China
| | - Yingyong Hou
- Department of Pathology, Zhongshan hospital, Fudan University, Shanghai200032, China
| | - Ruotong Tian
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Shasha Bian
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Microbiology, Key Laboratory of Medical Molecular Virology (Ministry of Education/ National Health Commission/ Chinese Academy of Medical Sciences), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Yuli Li
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Yinghua Dong
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Logistics, Dalian No.3 People’s hospital Affiliated to Dalian Medical University, Dalian116033, China
| | - Qian Liu
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Weiwei Dai
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Microbiology, Key Laboratory of Medical Molecular Virology (Ministry of Education/ National Health Commission/ Chinese Academy of Medical Sciences), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Zhuoyang Fan
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Rucheng Yan
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Binyang Pan
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai200040, China
| | - Siheng Feng
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Jing Wu
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai200040, China
| | - Fangzhen Chen
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai200040, China
| | - Changle Yang
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai200040, China
| | - Hanlin Wang
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Haochen Dai
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Minfeng Shu
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Microbiology, Key Laboratory of Medical Molecular Virology (Ministry of Education/ National Health Commission/ Chinese Academy of Medical Sciences), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
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4
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Damayanti NP, Saadatzadeh MR, Dobrota E, Ordaz JD, Bailey BJ, Pandya PH, Bijangi-Vishehsaraei K, Shannon HE, Alfonso A, Coy K, Trowbridge M, Sinn AL, Zhang ZY, Gallagher RI, Wulfkuhle J, Petricoin E, Richardson AM, Marshall MS, Lion A, Ferguson MJ, Balsara KE, Pollok KE. Establishment and characterization of patient-derived xenograft of a rare pediatric anaplastic pleomorphic xanthoastrocytoma (PXA) bearing a CDC42SE2-BRAF fusion. Sci Rep 2023; 13:9163. [PMID: 37280243 PMCID: PMC10244396 DOI: 10.1038/s41598-023-36107-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/30/2023] [Indexed: 06/08/2023] Open
Abstract
Pleomorphic xanthoastrocytoma (PXA) is a rare subset of primary pediatric glioma with 70% 5-year disease free survival. However, up to 20% of cases present with local recurrence and malignant transformation into more aggressive type anaplastic PXA (AXPA) or glioblastoma. The understanding of disease etiology and mechanisms driving PXA and APXA are limited, and there is no standard of care. Therefore, development of relevant preclinical models to investigate molecular underpinnings of disease and to guide novel therapeutic approaches are of interest. Here, for the first time we established, and characterized a patient-derived xenograft (PDX) from a leptomeningeal spread of a patient with recurrent APXA bearing a novel CDC42SE2-BRAF fusion. An integrated -omics analysis was conducted to assess model fidelity of the genomic, transcriptomic, and proteomic/phosphoproteomic landscapes. A stable xenoline was derived directly from the patient recurrent tumor and maintained in 2D and 3D culture systems. Conserved histology features between the PDX and matched APXA specimen were maintained through serial passages. Whole exome sequencing (WES) demonstrated a high degree of conservation in the genomic landscape between PDX and matched human tumor, including small variants (Pearson's r = 0.794-0.839) and tumor mutational burden (~ 3 mutations/MB). Large chromosomal variations including chromosomal gains and losses were preserved in PDX. Notably, chromosomal gain in chromosomes 4-9, 17 and 18 and loss in the short arm of chromosome 9 associated with homozygous 9p21.3 deletion involving CDKN2A/B locus were identified in both patient tumor and PDX sample. Moreover, chromosomal rearrangement involving 7q34 fusion; CDC42SE-BRAF t (5;7) (q31.1, q34) (5:130,721,239, 7:140,482,820) was identified in the PDX tumor, xenoline and matched human tumor. Transcriptomic profile of the patient's tumor was retained in PDX (Pearson r = 0.88) and in xenoline (Pearson r = 0.63) as well as preservation of enriched signaling pathways (FDR Adjusted P < 0.05) including MAPK, EGFR and PI3K/AKT pathways. The multi-omics data of (WES, transcriptome, and reverse phase protein array (RPPA) was integrated to deduce potential actionable pathways for treatment (FDR < 0.05) including KEGG01521, KEGG05202, and KEGG05200. Both xenoline and PDX were resistant to the MEK inhibitors trametinib or mirdametinib at clinically relevant doses, recapitulating the patient's resistance to such treatment in the clinic. This set of APXA models will serve as a preclinical resource for developing novel therapeutic regimens for rare anaplastic PXAs and pediatric high-grade gliomas bearing BRAF fusions.
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Affiliation(s)
- Nur P Damayanti
- Neuro-Oncology Program, Pediatric Neurosurgery, Department of Neurosurgery, Indiana University, Indianapolis, IN, 46202, USA
- Department of Neurosurgery, Indiana University, Indianapolis, IN, 46202, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA
| | - M Reza Saadatzadeh
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Erika Dobrota
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Josue D Ordaz
- Department of Neurosurgery, Indiana University, Indianapolis, IN, 46202, USA
| | - Barbara J Bailey
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Indiana University Simon Comprehensive Cancer Center Preclinical Modeling and Therapeutics Core, Indianapolis, USA
| | - Pankita H Pandya
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Khadijeh Bijangi-Vishehsaraei
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Translational Research Integrated Biology Laboratory/Indiana Pediatric Biobank, Riley Children Hospital, Indianapolis, IN, 46202, USA
| | - Harlan E Shannon
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Kathy Coy
- Indiana University Simon Comprehensive Cancer Center Preclinical Modeling and Therapeutics Core, Indianapolis, USA
| | - Melissa Trowbridge
- Indiana University Simon Comprehensive Cancer Center Preclinical Modeling and Therapeutics Core, Indianapolis, USA
| | - Anthony L Sinn
- Indiana University Simon Comprehensive Cancer Center Preclinical Modeling and Therapeutics Core, Indianapolis, USA
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, IN, 47907, USA
| | - Rosa I Gallagher
- Center for Applied Proteomics and Molecular Medicine, Institute for Biomedical Innovation, George Mason University, Manassas, VA, 20110, USA
| | - Julia Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, Institute for Biomedical Innovation, George Mason University, Manassas, VA, 20110, USA
| | - Emanuel Petricoin
- Center for Applied Proteomics and Molecular Medicine, Institute for Biomedical Innovation, George Mason University, Manassas, VA, 20110, USA
| | - Angela M Richardson
- Department of Neurosurgery, Indiana University, Indianapolis, IN, 46202, USA
- Indiana University Simon Comprehensive Cancer Center Preclinical Modeling and Therapeutics Core, Indianapolis, USA
| | - Mark S Marshall
- Pediatric Cancer Precision Genomics Program, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Alex Lion
- Division of Pediatric Hematology-Oncology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Michael J Ferguson
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA
- Pediatric Cancer Precision Genomics Program, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Division of Pediatric Hematology-Oncology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Karl E Balsara
- Neuro-Oncology Program, Pediatric Neurosurgery, Department of Neurosurgery, Indiana University, Indianapolis, IN, 46202, USA.
- Department of Neurosurgery, University of Oklahoma School of Medicine, Oklahoma City, OH, 73104, USA.
| | - Karen E Pollok
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA.
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
- Indiana University Simon Comprehensive Cancer Center Preclinical Modeling and Therapeutics Core, Indianapolis, USA.
- Pediatric Cancer Precision Genomics Program, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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5
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Wang YL, Zhao WW, Bai SM, Ma Y, Yin XK, Feng LL, Zeng GD, Wang F, Feng WX, Zheng J, Wang YN, Zeng B, Liu Q, Hung MC, Wan XB. DNA damage-induced paraspeckle formation enhances DNA repair and tumor radioresistance by recruiting ribosomal protein P0. Cell Death Dis 2022; 13:709. [PMID: 35974014 PMCID: PMC9381602 DOI: 10.1038/s41419-022-05092-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 01/21/2023]
Abstract
Paraspeckles are mammal-specific membraneless nuclear bodies that participate in various biological processes. NONO, a central paraspeckle component, has been shown to play pivotal roles in DNA double-strand breaks (DSB) repair, whereas its underlying mechanism needs to be further disclosed. Here, using co-immunoprecipitation and mass spectrum, we identified ribosomal protein P0 (RPLP0) as a DSB-induced NONO-binding protein; RPLP0 binds to the RRM1 and RRM2 domains of NONO. Similar to NONO, RPLP0 enhances non-homologous end joining-mediated DSB repair, which was ascribed to a ribosome-independent manner. Interestingly, paraspeckles were induced as early as 15 min after irradiation; it further recruited nuclear RPLP0 to enhance its interaction with NONO. Radiation-induced NONO/RPLP0 complex subsequently anchored at the damaged DNA and increased the autophosphorylation of DNA-PK at Thr2609, thereby enhancing DSB repair. Consistently, in vivo and in vitro experiments showed that depletion of NONO sensitizes tumor cells to radiation. For patients with locally advanced rectal cancer, NONO expression was remarkably increased in tumor tissues and correlated with a poor response to radiochemotherapy. Our findings suggest a pivotal role of radiation-induced paraspeckles in DNA repair and tumor radioresistance, and provide a new insight into the ribosome-independent function of ribosomal proteins.
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Affiliation(s)
- Yun-Long Wang
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China ,grid.12981.330000 0001 2360 039XDepartment of Radiation Oncology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Wan-Wen Zhao
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Shao-Mei Bai
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Yan Ma
- grid.12981.330000 0001 2360 039XDepartment of Radiation Oncology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Xin-Ke Yin
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Li-Li Feng
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Guang-Dong Zeng
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Fang Wang
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Wei-Xing Feng
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China ,grid.12981.330000 0001 2360 039XDepartment of Radiation Oncology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Jian Zheng
- grid.12981.330000 0001 2360 039XDepartment of Radiation Oncology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Ying-Nai Wang
- grid.240145.60000 0001 2291 4776Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Bing Zeng
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Quentin Liu
- grid.411971.b0000 0000 9558 1426Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044 People’s Republic of China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060 People’s Republic of China
| | - Mien-Chie Hung
- grid.240145.60000 0001 2291 4776Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA ,grid.254145.30000 0001 0083 6092Graduate Institute of Biomedical Sciences and Research Centers for Cancer Biology and Molecular Medicine, China Medical University, Taichung, 404 Taiwan ,grid.252470.60000 0000 9263 9645Department of Biotechnology, Asia University, Taichung, 413 Taiwan
| | - Xiang-Bo Wan
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China ,grid.12981.330000 0001 2360 039XDepartment of Radiation Oncology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
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6
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Azizidoost S, Ghaedrahmati F, Anbiyaee O, Ahmad Ali R, Cheraghzadeh M, Farzaneh M. Emerging roles for lncRNA-NEAT1 in colorectal cancer. Cancer Cell Int 2022; 22:209. [PMID: 35676702 PMCID: PMC9178824 DOI: 10.1186/s12935-022-02627-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/31/2022] [Indexed: 12/21/2022] Open
Abstract
Colorectal cancer (CRC) is the third cause of cancer death in the world that arises from the glandular and epithelial cells of the large intestine, during a series of genetic or epigenetic alternations. Recently, long non-coding RNAs (lncRNAs) has opened a separate window of research in molecular and translational medicine. Emerging evidence has supported that lncRNAs can regulate cell cycle of CRC cells. LncRNA NEAT1 has been verified to participate in colon cancer development and progression. NEAT1 as a competing endogenous RNA could suppress the expression of miRNAs, and then regulate molecules downstream of these miRNAs. In this review, we summarized emerging roles of NEAT1 in CRC cells.
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Affiliation(s)
- Shirin Azizidoost
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Farhoodeh Ghaedrahmati
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Omid Anbiyaee
- Cardiovascular Research Center, Nemazi Hospital, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Riyadh Ahmad Ali
- Department of Medical Laboratory Science, College of Health Science, Lebanese French University, Kurdistan Region, Iraq
| | - Maryam Cheraghzadeh
- Department of Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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7
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Sanbonmatsu K. Getting to the bottom of lncRNA mechanism: structure-function relationships. Mamm Genome 2022; 33:343-353. [PMID: 34642784 PMCID: PMC8509902 DOI: 10.1007/s00335-021-09924-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022]
Abstract
While long non-coding RNAs are known to play key roles in disease and development, relatively few structural studies have been performed for this important class of RNAs. Here, we review functional studies of long non-coding RNAs and expose the need for high-resolution 3-D structural studies, discussing the roles of long non-coding RNAs in the cell and how structure-function relationships might be used to elucidate further understanding. We then describe structural studies of other classes of RNAs using chemical probing, nuclear magnetic resonance, small-angle X-ray scattering, X-ray crystallography, and cryogenic electron microscopy (cryo-EM). Next, we review early structural studies of long non-coding RNAs to date and describe the way forward for the structural biology of long non-coding RNAs in terms of cryo-EM.
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8
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Liu C, Gao X, Li Y, Sun W, Xu Y, Tan Y, Du R, Zhong G, Zhao D, Liu Z, Jin X, Zhao Y, Wang Y, Yuan X, Pan J, Yuan G, Li Y, Xing W, Kan G, Wang Y, Li Q, Han X, Li J, Ling S, Li Y. The mechanosensitive lncRNA Neat1 promotes osteoblast function through paraspeckle-dependent Smurf1 mRNA retention. Bone Res 2022; 10:18. [PMID: 35210394 PMCID: PMC8873336 DOI: 10.1038/s41413-022-00191-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 11/01/2021] [Accepted: 12/14/2021] [Indexed: 12/21/2022] Open
Abstract
Mechanical stimulation plays an important role in bone remodeling. Exercise-induced mechanical loading enhances bone strength, whereas mechanical unloading leads to bone loss. Increasing evidence has demonstrated that long noncoding RNAs (lncRNAs) play key roles in diverse biological, physiological and pathological contexts. However, the roles of lncRNAs in mechanotransduction and their relationships with bone formation remain unknown. In this study, we screened mechanosensing lncRNAs in osteoblasts and identified Neat1, the most clearly decreased lncRNA under simulated microgravity. Of note, not only Neat1 expression but also the specific paraspeckle structure formed by Neat1 was sensitive to different mechanical stimulations, which were closely associated with osteoblast function. Paraspeckles exhibited small punctate aggregates under simulated microgravity and elongated prolate or larger irregular structures under mechanical loading. Neat1 knockout mice displayed disrupted bone formation, impaired bone structure and strength, and reduced bone mass. Neat1 deficiency in osteoblasts reduced the response of osteoblasts to mechanical stimulation. In vivo, Neat1 knockout in mice weakened the bone phenotypes in response to mechanical loading and hindlimb unloading stimulation. Mechanistically, paraspeckles promoted nuclear retention of E3 ubiquitin ligase Smurf1 mRNA and downregulation of their translation, thus inhibiting ubiquitination-mediated degradation of the osteoblast master transcription factor Runx2, a Smurf1 target. Our study revealed that Neat1 plays an essential role in osteoblast function under mechanical stimulation, which provides a paradigm for the function of the lncRNA-assembled structure in response to mechanical stimulation and offers a therapeutic strategy for long-term spaceflight- or bedrest-induced bone loss and age-related osteoporosis.
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Affiliation(s)
- Caizhi Liu
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Xingcheng Gao
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Yuheng Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China.,The Key Laboratory of Aerospace Medicine, Ministry of Education, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Weijia Sun
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Youjia Xu
- The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yingjun Tan
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Ruikai Du
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Guohui Zhong
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China.,The Key Laboratory of Aerospace Medicine, Ministry of Education, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Dingsheng Zhao
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Zizhong Liu
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Xiaoyan Jin
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Yinlong Zhao
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China.,College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Yinbo Wang
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China.,The Key Laboratory of Aerospace Medicine, Ministry of Education, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Xinxin Yuan
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Junjie Pan
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China.,Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Guodong Yuan
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China.,Medical School of Southeast University, Nanjing, Jiangsu, China
| | - Youyou Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China.,The Key Laboratory of Aerospace Medicine, Ministry of Education, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Wenjuan Xing
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China.,The Key Laboratory of Aerospace Medicine, Ministry of Education, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Guanghan Kan
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Yanqing Wang
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Qi Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Xuan Han
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Jianwei Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China.
| | - Shukuan Ling
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China.
| | - Yingxian Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China.
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9
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Sanbonmatsu K. Towards Molecular Mechanism in Long Non-coding RNAs: Linking Structure and Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:23-32. [PMID: 35220564 DOI: 10.1007/978-3-030-92034-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
While long non-coding RNAs play key roles in disease and development, few structural studies have been performed to date for this emerging class of RNAs. Here, we provide a brief review of functional studies of long non-coding RNAs, followed by a review of previous structural studies of long non-coding RNAs. We then describe structural studies of other classes of RNAs using chemical probing, nuclear magnetic resonance, small angle X-ray scattering, X-ray crystallography and cryogenic electron microscopy (cryo-EM). Next, we describe the way forward for the structural biology of long non-coding RNAs in terms of cryo-EM. Finally, we discuss of the roles of long non-coding RNAs in the cell and how structure-function relationships might be used to elucidate further understanding.
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10
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Bhatt U, Kretzmann AL, Guédin A, Ou A, Kobelke S, Bond CS, Evans CW, Hurley LH, Mergny JL, Iyer KS, Fox AH, Smith NM. The role of G-Quadruplex DNA in Paraspeckle formation in cancer. Biochimie 2021; 190:124-131. [PMID: 34329720 DOI: 10.1016/j.biochi.2021.07.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 12/11/2022]
Abstract
Paraspeckles are RNA-protein structures within the nucleus of mammalian cells, capable of orchestrating various biochemical processes. An overexpression of the architectural component of paraspeckles, a long non-coding RNA called NEAT1 (Nuclear Enriched Abundant Transcript 1), has been linked to a variety of cancers and is often associated with poor patient prognosis. Thus, there is an accumulating interest in the role of paraspeckles in carcinogenesis, however there is a limited understanding of how NEAT1 expression is regulated. Here, we demonstrate that both nuclear G-quadruplex (G4) and paraspeckle formation are significantly increased in a human breast cancer cell line compared to non-tumorigenic breast cells. Moreover, we identified and characterized G4-forming sequences within the NEAT1 promoter and demonstrate stabilization of G4 DNA with a G4-stabilizing small molecule results in a significant alteration in both paraspeckle formation and NEAT1 expression. This G4-mediated alteration of NEAT1 at both the transcriptional and post-transcriptional levels was evident in U2OS osteosarcoma cells, MCF-7 breast adenocarcinoma and MDA-MB-231 triple negative breast cancer cells.
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Affiliation(s)
- Uditi Bhatt
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Amy L Kretzmann
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Aurore Guédin
- ARNA Laboratory, IECB, INSERM U1212, CNRS UMR5320, Université de Bordeaux, Pessac, France
| | - Arnold Ou
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Simon Kobelke
- School of Human Sciences, The University of Western Australia, Perth, Australia
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | | | - Jean-Louis Mergny
- ARNA Laboratory, IECB, INSERM U1212, CNRS UMR5320, Université de Bordeaux, Pessac, France; Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 65, Czech Republic; Laboratoire D'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau Cedex, France
| | - K Swaminathan Iyer
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Archa H Fox
- School of Molecular Sciences, The University of Western Australia, Perth, Australia; School of Human Sciences, The University of Western Australia, Perth, Australia
| | - Nicole M Smith
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.
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11
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Plasek LM, Valadkhan S. lncRNAs in T lymphocytes: RNA regulation at the heart of the immune response. Am J Physiol Cell Physiol 2021; 320:C415-C427. [PMID: 33296288 PMCID: PMC8294623 DOI: 10.1152/ajpcell.00069.2020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genome-wide analyses in the last decade have uncovered the presence of a large number of long non-protein-coding transcripts that show highly tissue- and state-specific expression patterns. High-throughput sequencing analyses in diverse subsets of immune cells have revealed a complex and dynamic expression pattern for these long noncoding RNAs (lncRNAs) that correlate with the functional states of immune cells. Although the vast majority of lncRNAs expressed in immune cells remain unstudied, functional studies performed on a small subset have indicated that their state-specific expressions pattern frequently has a regulatory impact on the function of immune cells. In vivo and in vitro studies have pointed to the involvement of lncRNAs in a wide variety of cellular processes, including both the innate and adaptive immune response through mechanisms ranging from epigenetic and transcriptional regulation to sequestration of functional molecules in subcellular compartments. This review will focus mainly on the role of lncRNAs in CD4+ and CD8+ T cells, which play pivotal roles in adaptive immunity. Recent studies have pointed to key physiological functions for lncRNAs during several developmental and functional stages of the life cycle of lymphocytes. Although lncRNAs play important physiological roles in lymphocytic response to antigenic stimulation, differentiation into effector cells, and secretion of cytokines, their dysregulated expression can promote or sustain pathological states such as autoimmunity, chronic inflammation, cancer, and viremia. This, together with their highly cell type-specific expression patterns, makes lncRNAs ideal therapeutic targets and underscores the need for additional studies into the role of these understudied transcripts in adaptive immune response.
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12
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Xufei F, Xiujuan Z, Jianyi L, Liyan Y, Ting Y, Min H. Up-regulation of LncRNA NEAT1 induces apoptosis of human placental trophoblasts. Free Radic Res 2020; 54:678-686. [PMID: 32998583 DOI: 10.1080/10715762.2020.1826468] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The trophoblast apoptosis induced by placental oxidative stress is a contributor to the pathological development of preeclampsia (PE), whereas the molecular mechanism remains unclear. In this study, we explored the role and mechanism of Long non-coding RNA (LncRNA) NEAT1 in trophoblasts apoptosis. In the placenta tissues of PE patients and H2O2-treated human trophoblast cell line HTR-8/SVneo, the expressions of LncRNA NEAT1, p53, and estrogen receptor α (ESRα) were increased whereas miR-18a-5p expression was decreased. ESRα expression was up-regulated by LncRNA NEAT1 overexpression and down-regulated by miR-18a-5p overexpression in HTR-8/SVneo cells. LncRNA NEAT1 could release ESRα expression through sponging miR-18a-5p and the transcription of LncRNA NEAT1 was promoted by p53. miR-18a-5p overexpression suppressed H2O2-induced cell apoptosis in HTR-8/SVneo cells, while the inhibitory effect of miR-18a-5p overexpression on cell apoptosis was abrogated by LncRNA NEAT1 overexpression. In summary, LncRNA NEAT1 transcription was induced by p53 under oxidative stress condition, the high expression of LncRNA NEAT1 subsequently increased ESRα expression by sponging miR-18a-5p, thus inducing trophoblasts apoptosis.
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Affiliation(s)
- Fan Xufei
- Department of Obstetrics and Gynecology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Zheng Xiujuan
- Department of Obstetrics and Gynecology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Lou Jianyi
- Department of Obstetrics and Gynecology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Ye Liyan
- Department of Obstetrics and Gynecology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Yan Ting
- Department of Obstetrics and Gynecology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Hu Min
- Department of Obstetrics and Gynecology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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13
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Razin SV, Gavrilov AA, Iarovaia OV. Modification of Nuclear Compartments and the 3D Genome in the Course of a Viral Infection. Acta Naturae 2020; 12:34-46. [PMID: 33456976 PMCID: PMC7800604 DOI: 10.32607/actanaturae.11041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022] Open
Abstract
The review addresses the question of how the structural and functional compartmentalization of the cell nucleus and the 3D organization of the cellular genome are modified during the infection of cells with various viruses. Particular attention is paid to the role of the introduced changes in the implementation of the viral strategy to evade the antiviral defense systems and provide conditions for viral replication. The discussion focuses on viruses replicating in the cell nucleus. Cytoplasmic viruses are mentioned in cases when a significant reorganization of the nuclear compartments or the 3D genome structure occurs during an infection with these viruses.
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Affiliation(s)
- S. V. Razin
- Institute of Gene Biology Russian Academy of Sciences
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14
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Li W, Karwacki-Neisius V, Ma C, Tan L, Shi Y, Wu F, Shi YG. Nono deficiency compromises TET1 chromatin association and impedes neuronal differentiation of mouse embryonic stem cells. Nucleic Acids Res 2020; 48:4827-4838. [PMID: 32286661 PMCID: PMC7229820 DOI: 10.1093/nar/gkaa213] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 03/19/2020] [Accepted: 04/13/2020] [Indexed: 12/11/2022] Open
Abstract
NONO is a DNA/RNA-binding protein, which plays a critical regulatory role during cell stage transitions of mouse embryonic stem cells (mESCs). However, its function in neuronal lineage commitment and the molecular mechanisms of its action in such processes are largely unknown. Here we report that NONO plays a key role during neuronal differentiation of mESCs. Nono deletion impedes neuronal lineage commitment largely due to a failure of up-regulation of specific genes critical for neuronal differentiation. Many of the NONO regulated genes are also DNA demethylase TET1 targeted genes. Importantly, re-introducing wild type NONO to the Nono KO cells, not only restores the normal expression of the majority of NONO/TET1 coregulated genes but also rescues the defective neuronal differentiation of Nono-deficient mESCs. Mechanistically, our data shows that NONO directly interacts with TET1 via its DNA binding domain and recruits TET1 to genomic loci to regulate 5-hydroxymethylcytosine levels. Nono deletion leads to a significant dissociation of TET1 from chromatin and dysregulation of DNA hydroxymethylation of neuronal genes. Taken together, our findings reveal a key role and an epigenetic mechanism of action of NONO in regulation of TET1-targeted neuronal genes, offering new functional and mechanistic understanding of NONO in stem cell functions, lineage commitment and specification.
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Affiliation(s)
- Wenjing Li
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China, and Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, 201102, China.,Endocrinology Division, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA
| | - Violetta Karwacki-Neisius
- Division of Newborn Medicine and Program in Epigenetics, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Chun Ma
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China, and Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Li Tan
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China, and Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Yang Shi
- Division of Newborn Medicine and Program in Epigenetics, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Feizhen Wu
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China, and Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Yujiang Geno Shi
- Endocrinology Division, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA
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15
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Simko EAJ, Liu H, Zhang T, Velasquez A, Teli S, Haeusler AR, Wang J. G-quadruplexes offer a conserved structural motif for NONO recruitment to NEAT1 architectural lncRNA. Nucleic Acids Res 2020; 48:7421-7438. [PMID: 32496517 PMCID: PMC7367201 DOI: 10.1093/nar/gkaa475] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/02/2020] [Indexed: 12/11/2022] Open
Abstract
The long non-coding RNA NEAT1 serves as a scaffold for the assembly of paraspeckles, membraneless nuclear organelles involved in gene regulation. Paraspeckle assembly requires NEAT1 recruitment of the RNA-binding protein NONO, however the NEAT1 elements responsible for recruitment are unknown. Herein we present evidence that previously unrecognized structural features of NEAT1 serve an important role in these interactions. Led by the initial observation that NONO preferentially binds the G-quadruplex conformation of G-rich C9orf72 repeat RNA, we find that G-quadruplex motifs are abundant and conserved features of NEAT1. Furthermore, we determine that NONO binds NEAT1 G-quadruplexes with structural specificity and provide evidence that G-quadruplex motifs mediate NONO-NEAT1 association, with NONO binding sites on NEAT1 corresponding largely to G-quadruplex motifs, and treatment with a G-quadruplex-disrupting small molecule causing dissociation of native NONO-NEAT1 complexes. Together, these findings position G-quadruplexes as a primary candidate for the NONO-recruiting elements of NEAT1 and provide a framework for further investigation into the role of G-quadruplexes in paraspeckle formation and function.
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Affiliation(s)
- Eric A J Simko
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Honghe Liu
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tao Zhang
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Adan Velasquez
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shraddha Teli
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Aaron R Haeusler
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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16
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Wang J, Chen Y, Tang Z, Hu D, Yao C, Yang L. LncRNA NEAT1 regulated inflammation and apoptosis in a rat model of sepsis-induced acute kidney injury via MiR-27a-3p/TAB3 axis. Biosci Biotechnol Biochem 2020; 84:2215-2227. [PMID: 32698679 DOI: 10.1080/09168451.2020.1792760] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This study explored the mechanism of NEAT1 in sepsis-induced AKI rats. Cecal ligation punctures (CLP)-induced AKI rats were injected with siRNA-NEAT1 lentivirus. Kidney histopathology and apoptosis were evaluated via hematoxylin-eosin and TUNEL staining, respectively. ELISA determined the levels of Blood urea nitrogen (BUN), serum creatinine (SCr), neutrophil gelatinase-associated lipocalin (NGAL), kidney injury molecule-1 (KIM-1), TNF-α, Interleukin (IL)-1β, and IL-6. Colorimetry measured malondialdehyde (MDA), superoxide dismutase (SOD) activities. qPCR analyzed NEAT1, miR-27a-3p, TAB3, Bcl-2, and Bax expressions. siNEAT1 reversed the promotive effect of CLP on kidney histopathological injury, and BUN, SCr, NGAL, KIM-1, TNF-α, IL-1β, IL-6, MDA, and Bax levels and apoptosis, but raised CLP-downregulated SOD and Bcl-2 levels. NEAT1 sponged miR-27a-3p which targeted TAB3. siNEAT1 upregulated miR-27a-3p and downregulated TAB3 expression. TAB3 overexpression reversed the inhibitory effect of siNEAT1 on the LPS-induced apoptosis of HK-2 cells. siNEAT1 alleviated sepsis-induced AKI in rats and LPS-induced sepsis of cells via miR-27a-3p/TAB3 axis.
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Affiliation(s)
- Jiasheng Wang
- Department of Critical Medicine, The People's Hospital of Dazu District , Chongqing, China
| | - Yong Chen
- Department of Critical Medicine, The People's Hospital of Dazu District , Chongqing, China
| | - Ze Tang
- Department of Critical Care Medicine, Yongchuan Hospital of Chongqing Medical University , Chongqing, China
| | - Dabi Hu
- Department of Critical Medicine, The People's Hospital of Dazu District , Chongqing, China
| | - Caoyuan Yao
- Department of Respiratory and Critical Care Medicine, Yongchuan Hospital of Chongqing Medical University , Chongqing, China
| | - Lei Yang
- Department of Laboratory, The People's Hospital of Dazu District , Chongqing, China
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17
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Boros FA, Maszlag-Török R, Vécsei L, Klivényi P. Increased level of NEAT1 long non-coding RNA is detectable in peripheral blood cells of patients with Parkinson's disease. Brain Res 2020; 1730:146672. [PMID: 31953211 DOI: 10.1016/j.brainres.2020.146672] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/21/2019] [Accepted: 01/12/2020] [Indexed: 02/07/2023]
Abstract
Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder that poses serious burden to individuals and society as well. Although a number of PD associated genetic factors have been identified, the molecular mechanism of the disease so far has not been completely elucidated. Involvement of long non-coding RNAs (lncRNAs) in the pathology of neurodegenerative disorders is attracting increased interest because of the diverse mechanisms lncRNAs affect gene expression and cellular homeostasis at different levels. We aimed to test the feasibility of detecting alterations in lncRNA levels in easily accessible samples of PD patients by routine laboratory technique. By narrowing the number of selected lncRNAs implicated in neurodegeneration and increasing the number of PD samples included, we found one out of 41 lncRNAs readily detectable in increased level in peripheral blood of PD patients. We detected NEAT1 to be significantly up-regulated in PD patients in multiple comparisons. NEAT1 is the core element of nuclear paraspeckles and it plays role in regulation of transcription, mRNA and miRNA levels, mitochondrial and cellular homeostasis. Our finding is in accord with recent data demonstrating changes in the level of NEAT1 in neurons of PD patients and in several models of the disease. However, to our knowledge this is the first study to report NEAT1 up-regulation in blood of PD patients. Identification of altered expression of this lncRNA in the periphery might help to a better understanding of the mechanisms underlying PD, and can contribute to the identification of new therapeutic targets and disease markers.
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Affiliation(s)
- Fanni Annamária Boros
- Department of Neurology, Albert Szent-Györgyi Clinical Center, Faculty of Medicine, University of Szeged, Semmelweis u. 6, H-6725 Szeged, Hungary
| | - Rita Maszlag-Török
- Department of Neurology, Albert Szent-Györgyi Clinical Center, Faculty of Medicine, University of Szeged, Semmelweis u. 6, H-6725 Szeged, Hungary; MTA-SZTE Neuroscience Research Group, Semmelweis u. 6, H-6725 Szeged, Hungary
| | - László Vécsei
- Department of Neurology, Albert Szent-Györgyi Clinical Center, Faculty of Medicine, University of Szeged, Semmelweis u. 6, H-6725 Szeged, Hungary; MTA-SZTE Neuroscience Research Group, Semmelweis u. 6, H-6725 Szeged, Hungary
| | - Péter Klivényi
- Department of Neurology, Albert Szent-Györgyi Clinical Center, Faculty of Medicine, University of Szeged, Semmelweis u. 6, H-6725 Szeged, Hungary.
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18
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Deshar R, Yoo W, Cho EB, Kim S, Yoon JB. RNF8 mediates NONO degradation following UV-induced DNA damage to properly terminate ATR-CHK1 checkpoint signaling. Nucleic Acids Res 2019; 47:762-778. [PMID: 30445466 PMCID: PMC6344893 DOI: 10.1093/nar/gky1166] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/02/2018] [Indexed: 12/26/2022] Open
Abstract
RNF8 plays a critical role in DNA damage response (DDR) to initiate ubiquitination-dependent signaling. To better characterize the role of RNF8 in UV-induced DDR, we searched for novel substrates of RNF8 and identified NONO as one intriguing substrate. We found that: (i) RNF8 ubiquitinates NONO and (ii) UV radiation triggers NONO ubiquitination and its subsequent degradation. Depletion of RNF8 inhibited UV-induced degradation of NONO, suggesting that RNF8 targets NONO for degradation in response to UV damage. In addition, we found that 3 NONO lysine residues (positions 279, 290 and 295) are important for conferring its instability in UV-DDR. Depletion of RNF8 or expression of NONO with lysine to arginine substitutions at positions 279, 290 and 295 prolonged CHK1 phosphorylation over an extended period of time. Furthermore, expression of the stable mutant, but not wild-type NONO, induced a prolonged S phase following UV exposure. Stable cell lines expressing the stable NONO mutant showed increased UV sensitivity in a clonogenic survival assay. Since RNF8 recruitment to the UV-damaged sites is dependent on ATR, we propose that RNF8-mediated NONO degradation and subsequent inhibition of NONO-dependent chromatin loading of TOPBP1, a key activator of ATR, function as a negative feedback loop critical for turning off ATR-CHK1 checkpoint signaling in UV-DDR.
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Affiliation(s)
- Rakesh Deshar
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul 137-701, Korea
| | - Wonjin Yoo
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Eun-Bee Cho
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Sungjoo Kim
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul 137-701, Korea
| | - Jong-Bok Yoon
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 120-749, Korea
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19
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Yuan L, Zhou M, Lv H, Qin X, Zhou J, Mao X, Li X, Xu Y, Liu Y, Xing H. Involvement of NEAT1/miR‐133a axis in promoting cervical cancer progression via targeting SOX4. J Cell Physiol 2019; 234:18985-18993. [PMID: 30932200 DOI: 10.1002/jcp.28538] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 02/25/2019] [Accepted: 03/05/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Li‐Yun Yuan
- Department of Obstetrics and Gynecology Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science Xiangyang Hubei China
| | - Min Zhou
- Department of Obstetrics and Gynecology Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science Xiangyang Hubei China
| | - Huabing Lv
- Department of Obstetrics and Gynecology Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science Xiangyang Hubei China
| | - Xiaomin Qin
- Department of Obstetrics and Gynecology Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science Xiangyang Hubei China
| | - Jinting Zhou
- Department of Obstetrics and Gynecology Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science Xiangyang Hubei China
| | - Xiaogang Mao
- Department of Obstetrics and Gynecology Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science Xiangyang Hubei China
| | - Xianxian Li
- Department of Obstetrics and Gynecology Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science Xiangyang Hubei China
| | - Ying Xu
- Department of Obstetrics and Gynecology Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science Xiangyang Hubei China
| | - Yun Liu
- Department of Nephrology Huai'an Second People's Hospital and the Affiliated Huai'an Hospital of Xuzhou Medical University Huai'an China
| | - Hui Xing
- Department of Obstetrics and Gynecology Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science Xiangyang Hubei China
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20
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Katsel P, Roussos P, Fam P, Khan S, Tan W, Hirose T, Nakagawa S, Pletnikov MV, Haroutunian V. The expression of long noncoding RNA NEAT1 is reduced in schizophrenia and modulates oligodendrocytes transcription. NPJ SCHIZOPHRENIA 2019; 5:3. [PMID: 30696826 PMCID: PMC6386752 DOI: 10.1038/s41537-019-0071-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/08/2019] [Indexed: 01/22/2023]
Abstract
Oligodendrocyte (OLG)-related abnormalities have been broadly observed in schizophrenia (SZ); however, the etiology of these abnormalities remains unknown. As SZ is broadly believed to be a developmental disorder, the etiology of the myelin abnormalities in SZ may be related to OLG fate specification during development. Noncoding RNAs (ncRNAs) are an important part of multifaceted transcriptional complexes participating in neurogenic commitment and regulation of postmitotic cell function. The long ncRNA, NEAT1, is a structural component of paraspeckles (subnuclear bodies in interchromatin regions) that may control activity of developmental enhancers of OLG fate specification. Gene expression studies of multiple cortical regions from individuals with SZ showed strong downregulation of NEAT1 levels relative to controls. NEAT1-deficient mice show significant decreases in the numbers of OLG-lineage cells in the frontal cortex. To gain further insight into biological processes affected by NEAT1 deficiency, we analyzed RNA-seq data from frontal cortex of NEAT1-/- mice. Analyses of differentially expressed gene signature from NEAT1-/- mice revealed a significant impact on processes related to OLG differentiation and RNA posttranscriptional modification with the underlying mechanisms involving Wnt signaling, cell contact interactions, and regulation of cholesterol/lipid metabolism. Additional studies revealed evidence of co-expression of SOX10, an OLG transcription factor, and NEAT1, and showed enrichment of OLG-specific transcripts in NEAT1 purified chromatin isolates from human frontal cortex. Reduced nuclear retention of quaking isoform 5 in NEAT1-/- mice shed light on possible mechanism(s) responsible for reduced expression of OLG/myelin proteins and supported the involvement of NEAT1 in oligodendrocyte function.
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Affiliation(s)
- Pavel Katsel
- Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Panos Roussos
- Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology Friedman Brain Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mental Illness Research, Education and Clinical Center (MIRECC), James J Peters VA Medical Center, Bronx, NY, USA
| | - Peter Fam
- Mental Illness Research, Education and Clinical Center (MIRECC), James J Peters VA Medical Center, Bronx, NY, USA
| | - Sonia Khan
- Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Weilun Tan
- Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tetsuro Hirose
- Institute for Genetic Medicine, RNA Biology Laboratory, Hokkaido University, Sapporo, 060-0815, Japan
| | - Shinichi Nakagawa
- Institute for Genetic Medicine, RNA Biology Laboratory, Hokkaido University, Sapporo, 060-0815, Japan.,RIKEN, RNA Biology Laboratory, Wako, Saitama, Japan
| | - Mikhail V Pletnikov
- Departments of Psychiatry, Neuroscience, Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vahram Haroutunian
- Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mental Illness Research, Education and Clinical Center (MIRECC), James J Peters VA Medical Center, Bronx, NY, USA.,Department of Neuroscience, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
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21
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Vito D, Smales CM. The Long Non-Coding RNA Transcriptome Landscape in CHO Cells Under Batch and Fed-Batch Conditions. Biotechnol J 2018; 13:e1800122. [PMID: 29781203 DOI: 10.1002/biot.201800122] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/16/2018] [Indexed: 12/18/2022]
Abstract
The role of non-coding RNAs in determining growth, productivity, and recombinant product quality attributes in Chinese hamster ovary (CHO) cells has received much attention in recent years, exemplified by studies into microRNAs in particular. However, other classes of non-coding RNAs have received less attention. One such class are the non-coding RNAs known collectively as long non-coding RNAs (lncRNAs). The authors have undertaken the first landscape analysis of the lncRNA transcriptome in CHO using a mouse based microarray that also provided for the surveillance of the coding transcriptome. The authors report on those lncRNAs present in a model host CHO cell line under batch and fed-batch conditions on two different days and relate the expression of different lncRNAs to each other. The authors demonstrate that the mouse microarray is suitable for the detection and analysis of thousands of CHO lncRNAs and validated a number of these by qRT-PCR. The authors then further analyzed the data to identify those lncRNAs whose expression changed the most between growth and stationary phases of culture or between batch and fed-batch culture to identify potential lncRNA targets for further functional studies with regard to their role in controlling growth of CHO cells. The authors discuss the implications for the publication of this rich dataset and how this may be used by the community.
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Affiliation(s)
- Davide Vito
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, CT2 7NJ, Kent, UK
| | - Christopher Mark Smales
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, CT2 7NJ, Kent, UK
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22
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23
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Schaub A, Glasmacher E. Splicing in immune cells-mechanistic insights and emerging topics. Int Immunol 2018; 29:173-181. [PMID: 28498981 PMCID: PMC5890895 DOI: 10.1093/intimm/dxx026] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 04/27/2017] [Indexed: 11/26/2022] Open
Abstract
Differential splicing of mRNAs not only enables regulation of gene expression levels, but also ensures a high degree of gene-product diversity. The extent to which splicing of mRNAs is utilized as a mechanism in immune cells has become evident within the last few years. Still, only a few of these mechanisms have been well studied. In this review, we discuss some of the best-understood mechanisms, for instance the differential splicing of CD45 in T cells, as well as immunoglobulin genes in B cells. Beyond that we provide general mechanistic insights on how, when and where this process takes place and discuss the current knowledge regarding these topics in immune cells. We also highlight some of the reported links to immune-related diseases, genome-wide sequencing studies that revealed thousands of differentially spliced transcripts, as well as splicing studies on immune cells that remain mechanistically not fully understood. We thereby display potential emerging topics for future studies centered on splicing mechanisms in immune cells.
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Affiliation(s)
- Annalisa Schaub
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
| | - Elke Glasmacher
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
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24
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Hicks JA, Li L, Matsui M, Chu Y, Volkov O, Johnson KC, Corey DR. Human GW182 Paralogs Are the Central Organizers for RNA-Mediated Control of Transcription. Cell Rep 2018; 20:1543-1552. [PMID: 28813667 DOI: 10.1016/j.celrep.2017.07.058] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/10/2017] [Accepted: 07/20/2017] [Indexed: 01/21/2023] Open
Abstract
In the cytoplasm, small RNAs can control mammalian translation by regulating the stability of mRNA. In the nucleus, small RNAs can also control transcription and splicing. The mechanisms for RNA-mediated nuclear regulation are not understood and remain controversial, hindering the effective application of nuclear RNAi and investigation of its natural regulatory roles. Here, we reveal that the human GW182 paralogs TNRC6A/B/C are central organizing factors critical to RNA-mediated transcriptional activation. Mass spectrometry of purified nuclear lysates followed by experimental validation demonstrates that TNRC6A interacts with proteins involved in protein degradation, RNAi, the CCR4-NOT complex, the mediator complex, and histone-modifying complexes. Functional analysis implicates TNRC6A, NAT10, MED14, and WDR5 in RNA-mediated transcriptional activation. These findings describe protein complexes capable of bridging RNA-mediated sequence-specific recognition of noncoding RNA transcripts with the regulation of gene transcription.
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Affiliation(s)
- Jessica A Hicks
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Liande Li
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Masayuki Matsui
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Yongjun Chu
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Oleg Volkov
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Krystal C Johnson
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - David R Corey
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA.
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25
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The Hepatitis Delta Virus accumulation requires paraspeckle components and affects NEAT1 level and PSP1 localization. Sci Rep 2018; 8:6031. [PMID: 29662142 PMCID: PMC5902443 DOI: 10.1038/s41598-018-24500-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/03/2018] [Indexed: 12/12/2022] Open
Abstract
The Hepatitis Delta Virus (HDV) relies mainly on host proteins for its replication. We previously identified that PSF and p54nrb associate with the HDV RNA genome during viral replication. Together with PSP1, these proteins are part of paraspeckles, which are subnuclear bodies nucleated by the long non-coding RNA NEAT1. In this work, we established the requirement for PSF, p54nrb and PSP1 in HDV replication using RNAi-mediated knockdown in HEK-293 cells replicating the HDV RNA genome. We determined that HDV replication induces the delocalization of PSP1 to cytoplasmic foci containing PABP and increases NEAT1 level causing an enlargement of NEAT1 foci. Overall, our data support a role for the main paraspeckles proteins in HDV life cycle and indicate that HDV replication causes a cellular stress and induces both a delocalization of the PSP1 to the cytoplasm and a disruption of paraspeckles.
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26
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Chen Y, Qiu J, Chen B, Lin Y, Chen Y, Xie G, Qiu J, Tong H, Jiang D. RETRACTED: Long non-coding RNA NEAT1 plays an important role in sepsis-induced acute kidney injury by targeting miR-204 and modulating the NF-κB pathway. Int Immunopharmacol 2018; 59:252-260. [PMID: 29669307 DOI: 10.1016/j.intimp.2018.03.023] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 02/09/2018] [Accepted: 03/20/2018] [Indexed: 01/17/2023]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal).
This article has been retracted at the request of authors with the approval of the Editor-in-Chief.
Panel ‘LPS+sh-NEAT1’ from Figure 2C appears similar to panel ‘si-PVT1’ from Figure 2A of the article published by Wei Huang, Xiuwen Lan, Xueting Li, Dawei Wang, Yinghao Sun, Qian Wang, Hong Gao and Kaijiang Yu in the International Immunopharmacology 47 (2017) 134-140 http://dx.doi.org/10.1016/j.intimp.2017.03.030 and panel ‘Control’ from Figure 1D of the article published by Xiaodi Liu, Chengying Hong, Shipin Wu, Shiling Song, Zhi Yang, Lin Cao, Tongwei Song and Ying Yang in the Journal of Cellular Biochemistry 120 (2019) 11331-11341 https://doi.org/10.1002/jcb.28409.
Given the comments of Dr Elisabeth Bik https://scienceintegritydigest.com/2020/02/21/the-tadpole-paper-mill/ regarding this article, the journal requested the corresponding author to provide the raw data. However, the author was not able to fulfil this request.
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Affiliation(s)
- Yi Chen
- Department of Critical Care Medicine, The Fifth People's Hospital of Dongguan, Dongguan Hospital Affiliated to Medical College of Jinan University, Dongguan 523900, China
| | - Jialing Qiu
- Department of Critical Care Medicine, Medical College of Jinan University, Jinan, Guangzhou 510000, China
| | - Bin Chen
- Department of Critical Care Medicine, The Fifth People's Hospital of Dongguan, Dongguan Hospital Affiliated to Medical College of Jinan University, Dongguan 523900, China
| | - Youping Lin
- Department of Critical Care Medicine, The Fifth People's Hospital of Dongguan, Dongguan Hospital Affiliated to Medical College of Jinan University, Dongguan 523900, China
| | - Yulan Chen
- Department of Critical Care Medicine, The Fifth People's Hospital of Dongguan, Dongguan Hospital Affiliated to Medical College of Jinan University, Dongguan 523900, China
| | - Guojin Xie
- Department of Critical Care Medicine, The Fifth People's Hospital of Dongguan, Dongguan Hospital Affiliated to Medical College of Jinan University, Dongguan 523900, China
| | - Junming Qiu
- Department of ICU, General Hospital of Guangzhou Military Command, Key Laboratory of Tropical Zone Trauma Care and Tissue Repair of PLA, Guangzhou, Guangdong, China
| | - Huasheng Tong
- Department of ICU, General Hospital of Guangzhou Military Command, Key Laboratory of Tropical Zone Trauma Care and Tissue Repair of PLA, Guangzhou, Guangdong, China
| | - Dongxin Jiang
- Department of Critical Care Medicine, The Fifth People's Hospital of Dongguan, Dongguan Hospital Affiliated to Medical College of Jinan University, Dongguan 523900, China.
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27
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Lakhotia SC. From Heterochromatin to Long Noncoding RNAs in Drosophila: Expanding the Arena of Gene Function and Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:75-118. [PMID: 28815537 DOI: 10.1007/978-981-10-5203-3_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc. There has been a rapid increase in the number of identified lncRNAs, although a much larger number still remains unknown. The diversity of modes of actions and functions of the limited number of Drosophila lncRNAs, which have been examined, already reflects the profound roles of such RNAs in generating and sustaining the biological complexities of eukaryotes. Several of the known Drosophila lncRNAs originate as independent sense or antisense transcripts from promoter or intergenic, intronic, or 5'/3'-UTR regions, while many of them are independent genes that produce only lncRNAs or coding as well as noncoding RNAs. The different lncRNAs affect chromatin organization (local or large-scale pan-chromosomal), transcription, RNA processing/stability, or translation either directly through interaction with their target DNA sequences or indirectly by acting as intermediary molecules for specific regulatory proteins or may act as decoys/sinks, or storage sites for specific proteins or groups of proteins, or may provide a structural framework for the assembly of substructures in nucleus/cytoplasm. It is interesting that many of the "functions" alluded to heterochromatin in earlier cytogenetic studies appear to find correlates with the known subtle as well as far-reaching actions of the different small and long noncoding RNAs. Further studies exploiting the very rich and powerful genetic and molecular resources available for the Drosophila model are expected to unravel the mystery underlying the long reach of ncRNAs.
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Affiliation(s)
- Subhash C Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.
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28
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Mello SS, Attardi LD. Deciphering p53 signaling in tumor suppression. Curr Opin Cell Biol 2017; 51:65-72. [PMID: 29195118 DOI: 10.1016/j.ceb.2017.11.005] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/07/2017] [Accepted: 11/09/2017] [Indexed: 12/20/2022]
Abstract
The p53 transcription factor is mutated in over half of human cancers, and p53-null mice are highly predisposed to cancer, highlighting p53s essential role in tumor suppression. Studies in mouse models have revealed that p53 cell cycle arrest and apoptosis responses to acute DNA damage signals are dispensable for tumor suppression, prompting a search for new mechanisms underlying p53-mediated cancer suppression. p53 responds to other types of stress signals and regulates a host other cellular processes, including maintenance of genomic stability, metabolism, stemness, non-apoptotic cell death, migration/invasion, and cell signaling, any or all of which could be fundamental for suppressing carcinogenesis. The ability of p53 to govern numerous transcriptional programs and cellular functions likely explains its potent tumor suppressor activity.
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Affiliation(s)
- Stephano S Mello
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura D Attardi
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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29
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Elucidating the Role of Host Long Non-Coding RNA during Viral Infection: Challenges and Paths Forward. Vaccines (Basel) 2017; 5:vaccines5040037. [PMID: 29053596 PMCID: PMC5748604 DOI: 10.3390/vaccines5040037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/12/2017] [Accepted: 10/17/2017] [Indexed: 12/31/2022] Open
Abstract
Research over the past decade has clearly shown that long non-coding RNAs (lncRNAs) are functional. Many lncRNAs can be related to immunity and the host response to viral infection, but their specific functions remain largely elusive. The vast majority of lncRNAs are annotated with extremely limited knowledge and tend to be expressed at low levels, making ad hoc experimentation difficult. Changes to lncRNA expression during infection can be systematically profiled using deep sequencing; however, this often produces an intractable number of candidate lncRNAs, leaving no clear path forward. For these reasons, it is especially important to prioritize lncRNAs into high-confidence “hits” by utilizing multiple methodologies. Large scale perturbation studies may be used to screen lncRNAs involved in phenotypes of interest, such as resistance to viral infection. Single cell transcriptome sequencing quantifies cell-type specific lncRNAs that are less abundant in a mixture. When coupled with iterative experimental validations, new computational strategies for efficiently integrating orthogonal high-throughput data will likely be the driver for elucidating the functional role of lncRNAs during viral infection. This review highlights new high-throughput technologies and discusses the potential for integrative computational analysis to streamline the identification of infection-related lncRNAs and unveil novel targets for antiviral therapeutics.
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30
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Ebnet K. Junctional Adhesion Molecules (JAMs): Cell Adhesion Receptors With Pleiotropic Functions in Cell Physiology and Development. Physiol Rev 2017; 97:1529-1554. [PMID: 28931565 DOI: 10.1152/physrev.00004.2017] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/04/2017] [Accepted: 05/11/2017] [Indexed: 02/06/2023] Open
Abstract
Junctional adhesion molecules (JAM)-A, -B and -C are cell-cell adhesion molecules of the immunoglobulin superfamily which are expressed by a variety of tissues, both during development and in the adult organism. Through their extracellular domains, they interact with other adhesion receptors on opposing cells. Through their cytoplasmic domains, they interact with PDZ domain-containing scaffolding and signaling proteins. In combination, these two properties regulate the assembly of signaling complexes at specific sites of cell-cell adhesion. The multitude of molecular interactions has enabled JAMs to adopt distinct cellular functions such as the regulation of cell-cell contact formation, cell migration, or mitotic spindle orientation. Not surprisingly, JAMs regulate diverse processes such as epithelial and endothelial barrier formation, hemostasis, angiogenesis, hematopoiesis, germ cell development, and the development of the central and peripheral nervous system. This review summarizes the recent progress in the understanding of JAMs, including their characteristic structural features, their molecular interactions, their cellular functions, and their contribution to a multitude of processes during vertebrate development and homeostasis.
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Affiliation(s)
- Klaus Ebnet
- Institute-Associated Research Group "Cell Adhesion and Cell Polarity", Institute of Medical Biochemistry, ZMBE, Cells-In-Motion Cluster of Excellence (EXC1003-CiM), and Interdisciplinary Clinical Research Center (IZKF), University of Münster, Münster, Germany
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31
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Li W, Zhang Z, Liu X, Cheng X, Zhang Y, Han X, Zhang Y, Liu S, Yang J, Xu B, He L, Sun L, Liang J, Shang Y. The FOXN3-NEAT1-SIN3A repressor complex promotes progression of hormonally responsive breast cancer. J Clin Invest 2017; 127:3421-3440. [PMID: 28805661 DOI: 10.1172/jci94233] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/29/2017] [Indexed: 12/28/2022] Open
Abstract
The pathophysiological function of the forkhead transcription factor FOXN3 remains to be explored. Here we report that FOXN3 is a transcriptional repressor that is physically associated with the SIN3A repressor complex in estrogen receptor-positive (ER+) cells. RNA immunoprecipitation-coupled high-throughput sequencing identified that NEAT1, an estrogen-inducible long noncoding RNA, is required for FOXN3 interactions with the SIN3A complex. ChIP-Seq and deep sequencing of RNA genomic targets revealed that the FOXN3-NEAT1-SIN3A complex represses genes including GATA3 that are critically involved in epithelial-to-mesenchymal transition (EMT). We demonstrated that the FOXN3-NEAT1-SIN3A complex promotes EMT and invasion of breast cancer cells in vitro as well as dissemination and metastasis of breast cancer in vivo. Interestingly, the FOXN3-NEAT1-SIN3A complex transrepresses ER itself, forming a negative-feedback loop in transcription regulation. Elevation of both FOXN3 and NEAT1 expression during breast cancer progression corresponded to diminished GATA3 expression, and high levels of FOXN3 and NEAT1 strongly correlated with higher histological grades and poor prognosis. Our experiments uncovered that NEAT1 is a facultative component of the SIN3A complex, shedding light on the mechanistic actions of NEAT1 and the SIN3A complex. Further, our study identified the ERα-NEAT1-FOXN3/NEAT1/SIN3A-GATA3 axis that is implicated in breast cancer metastasis, providing a mechanistic insight into the pathophysiological function of FOXN3.
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Affiliation(s)
- Wanjin Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Zihan Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xinhua Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xiao Cheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yi Zhang
- Center for Genome Analysis, ABLife Inc., Wuhan, Hubei, China
| | - Xiao Han
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yu Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Shumeng Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jianguo Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Bosen Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Lin He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Luyang Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jing Liang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yongfeng Shang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
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Long noncoding RNAs: lincs between human health and disease. Biochem Soc Trans 2017; 45:805-812. [PMID: 28620042 DOI: 10.1042/bst20160376] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 03/31/2017] [Accepted: 04/06/2017] [Indexed: 12/21/2022]
Abstract
Long noncoding RNAs (lncRNAs) represent one of the largest classes of transcripts and are highly diverse in terms of characteristics and functions. Advances in high-throughput sequencing platforms have enabled the rapid discovery and identification of lncRNAs as key regulatory molecules involved in various cellular processes and their dysregulation in various human diseases. Here, we summarize the current knowledge of the functions and underlying mechanisms of lncRNA activity with a particular focus on cancer biology. We also discuss the potential of lncRNAs as diagnostic and therapeutic targets for clinical applications.
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Morchikh M, Cribier A, Raffel R, Amraoui S, Cau J, Severac D, Dubois E, Schwartz O, Bennasser Y, Benkirane M. HEXIM1 and NEAT1 Long Non-coding RNA Form a Multi-subunit Complex that Regulates DNA-Mediated Innate Immune Response. Mol Cell 2017; 67:387-399.e5. [PMID: 28712728 DOI: 10.1016/j.molcel.2017.06.020] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 05/15/2017] [Accepted: 06/16/2017] [Indexed: 12/23/2022]
Abstract
The DNA-mediated innate immune response underpins anti-microbial defenses and certain autoimmune diseases. Here we used immunoprecipitation, mass spectrometry, and RNA sequencing to identify a ribonuclear complex built around HEXIM1 and the long non-coding RNA NEAT1 that we dubbed the HEXIM1-DNA-PK-paraspeckle components-ribonucleoprotein complex (HDP-RNP). The HDP-RNP contains DNA-PK subunits (DNAPKc, Ku70, and Ku80) and paraspeckle proteins (SFPQ, NONO, PSPC1, RBM14, and MATRIN3). We show that binding of HEXIM1 to NEAT1 is required for its assembly. We further demonstrate that the HDP-RNP is required for the innate immune response to foreign DNA, through the cGAS-STING-IRF3 pathway. The HDP-RNP interacts with cGAS and its partner PQBP1, and their interaction is remodeled by foreign DNA. Remodeling leads to the release of paraspeckle proteins, recruitment of STING, and activation of DNAPKc and IRF3. Our study establishes the HDP-RNP as a key nuclear regulator of DNA-mediated activation of innate immune response through the cGAS-STING pathway.
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Affiliation(s)
- Mehdi Morchikh
- Institut de Génétique Humaine, Laboratoire de Virologie Moléculaire, Université de Montpellier, CNRS UMR9002, 34000 Montpellier, France.
| | - Alexandra Cribier
- Institut de Génétique Humaine, Laboratoire de Virologie Moléculaire, Université de Montpellier, CNRS UMR9002, 34000 Montpellier, France.
| | - Raoul Raffel
- Institut de Génétique Humaine, Laboratoire de Virologie Moléculaire, Université de Montpellier, CNRS UMR9002, 34000 Montpellier, France
| | - Sonia Amraoui
- Institut Pasteur, Virus and Immunity Unit, URA CNRS 3015, 75015 Paris, France
| | - Julien Cau
- MRI-Montpellier, Biocampus, Montpellier, 34095 France; IGH CNRS- Université de Montpellier, UMR9002, 34396 Montpellier, France
| | - Dany Severac
- MGX-Montpellier GenomiX, 34094 Montpellier, France
| | | | - Olivier Schwartz
- Institut Pasteur, Virus and Immunity Unit, URA CNRS 3015, 75015 Paris, France
| | - Yamina Bennasser
- Institut de Génétique Humaine, Laboratoire de Virologie Moléculaire, Université de Montpellier, CNRS UMR9002, 34000 Montpellier, France
| | - Monsef Benkirane
- Institut de Génétique Humaine, Laboratoire de Virologie Moléculaire, Université de Montpellier, CNRS UMR9002, 34000 Montpellier, France.
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Torres M, Becquet D, Blanchard MP, Guillen S, Boyer B, Moreno M, Franc JL, François-Bellan AM. Paraspeckles as rhythmic nuclear mRNA anchorages responsible for circadian gene expression. Nucleus 2017; 8:249-254. [PMID: 28060565 DOI: 10.1080/19491034.2016.1277304] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Circadian clocks regulate rhythmic gene expression levels by means of mRNA oscillations that are mainly driven by post-transcriptional regulation. We identified a new post-transcriptional mechanism, which involves nuclear bodies called paraspeckles. Major components of paraspeckles including the long noncoding RNA Neat1, which is the structural component, and its major protein partners, as well as the number of paraspeckles, follow a circadian pattern in pituitary cells. Paraspeckles are known to retain within the nucleus RNAs containing inverted repeats of Alu sequences. We showed that a reporter gene in which these RNA duplex elements were inserted in the 3'-UTR region displayed a circadian expression. Moreover, circadian endogenous mRNA associated with paraspeckles lost their circadian pattern when paraspeckles were disrupted. This work not only highlights a new paraspeckle-based post-transcriptional mechanism involved in circadian gene expression but also provides the list of all mRNA associated with paraspeckles in the nucleus of pituitary cells.
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Affiliation(s)
- Manon Torres
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Denis Becquet
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Marie-Pierre Blanchard
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Séverine Guillen
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Bénédicte Boyer
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Mathias Moreno
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Jean-Louis Franc
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
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Gerstner JR, Koberstein JN, Watson AJ, Zapero N, Risso D, Speed TP, Frank MG, Peixoto L. Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex. BMC Genomics 2016; 17:727. [PMID: 27801296 PMCID: PMC5088519 DOI: 10.1186/s12864-016-3065-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Why we sleep is still one of the most perplexing mysteries in biology. Strong evidence indicates that sleep is necessary for normal brain function and that sleep need is a tightly regulated process. Surprisingly, molecular mechanisms that determine sleep need are incompletely described. Moreover, very little is known about transcriptional changes that specifically accompany the accumulation and discharge of sleep need. Several studies have characterized differential gene expression changes following sleep deprivation. Much less is known, however, about changes in gene expression during the compensatory response to sleep deprivation (i.e. recovery sleep). RESULTS In this study we present a comprehensive analysis of the effects of sleep deprivation and subsequent recovery sleep on gene expression in the mouse cortex. We used a non-traditional analytical method for normalization of genome-wide gene expression data, Removal of Unwanted Variation (RUV). RUV improves detection of differential gene expression following sleep deprivation. We also show that RUV normalization is crucial to the discovery of differentially expressed genes associated with recovery sleep. Our analysis indicates that the majority of transcripts upregulated by sleep deprivation require 6 h of recovery sleep to return to baseline levels, while the majority of downregulated transcripts return to baseline levels within 1-3 h. We also find that transcripts that change rapidly during recovery (i.e. within 3 h) do so on average with a time constant that is similar to the time constant for the discharge of sleep need. CONCLUSIONS We demonstrate that proper data normalization is essential to identify changes in gene expression that are specifically linked to sleep deprivation and recovery sleep. Our results provide the first evidence that recovery sleep is comprised of two waves of transcriptional regulation that occur at different times and affect functionally distinct classes of genes.
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Affiliation(s)
- Jason R Gerstner
- Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA
| | - John N Koberstein
- Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA
| | - Adam J Watson
- Department of Neuroscience, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nikolai Zapero
- Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA
| | - Davide Risso
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Terence P Speed
- Department of Statistics, University of California, Berkeley, CA, USA.,Department of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Marcos G Frank
- Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA.
| | - Lucia Peixoto
- Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA.
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36
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Sun C, Li S, Zhang F, Xi Y, Wang L, Bi Y, Li D. Long non-coding RNA NEAT1 promotes non-small cell lung cancer progression through regulation of miR-377-3p-E2F3 pathway. Oncotarget 2016; 7:51784-51814. [PMID: 27351135 PMCID: PMC5239515 DOI: 10.18632/oncotarget.10108] [Citation(s) in RCA: 259] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/05/2016] [Indexed: 01/17/2023] Open
Abstract
Recently, the long non-coding RNA (lncRNA) NEAT1 has been identified as an oncogenic gene in multiple cancer types and elevated expression of NEAT1 was tightly linked to tumorigenesis and cancer progression. However, the molecular basis for this observation has not been characterized in progression of non-small cell lung cancer (NSCLC). In our studies, we identified NEAT1 was highly expressed in patients with NSCLC and was a novel regulator of NSCLC progression. Patients whose tumors had high NEAT1 expression had a shorter overall survival than patients whose tumors had low NEAT1 expression. Further, NEAT1 significantly accelerates NSCLC cell growth and metastasis in vitro and tumor growth in vivo. Additionally, by using bioinformatics study and RNA pull down combined with luciferase reporter assays, we demonstrated that NEAT1 functioned as a competing endogenous RNA (ceRNA) for hsa-miR-377-3p, antagonized its functions and led to the de-repression of its endogenous targets E2F3, which was a core oncogene in promoting NSCLC progression. Taken together, these observations imply that the NEAT1 modulated the expression of E2F3 gene by acting as a ceRNA, which may build up the missing link between the regulatory miRNA network and NSCLC progression.
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Affiliation(s)
- Chengcao Sun
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan, P. R. China
| | - Shujun Li
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan, P. R. China
- Wuhan Hospital for the Prevention and Treatment of Occupational Diseases, Wuhan, P. R. China
| | - Feng Zhang
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan, P. R. China
| | - Yongyong Xi
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan, P. R. China
| | - Liang Wang
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan, P. R. China
| | - Yongyi Bi
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan, P. R. China
| | - Dejia Li
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan, P. R. China
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Abstract
The number of long noncoding RNAs (lncRNAs) has grown rapidly; however, our understanding of their function remains limited. Although cultured cells have facilitated investigations of lncRNA function at the molecular level, the use of animal models provides a rich context in which to investigate the phenotypic impact of these molecules. Promising initial studies using animal models demonstrated that lncRNAs influence a diverse number of phenotypes, ranging from subtle dysmorphia to viability. Here, we highlight the diversity of animal models and their unique advantages, discuss the use of animal models to profile lncRNA expression, evaluate experimental strategies to manipulate lncRNA function in vivo, and review the phenotypes attributable to lncRNAs. Despite a limited number of studies leveraging animal models, lncRNAs are already recognized as a notable class of molecules with important implications for health and disease.
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38
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Torres M, Becquet D, Blanchard MP, Guillen S, Boyer B, Moreno M, Franc JL, François-Bellan AM. Circadian RNA expression elicited by 3'-UTR IRAlu-paraspeckle associated elements. eLife 2016; 5. [PMID: 27441387 PMCID: PMC4987140 DOI: 10.7554/elife.14837] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 07/20/2016] [Indexed: 12/31/2022] Open
Abstract
Paraspeckles are nuclear bodies form around the long non-coding RNA, Neat1, and RNA-binding proteins. While their role is not fully understood, they are believed to control gene expression at a post-transcriptional level by means of the nuclear retention of mRNA containing in their 3’-UTR inverted repeats of Alu sequences (IRAlu). In this study, we found that, in pituitary cells, all components of paraspeckles including four major proteins and Neat1 displayed a circadian expression pattern. Furthermore the insertion of IRAlu at the 3’-UTR of the EGFP cDNA led to a rhythmic circadian nuclear retention of the egfp mRNA that was lost when paraspeckles were disrupted whereas insertion of a single antisense Alu had only a weak effect. Using real-time video-microscopy, these IRAlu were further shown to drive a circadian expression of EGFP protein. This study shows that paraspeckles, thanks to their circadian expression, control circadian gene expression at a post-transcriptional level. DOI:http://dx.doi.org/10.7554/eLife.14837.001 Many biological features of animals, including body temperature and hormone levels, follow daily rhythms that repeat every 24 hours. These so-called circadian rhythms are driven by an internal body clock and are essential for the organism to adapt to the daily cycle of light and dark. Circadian rhythms also take place inside individual cells – for example, the amount of a given protein in a cell often rises and falls over each 24-hour period. To generate these daily fluctuations, the processes used to make proteins based on the instructions encoded within a gene must be carefully controlled. Genes are first copied or ‘transcribed' into intermediate molecules called messenger RNAs (mRNAs). These mRNA molecules must then travel out of the cell’s nucleus before they can be de-coded to produce proteins. This means that daily fluctuations in mRNA and protein levels could occur because the rate at which the DNA is transcribed fluctuates or because controlling the steps that occur after transcription. However it is not clear how much these post-transcriptional steps contribute to circadian rhythms inside cells. Recently, structures called paraspeckles were seen inside the nucleus. These structures are made from a long RNA molecule that does not code for a protein, and a number of proteins that can bind mRNA molecules. Paraspeckles are thought to prevent certain mRNAs from leaving the nucleus and therefore stop them from being decoded to make proteins. Torres et al. have now investigated whether paraspeckles may play a role in circadian rhythms. Torres et al. looked at the long non-coding RNA and several proteins that are known to be components of paraspeckles in cells taken from the pituitary glands of rats using a variety of techniques. These cells were chosen because they were known to have a working circadian clock. The analysis showed that the levels of these components, as well as the number of paraspeckles within the nucleus, changed over the course of a daily cycle. Torres et al. then confirmed that mRNAs containing a sequence that is known to recruit mRNAs to paraspeckes (the IRAlu sequence) could be also retained in the nucleus or released with a circadian rhythm. This pattern was lost when the paraspeckles were disrupted. These findings suggest that daily fluctuations in protein levels can be post-transcriptionally controlled by paraspeckles rhythmically retaining mRNAs in the nucleus. Future studies could explore whether it may be possible to control circadian rhythms by targeting the paraspeckles, which could help to improve conditions where the internal body clock goes wrong. DOI:http://dx.doi.org/10.7554/eLife.14837.002
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Affiliation(s)
- Manon Torres
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Denis Becquet
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Marie-Pierre Blanchard
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Séverine Guillen
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Bénédicte Boyer
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Mathias Moreno
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Jean-Louis Franc
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
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Knott GJ, Bond CS, Fox AH. The DBHS proteins SFPQ, NONO and PSPC1: a multipurpose molecular scaffold. Nucleic Acids Res 2016; 44:3989-4004. [PMID: 27084935 PMCID: PMC4872119 DOI: 10.1093/nar/gkw271] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/05/2016] [Indexed: 12/23/2022] Open
Abstract
Nuclear proteins are often given a concise title that captures their function, such as 'transcription factor,' 'polymerase' or 'nuclear-receptor.' However, for members of the Drosophila behavior/human splicing (DBHS) protein family, no such clean-cut title exists. DBHS proteins are frequently identified engaging in almost every step of gene regulation, including but not limited to, transcriptional regulation, RNA processing and transport, and DNA repair. Herein, we present a coherent picture of DBHS proteins, integrating recent structural insights on dimerization, nucleic acid binding modalities and oligomerization propensity with biological function. The emerging paradigm describes a family of dynamic proteins mediating a wide range of protein-protein and protein-nucleic acid interactions, on the whole acting as a multipurpose molecular scaffold. Overall, significant steps toward appreciating the role of DBHS proteins have been made, but we are only beginning to understand the complexity and broader importance of this family in cellular biology.
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Affiliation(s)
- Gavin J Knott
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia
| | - Archa H Fox
- School of Anatomy, Physiology and Human Biology, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
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40
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Jin C, Peng X, Xie T, Lu X, Liu F, Wu H, Yang Z, Wang J, Cheng L, Wu N. Detection of the long noncoding RNAs nuclear-enriched autosomal transcript 1 (NEAT1) and metastasis associated lung adenocarcinoma transcript 1 in the peripheral blood of HIV-1-infected patients. HIV Med 2016; 17:68-72. [PMID: 26139386 DOI: 10.1111/hiv.12276] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2015] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Long noncoding RNAs (lncRNAs) in HIV-1 infection have not been extensively studied. Here we detected two lncRNAs, nuclear-enriched autosomal transcript 1 (NEAT1) and metastasis associated lung adenocarcinoma transcript 1 (MALAT1), in peripheral blood mononuclear cells (PBMCs) and plasma of HIV-1-infected patients. METHODS Fifty-nine HIV-1-infected patients and 21 healthy controls were recruited for the study, of whom 31 patients were highly active antiretroviral therapy (HAART)-naïve and 28 patients had been receiving HAART for more than 1 year with undetectable viral loads. Total RNA was extracted from PBMCs and plasma, and levels of NEAT1 and MALAT1 were determined by quantitative real-time polymerase chain reaction. RESULTS We found that the levels of NEAT1 and MALAT1 in PBMCs were up-regulated in HAART-naïve patients and were reduced in patients receiving HAART. NEAT1 was down-regulated in the plasma of infected patients and expression was correlated with CD4 T-cell count. CONCLUSIONS Our findings suggest that NEAT1 and MALAT1 may interact with HIV-1 in vivo and that the presence of NEAT1 in plasma is a potential biomarker of HIV-1 infection.
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Affiliation(s)
- C Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - X Peng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - T Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - X Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - F Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - H Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Z Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - J Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - L Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - N Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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Dobson L, Nyitray L, Gáspári Z. A conserved charged single α-helix with a putative steric role in paraspeckle formation. RNA (NEW YORK, N.Y.) 2015; 21:2023-2029. [PMID: 26428695 PMCID: PMC4647456 DOI: 10.1261/rna.053058.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/27/2015] [Indexed: 06/05/2023]
Abstract
Paraspeckles are subnuclear particles involved in the regulation of mRNA expression. They are formed by the association of DBHS family proteins and the NEAT1 long noncoding RNA. Here, we show that a recently identified structural motif, the charged single α-helix, is largely conserved in the DBHS family. Based on the available structural data and a previously suggested multimerization scheme of DBHS proteins, we built a structural model of a (PSPC1/NONO)(n) multimer that might have relevance in paraspeckle formation. Our model contains an extended coiled-coil region that is followed by and partially overlaps with the predicted charged single α-helix. We suggest that the charged single α-helix can act as an elastic ruler governing the exact positioning of the dimeric core structures relative to each other during paraspeckle assembly along the NEAT1 noncoding RNA.
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Affiliation(s)
- László Dobson
- Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, H-1083 Budapest, Hungary
| | - László Nyitray
- Eötvös Loránd University, Department of Biochemistry, H-1117 Budapest, Hungary
| | - Zoltán Gáspári
- Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, H-1083 Budapest, Hungary
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Mircsof D, Langouët M, Rio M, Moutton S, Siquier-Pernet K, Bole-Feysot C, Cagnard N, Nitschke P, Gaspar L, Žnidarič M, Alibeu O, Fritz AK, Wolfer DP, Schröter A, Bosshard G, Rudin M, Koester C, Crestani F, Seebeck P, Boddaert N, Prescott K, Hines R, Moss SJ, Fritschy JM, Munnich A, Amiel J, Brown SA, Tyagarajan SK, Colleaux L. Mutations in NONO lead to syndromic intellectual disability and inhibitory synaptic defects. Nat Neurosci 2015; 18:1731-6. [PMID: 26571461 PMCID: PMC5392243 DOI: 10.1038/nn.4169] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/15/2015] [Indexed: 12/14/2022]
Abstract
The NONO protein has been characterized as an important transcriptional regulator in diverse cellular contexts. Here we show that loss of NONO function is a likely cause of human intellectual disability and that NONO-deficient mice have cognitive and affective deficits. Correspondingly, we find specific defects at inhibitory synapses, where NONO regulates synaptic transcription and gephyrin scaffold structure. Our data identify NONO as a possible neurodevelopmental disease gene and highlight the key role of the DBHS protein family in functional organization of GABAergic synapses.
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Affiliation(s)
- Dennis Mircsof
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland.,Neuromorphology Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - Maéva Langouët
- INSERM UMR 1163, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, Paris, France
| | - Marlène Rio
- INSERM UMR 1163, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, Paris, France.,Service de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Sébastien Moutton
- INSERM UMR 1163, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, Paris, France
| | - Karine Siquier-Pernet
- INSERM UMR 1163, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, Paris, France
| | - Christine Bole-Feysot
- Genomic Platform, INSERM UMR 1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, Paris, France
| | - Nicolas Cagnard
- Bioinformatic Platform, INSERM UMR 1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, Paris, France
| | - Patrick Nitschke
- Bioinformatic Platform, INSERM UMR 1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, Paris, France
| | - Ludmila Gaspar
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - Matej Žnidarič
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - Olivier Alibeu
- Genomic Platform, INSERM UMR 1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, Paris, France
| | - Ann-Kristina Fritz
- Institute of Anatomy, University of Zürich and Institute of Human Movement Sciences and Sport, ETH Zürich, Switzerland
| | - David P Wolfer
- Institute of Anatomy, University of Zürich and Institute of Human Movement Sciences and Sport, ETH Zürich, Switzerland
| | - Aileen Schröter
- Molecular Imaging and Functional Pharmacology Group, University of Zürich, Zürich, Switzerland
| | - Giovanna Bosshard
- Neuromorphology Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - Markus Rudin
- Molecular Imaging and Functional Pharmacology Group, University of Zürich, Zürich, Switzerland
| | - Christina Koester
- Neuromorphology Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - Florence Crestani
- Neuromorphology Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - Petra Seebeck
- Center for Integrative Rodent Physiology, University of Zürich, Zürich, Switzerland
| | - Nathalie Boddaert
- INSERM UMR 1163, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, Paris, France.,Service de radiologie pédiatrique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Katrina Prescott
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals National Health Service Trust, Department of Clinical Genetics, Chapel Allerton Hospital, Chapeltown Road, Leeds, UK
| | | | - Rochelle Hines
- Tufts University, Sackler School of Graduate Biomedical Sciences, Boston, Massachusetts, USA
| | - Steven J Moss
- Tufts University, Sackler School of Graduate Biomedical Sciences, Boston, Massachusetts, USA
| | - Jean-Marc Fritschy
- Neuromorphology Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - Arnold Munnich
- INSERM UMR 1163, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, Paris, France
| | - Jeanne Amiel
- INSERM UMR 1163, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, Paris, France.,Service de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Steven A Brown
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - Shiva K Tyagarajan
- Neuromorphology Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - Laurence Colleaux
- INSERM UMR 1163, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital, Paris, France
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Mito M, Kawaguchi T, Hirose T, Nakagawa S. Simultaneous multicolor detection of RNA and proteins using super-resolution microscopy. Methods 2015; 98:158-165. [PMID: 26564236 DOI: 10.1016/j.ymeth.2015.11.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 11/04/2015] [Accepted: 11/07/2015] [Indexed: 11/19/2022] Open
Abstract
A number of non-membranous cellular bodies have been identified in higher eukaryotes, and these bodies contain a specific set of proteins and RNAs that are used to fulfill their functions. The size of these RNA-containing cellular bodies is usually on a submicron scale, making it difficult to observe fine structures using optical microscopy due to the diffraction limitation of visible light. Recently, microscope companies have released super-resolution microscopes that were developed using different principles, enabling the observation of sub-micron structures not resolvable in conventional fluorescent microscopy. Here, we describe multi-color fluorescent in situ hybridization techniques optimized for the simultaneous detection of RNA and proteins using super-resolution microscopy, namely structured illumination microscopy (SIM).
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Affiliation(s)
- Mari Mito
- RNA Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tetsuya Kawaguchi
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
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Wu Y, Yang L, Zhao J, Li C, Nie J, Liu F, Zhuo C, Zheng Y, Li B, Wang Z, Xu Y. Nuclear-enriched abundant transcript 1 as a diagnostic and prognostic biomarker in colorectal cancer. Mol Cancer 2015; 14:191. [PMID: 26552600 PMCID: PMC4640217 DOI: 10.1186/s12943-015-0455-5] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 10/13/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND High expression of the long non-coding RNA nuclear-enriched abundant transcript 1 (NEAT1) in whole blood has been reported in colorectal cancer patients; however, its' clinical significance and origin are unclear. We evaluated the diagnostic and prognostic value, and origin of whole blood NEAT1 in colorectal cancer. METHODS Expression of NEAT1 variants, NEAT1_v1 and NEAT1_v2 were determined using real-time quantitative PCR. The diagnostic value of whole blood NEAT1 expression was evaluated in test (n = 60) and validation (n = 200) cohorts of colorectal cancer patients and normal controls (NCs). To identify the origin of NEAT1, its expression was analyzed in blood, matched primary tumor tissues, para-tumor tissues, metastatic tissues, and also immune cells from patients or NCs. Function of NEAT1 in colorectal cell lines was also assessed. The correlation of NEAT1 expression with clinical outcomes was assessed in 191 patients. RESULTS Whole blood NEAT1 expression was significantly higher in colorectal cancer patients than in NCs. NEAT1_v1 and NEAT1_v2 expression were highly accurate in distinguishing colorectal cancer patients from NCs (area under the curve: 0.787 and 0.871, respectively). Knockdown of NEAT1_v1 in vitro could inhibit cell invasion and proliferation, while knockdown of NEAT1_v2 promoted cell growth. However, whole blood expression was not correlated with matched tissues. An elevated expression was seen in neutrophils from CRC patients. Furthermore, high expression of NEAT1_v1 was correlated with worse overall survival. In contrast, high expression of NEAT1_v2 alone was correlated with better overall survival. CONCLUSION Whole blood NEAT1 expression is a novel diagnostic and prognostic biomarker of overall survival in colorectal cancer. Elevated NEAT1 may derive from neutrophils.
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Affiliation(s)
- Yuchen Wu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, No. 270 Dong-an Road, Shanghai, 20032, People's Republic of China.
| | - Li Yang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, No. 270 Dong-an Road, Shanghai, 20032, People's Republic of China.
| | - Jiang Zhao
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, No. 270 Dong-an Road, Shanghai, 20032, People's Republic of China.
| | - Cong Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, No. 270 Dong-an Road, Shanghai, 20032, People's Republic of China.
| | - Jia Nie
- Key Laboratory of Molecular Virology & Immunology, Unit of Molecular Immunology, Institut Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, No. 320 Yue-yang Road, Shanghai, 20031, People's Republic of China.
| | - Fangqi Liu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, No. 270 Dong-an Road, Shanghai, 20032, People's Republic of China.
| | - Changhua Zhuo
- Department of Surgical Oncology, Fujian Provincial Cancer Hospital, Teaching Hospital of Fujian Medical University, No. 420 Fu-ma Road, Fuzhou, 350014, People's Republic of China.
| | - Yaxin Zheng
- Eastern Hepatobiliary Hospital, Second Military Medical University, No. 225 Chang-hai Road, Shanghai, 200438, People's Republic of China.
| | - Bin Li
- Key Laboratory of Molecular Virology & Immunology, Unit of Molecular Immunology, Institut Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, No. 320 Yue-yang Road, Shanghai, 20031, People's Republic of China.
| | - Zhimin Wang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute (SITI), No. 250 Bi-bo Road, Shanghai, 201203, People's Republic of China.
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, No. 270 Dong-an Road, Shanghai, 20032, People's Republic of China.
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Towards structural classification of long non-coding RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:41-5. [PMID: 26537437 DOI: 10.1016/j.bbagrm.2015.09.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/10/2015] [Accepted: 09/28/2015] [Indexed: 01/16/2023]
Abstract
While long non-coding RNAs play key roles in disease and development, few structural studies have been performed to date for this emerging class of RNAs. Previous structural studies are reviewed, and a pipeline is presented to determine secondary structures of long non-coding RNAs. Similar to riboswitches, experimentally determined secondary structures of long non-coding RNAs for one species, may be used to improve sequence/structure alignments for other species. As riboswitches have been classified according to their secondary structure, a similar scheme could be used to classify long non-coding RNAs. This article is part of a Special Issue titled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Yoshimoto R, Mayeda A, Yoshida M, Nakagawa S. MALAT1 long non-coding RNA in cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:192-9. [PMID: 26434412 DOI: 10.1016/j.bbagrm.2015.09.012] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/24/2015] [Accepted: 09/28/2015] [Indexed: 02/09/2023]
Abstract
A recent massive parallel sequencing analysis has shown the fact that more than 80% of the human genome is transcribed into RNA. Among many kinds of the non-protein coding RNAs, we focus on the metastasis associated lung adenocarcinoma transcript 1 (MALAT1) that is a long non-coding RNA upregulated in metastatic carcinoma cells. Two molecular functions of MALAT1 have been proposed, one is the control of alternative splicing and the other is the transcriptional regulation. In this review, we document the molecular characteristics and functions of MALAT1 and shed light on the implication in the molecular pathology of various cancers. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Rei Yoshimoto
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan; Chemical Genetics Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Minoru Yoshida
- Chemical Genetics Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan
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Abstract
Messenger ribonucleoprotein (mRNP) granules are dynamic, self-assembling structures that harbor non-translating mRNAs bound by various proteins that regulate mRNA translation, localization, and turnover. Their importance in gene expression regulation is far reaching, ranging from precise spatial-temporal control of mRNAs that drive developmental programs in oocytes and embryos, to similarly exquisite control of mRNAs in neurons that underpin synaptic plasticity, and thus, memory formation. Analysis of mRNP granules in their various contexts has revealed common themes of assembly, disassembly, and modes of mRNA regulation, yet new studies continue to reveal unexpected and important findings, such as links between aberrant mRNP granule assembly and neurodegenerative disease. Continued study of these enigmatic structures thus promises fascinating new insights into cellular function, and may also suggest novel therapeutic strategies in various disease states.
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Affiliation(s)
- J Ross Buchan
- a Department of Molecular and Cellular Biology ; University of Arizona ; Tucson , AZ USA
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Nakagawa S. Lessons from reverse-genetic studies of lncRNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:177-83. [PMID: 26117798 DOI: 10.1016/j.bbagrm.2015.06.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/16/2015] [Accepted: 06/18/2015] [Indexed: 11/18/2022]
Abstract
The functions of long noncoding RNAs (lncRNAs) have mainly been studied using cultured cell lines, and this approach has revealed the involvement of lncRNAs in a variety of biological processes, including the epigenetic control of gene expression, post-transcriptional regulation of mRNA, and cellular proliferation and differentiation. Recently, increasing numbers of studies have investigated the functions of lncRNAs using gene-targeted model mice, largely confirming the physiological importance of lncRNA-mediated regulation in individual animals. In some cases, however, the results obtained by studies using knockout mice have been somewhat inconsistent with those of the preceding cell-based analyses. In this review, I will summarize the lessons that we are learning from the reverse-genetic studies of lncRNAs, namely the importance of noncoding DNA elements, the weak correlation between expression level and phenotypic prominence, the existence of tissue- and condition-specific phenotypes and incomplete penetrance, and the function of lncRNAs as precursor molecules. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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Chaoui A, Kavo A, Baral V, Watanabe Y, Lecerf L, Colley A, Mendoza-Londono R, Pingault V, Bondurand N. Subnuclear re-localization of SOX10 and p54NRB correlates with a unique neurological phenotype associated with SOX10 missense mutations. Hum Mol Genet 2015; 24:4933-47. [PMID: 26060192 DOI: 10.1093/hmg/ddv215] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 06/04/2015] [Indexed: 11/12/2022] Open
Abstract
SOX10 is a transcription factor with well-known functions in neural crest and oligodendrocyte development. Mutations in SOX10 were first associated with Waardenburg-Hirschsprung disease (WS4; deafness, pigmentation defects and intestinal aganglionosis). However, variable phenotypes that extend beyond the WS4 definition are now reported. The neurological phenotypes associated with some truncating mutations are suggested to be the result of escape from the nonsense-mediated mRNA decay pathway; but, to date, no mechanism has been suggested for missense mutations, of which approximately 20 have now been reported, with about half of the latter shown to be redistributed to nuclear bodies of undetermined nature and function in vitro. Here, we report that p54NRB, which plays a crucial role in the regulation of gene expression during many cellular processes including differentiation, interacts synergistically with SOX10 to regulate several target genes. Interestingly, this paraspeckle protein, as well as two other members of the Drosophila behavior human splicing (DBHS) protein family, co-localize with SOX10 mutants in nuclear bodies, suggesting the possible paraspeckle nature of these foci or re-localization of the DBHS members to other subnuclear compartments. Remarkably, the co-transfection of wild-type and mutant SOX10 constructs led to the sequestration of wild-type protein in mutant-induced foci. In contrast to mutants presenting with additional cytoplasmic re-localization, those exclusively found in the nucleus alter synergistic activity between SOX10 and p54NRB. We propose that such a dominant negative effect may contribute to or be at the origin of the unique progressive and severe neurological phenotype observed in affected patients.
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Affiliation(s)
- Asma Chaoui
- INSERM, U955, Equipe 6, 51 Avenue du Maréchal de Lattre de Tassigny, F-94000 Créteil, France, Université Paris-Est, UPEC, F-94000 Créteil, France, DHU Ageing-Thorax-Vessel-Blood, F-94000 Créteil, France
| | - Anthula Kavo
- INSERM, U955, Equipe 6, 51 Avenue du Maréchal de Lattre de Tassigny, F-94000 Créteil, France, Université Paris-Est, UPEC, F-94000 Créteil, France, DHU Ageing-Thorax-Vessel-Blood, F-94000 Créteil, France
| | - Viviane Baral
- INSERM, U955, Equipe 6, 51 Avenue du Maréchal de Lattre de Tassigny, F-94000 Créteil, France, Université Paris-Est, UPEC, F-94000 Créteil, France, DHU Ageing-Thorax-Vessel-Blood, F-94000 Créteil, France
| | - Yuli Watanabe
- INSERM, U955, Equipe 6, 51 Avenue du Maréchal de Lattre de Tassigny, F-94000 Créteil, France, Université Paris-Est, UPEC, F-94000 Créteil, France, DHU Ageing-Thorax-Vessel-Blood, F-94000 Créteil, France
| | - Laure Lecerf
- INSERM, U955, Equipe 6, 51 Avenue du Maréchal de Lattre de Tassigny, F-94000 Créteil, France, Université Paris-Est, UPEC, F-94000 Créteil, France, DHU Ageing-Thorax-Vessel-Blood, F-94000 Créteil, France
| | - Alison Colley
- Department of Clinical Genetics, Liverpool Hospital, Australia and
| | - Roberto Mendoza-Londono
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Veronique Pingault
- INSERM, U955, Equipe 6, 51 Avenue du Maréchal de Lattre de Tassigny, F-94000 Créteil, France, Université Paris-Est, UPEC, F-94000 Créteil, France, DHU Ageing-Thorax-Vessel-Blood, F-94000 Créteil, France
| | - Nadege Bondurand
- INSERM, U955, Equipe 6, 51 Avenue du Maréchal de Lattre de Tassigny, F-94000 Créteil, France, Université Paris-Est, UPEC, F-94000 Créteil, France, DHU Ageing-Thorax-Vessel-Blood, F-94000 Créteil, France,
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New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription. J Virol 2015; 89:7120-32. [PMID: 25926645 DOI: 10.1128/jvi.00608-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/22/2015] [Indexed: 01/25/2023] Open
Abstract
UNLABELLED We have previously shown that the Epstein-Barr virus (EBV) likely encodes hundreds of viral long noncoding RNAs (vlncRNAs) that are expressed during reactivation. Here we show that the EBV latency origin of replication (oriP) is transcribed bi-directionally during reactivation and that both leftward (oriPtLs) and rightward (oriPtRs) transcripts are largely localized in the nucleus. While the oriPtLs are most likely noncoding, at least some of the oriPtRs contain the BCRF1/vIL10 open reading frame. Nonetheless, oriPtR transcripts with long 5' untranslated regions may partially serve noncoding functions. Both oriPtL and oriPtR transcripts are expressed with late kinetics, and their expression is inhibited by phosphonoacetic acid. RNA sequencing (RNA-seq) analysis showed that oriPtLs and oriPtRs exhibited extensive "hyperediting" at their Family of Repeat (FR) regions. RNA secondary structure prediction revealed that the FR region of both oriPtLs and oriPtRs may form large evolutionarily conserved and thermodynamically stable hairpins. The double-stranded RNA-binding protein and RNA-editing enzyme ADAR was found to bind to oriPtLs, likely facilitating editing of the FR hairpin. Further, the multifunctional paraspeckle protein, NONO, was found to bind to oriPt transcripts, suggesting that oriPts interact with the paraspeckle-based innate antiviral immune pathway. Knockdown and ectopic expression of oriPtLs showed that it contributes to global viral lytic gene expression and viral DNA replication. Together, these results show that these new vlncRNAs interact with cellular innate immune pathways and that they help facilitate progression of the viral lytic cascade. IMPORTANCE Recent studies have revealed that the complexity of lytic herpesviral transcriptomes is significantly greater than previously appreciated with hundreds of viral long noncoding RNAs (vlncRNAs) being recently discovered. Work on cellular lncRNAs over the past several years has just begun to give us an initial appreciation for the array of functions they play in complex formation and regulatory processes in the cell. The newly identified herpesvirus lncRNAs are similarly likely to play a variety of different functions, although these functions are likely tailored to specific needs of the viral infection cycles. Here we describe novel transcripts derived from the EBV latency origin of replication. We show that they are hyperedited, that they interact with a relatively newly appreciated antiviral pathway, and that they play a role in facilitating viral lytic gene expression. These investigations are a starting point to unraveling the complex arena of vlncRNA function in herpesvirus lytic replication.
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