1
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Ye X, Yang Y, Yao J, Wang M, Liu Y, Xie G, Zeng Z, Zhang XK, Zhou H. Nuclear receptor RXRα binds the precursor of miR-103 to inhibit its maturation. BMC Biol 2023; 21:197. [PMID: 37735649 PMCID: PMC10512521 DOI: 10.1186/s12915-023-01701-3] [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: 09/18/2022] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND The maturation of microRNAs (miRNAs) successively undergoes Drosha, Dicer, and Argonaute -mediated processing, however, the intricate regulations of the individual miRNA maturation are largely unknown. Retinoid x receptor alpha (RXRα) belongs to nuclear receptors that regulate gene transcription by binding to DNA elements, however, whether RXRα binds to miRNAs to exert physiological functions is not known. RESULTS In this work, we found that RXRα directly binds to the precursor of miR-103 (pre-miR-103a-2) via its DNA-binding domain with a preferred binding sequence of AGGUCA. The binding of RXRα inhibits the processing of miR-103 maturation from pre-miR-103a-2. Mechanistically, RXRα prevents the nuclear export of pre-miR-103a-2 for further processing by inhibiting the association of exportin-5 with pre-miR-103a-2. Pathophysiologically, the negative effect of RXRα on miR-103 maturation correlates to the positive effects of RXRα on the expression of Dicer, a target of miR-103, and on the inhibition of breast cancer. CONCLUSIONS Our findings unravel an unexpected role of transcription factor RXRα in specific miRNA maturation at post-transcriptional level through pre-miRNA binding, and present a mechanistic insight regarding RXRα role in breast cancer progression.
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Affiliation(s)
- Xiaohong Ye
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, 361102, Fujian, China
- High Throughput Drug Screening Platform, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yun Yang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, 361102, Fujian, China
| | - Jiayue Yao
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, 361102, Fujian, China
| | - Mo Wang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yixin Liu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, 361102, Fujian, China
| | - Guobin Xie
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, 361102, Fujian, China
| | - Zhiping Zeng
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, 361102, Fujian, China
- High Throughput Drug Screening Platform, Xiamen University, Xiamen, 361102, Fujian, China
| | - Xiao-Kun Zhang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, 361102, Fujian, China
- High Throughput Drug Screening Platform, Xiamen University, Xiamen, 361102, Fujian, China
| | - Hu Zhou
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, 361102, Fujian, China.
- High Throughput Drug Screening Platform, Xiamen University, Xiamen, 361102, Fujian, China.
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2
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Aerobic exercise improves adipogenesis in diet-induced obese mice via the LncSRA/p38/JNK/PPARγ pathway. Nutr Res 2022; 105:20-32. [DOI: 10.1016/j.nutres.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 11/20/2022]
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3
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Yin L, Zhu X, Novák P, Zhou L, Gao L, Yang M, Zhao G, Yin K. The epitranscriptome of long noncoding RNAs in metabolic diseases. Clin Chim Acta 2021; 515:80-89. [PMID: 33422492 DOI: 10.1016/j.cca.2021.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) have abundant content and extensive functions that regulate the expression of genes at multiple levels. Recently, transcriptome-wide analysis confirmed that RNA can undergo various chemical modifications in response to stimulation by the environment that further determine the action mechanisms of RNAs and expand the diversity of the transcriptome. Modifications that occur in lncRNAs can affect their expression and the regulation of downstream molecules by changing the secondary structure, splicing, degradation or molecular stability of lncRNAs. During the development of metabolic diseases, reversible RNA modifications show a complex transcriptional landscape. Although a wide quantity and variety of lncRNA modifications have been identified, the knowledge regarding their underlying actions in alcohol use disorders (AUDs), osteoporosis, obesity, and cardiovascular disease (CVD) is still in its infancy. Herein, we will focus on the epitranscriptomic modifications that occur on lncRNAs and the crosstalk between them that affect metabolic diseases.
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Affiliation(s)
- Linjie Yin
- Research Lab for Clinical & Translational Medicine, Medical School, University of South China, Hengyang 421001, China; The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Xiao Zhu
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Petr Novák
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Le Zhou
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Ling Gao
- Research Lab for Clinical & Translational Medicine, Medical School, University of South China, Hengyang 421001, China
| | - Min Yang
- Research Lab for Clinical & Translational Medicine, Medical School, University of South China, Hengyang 421001, China; The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - GuoJun Zhao
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan City People's Hospital, Qingyuan 511518, China.
| | - Kai Yin
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China.
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4
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Clocchiatti A, Ghosh S, Procopio MG, Mazzeo L, Bordignon P, Ostano P, Goruppi S, Bottoni G, Katarkar A, Levesque M, Kölblinger P, Dummer R, Neel V, Özdemir BC, Dotto GP. Androgen receptor functions as transcriptional repressor of cancer-associated fibroblast activation. J Clin Invest 2018; 128:5531-5548. [PMID: 30395538 DOI: 10.1172/jci99159] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 09/26/2018] [Indexed: 01/16/2023] Open
Abstract
The aging-associated increase of cancer risk is linked with stromal fibroblast senescence and concomitant cancer-associated fibroblast (CAF) activation. Surprisingly little is known about the role of androgen receptor (AR) signaling in this context. We have found downmodulated AR expression in dermal fibroblasts underlying premalignant skin cancer lesions (actinic keratoses and dysplastic nevi) as well as in CAFs from the 3 major skin cancer types, squamous cell carcinomas (SCCs), basal cell carcinomas, and melanomas. Functionally, decreased AR expression in primary human dermal fibroblasts (HDFs) from multiple individuals induced early steps of CAF activation, and in an orthotopic skin cancer model, AR loss in HDFs enhanced tumorigenicity of SCC and melanoma cells. Forming a complex, AR converged with CSL/RBP-Jκ in transcriptional repression of key CAF effector genes. AR and CSL were positive determinants of each other's expression, with BET inhibitors, which counteract the effects of decreased CSL, restoring AR expression and activity in CAFs. Increased AR expression in these cells overcame the consequences of CSL loss and was by itself sufficient to block the growth and tumor-enhancing effects of CAFs on neighboring cancer cells. As such, the findings establish AR as a target for stroma-focused cancer chemoprevention and treatment.
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Affiliation(s)
- Andrea Clocchiatti
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Dermatology, Harvard Medical School, Boston, Massachusetts, USA
| | - Soumitra Ghosh
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | | | - Luigi Mazzeo
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Pino Bordignon
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Paola Ostano
- Cancer Genomics Laboratory, Edo and Elvo Tempia Valenta Foundation, Biella, Italy
| | - Sandro Goruppi
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Dermatology, Harvard Medical School, Boston, Massachusetts, USA
| | - Giulia Bottoni
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Atul Katarkar
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Mitchell Levesque
- Department of Dermatology, University Hospital Zürich, Zürich, Switzerland
| | - Peter Kölblinger
- Department of Dermatology, University Hospital Zürich, Zürich, Switzerland.,Department of Dermatology, Paracelsus Medical University, Salzburg, Austria
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zürich, Zürich, Switzerland
| | - Victor Neel
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Berna C Özdemir
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.,International Cancer Prevention Institute, Epalinges, Switzerland
| | - G Paolo Dotto
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Biochemistry, University of Lausanne, Epalinges, Switzerland.,International Cancer Prevention Institute, Epalinges, Switzerland
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5
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Sheng L, Ye L, Zhang D, Cawthorn WP, Xu B. New Insights Into the Long Non-coding RNA SRA: Physiological Functions and Mechanisms of Action. Front Med (Lausanne) 2018; 5:244. [PMID: 30238005 PMCID: PMC6135885 DOI: 10.3389/fmed.2018.00244] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (lncRNA) are emerging as new genetic/epigenetic regulators that can impact almost all physiological functions. Here, we focus on the long non-coding steroid receptor RNA activator (SRA), including new insights into its effects on gene expression, the cell cycle, and differentiation; how these relate to physiology and disease; and the mechanisms underlying these effects. We discuss how SRA acts as an RNA coactivator in nuclear receptor signaling; its effects on steroidogenesis, adipogenesis, and myocyte differentiation; the impact on breast and prostate cancer tumorigenesis; and, finally, its ability to modulate hepatic steatosis through several signaling pathways. Genome-wide analysis reveals that SRA regulates hundreds of target genes in adipocytes and breast cancer cells and binds to thousands of genomic sites in human pluripotent stem cells. Recent studies indicate that SRA acts as a molecular scaffold and forms networks with numerous coregulators and chromatin-modifying regulators in both activating and repressive complexes. We discuss how modifications to SRA's unique stem-loop secondary structure are important for SRA function, and highlight the various SRA isoforms and mutations that have clinical implications. Finally, we discuss the future directions for better understanding the molecular mechanisms of SRA action and how this might lead to new diagnostic and therapeutic approaches.
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Affiliation(s)
- Liang Sheng
- Department of Pharmacology, School of Basic Medical Science, Nanjing Medical University, Nanjing, China.,Neuroprotective Drug Discovery Key Laboratory of Nanjing Medical University, Nanjing, China
| | - Lan Ye
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Dong Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - William P Cawthorn
- University/British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Bin Xu
- Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, University of Michigan Medical Center Ann Arbor, MI, United States
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6
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Li Y, Wang H, Zhou D, Shuang T, Zhao H, Chen B. Up-Regulation of Long Noncoding RNA SRA Promotes Cell Growth, Inhibits Cell Apoptosis, and Induces Secretion of Estradiol and Progesterone in Ovarian Granular Cells of Mice. Med Sci Monit 2018; 24:2384-2390. [PMID: 29674607 PMCID: PMC5928913 DOI: 10.12659/msm.907138] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Increasing evidence indicates that long noncoding RNAs (LncRNAs) play a key role in multiple pathological processes. It has been shown that LncRNA steroid receptor RNA activator (SRA) is elevated in peripheral blood of patients with polycystic ovary syndrome (PCOS). The aim of this study was to assess the effect of elevated LncRNA SRA on ovarian granular cells of mice in vitro. MATERIAL AND METHODS We firstly isolated granular cells from mouse ovaries and over-expressed the LncRNA SRA by means of lentiviral transfection in this cell line. Then, we assessed the effects of LncRNA SRA on granular cells through real-time PCR, CCK-8 assay, flow cytometry, Hoechst staining, and Western blot assay. RESULTS We demonstrated that elevated LncRNA SRA stimulated cell growth, changed distribution of cell cycle phases with increase of Cyclin B, Cyclin E, and Cyclin D1, and inhibited cell apoptosis with up-regulation of bcl2 and down-regulation of bax, cleaved-caspase 3, and cleaved-PARP. Moreover, the contents of estradiol (E2) and progesterone (PG) and expressions of their key enzymes (CYP19A1 and CYP11A1) were up-regulated following over-expression of LncRNA SRA. CONCLUSIONS Taken together, our results indicate that abnormal LncRNA SRA may be a risk factor for evoking PCOS.
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Affiliation(s)
- Yan Li
- Department of Obstetrics and Gynecology, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China (mainland)
| | - Haixu Wang
- Department of Obstetrics and Gynecology, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China (mainland)
| | - Dangxia Zhou
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, China (mainland)
| | - Ting Shuang
- Department of Obstetrics and Gynecology, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China (mainland)
| | - Haibo Zhao
- Department of Obstetrics and Gynecology, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China (mainland)
| | - Biliang Chen
- Department of Obstetrics and Gynecology, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China (mainland)
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7
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Giurato G, Nassa G, Salvati A, Alexandrova E, Rizzo F, Nyman TA, Weisz A, Tarallo R. Quantitative mapping of RNA-mediated nuclear estrogen receptor β interactome in human breast cancer cells. Sci Data 2018; 5:180031. [PMID: 29509190 PMCID: PMC5839158 DOI: 10.1038/sdata.2018.31] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/22/2018] [Indexed: 12/13/2022] Open
Abstract
The nuclear receptor estrogen receptor 2 (ESR2, ERβ) modulates cancer cell proliferation and tumor growth, exerting an oncosuppressive role in breast cancer (BC). Interaction proteomics by tandem affinity purification coupled to mass spectrometry was previously applied in BC cells to identify proteins acting in concert with ERβ to control key cellular functions, including gene transcription, RNA splicing and post-transcriptional mRNA regulation. These studies revealed an involvement of RNA in ERβ interactome assembly and functions. By applying native protein complex purification followed by nano LC-MS/MS before and after in vitro RNA removal, we generated a large dataset of newly identified nuclear ERβ interactors, including a subset associating with the receptor via RNA bridging. These datasets will be useful to investigate further the role of ERβ, nuclear RNAs and the other proteins identified here in BC and other cell types.
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Affiliation(s)
- Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081 Baronissi (SA), Italy.,Genomix4Life srl, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi (SA), Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081 Baronissi (SA), Italy
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081 Baronissi (SA), Italy
| | - Elena Alexandrova
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081 Baronissi (SA), Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081 Baronissi (SA), Italy
| | - Tuula A Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo, 0372 Oslo, Norway
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081 Baronissi (SA), Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081 Baronissi (SA), Italy
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8
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Zhao Y, Dunker W, Yu YT, Karijolich J. The Role of Noncoding RNA Pseudouridylation in Nuclear Gene Expression Events. Front Bioeng Biotechnol 2018; 6:8. [PMID: 29473035 PMCID: PMC5809436 DOI: 10.3389/fbioe.2018.00008] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/22/2018] [Indexed: 12/23/2022] Open
Abstract
Pseudouridine is the most abundant internal RNA modification in stable noncoding RNAs (ncRNAs). It can be catalyzed by both RNA-dependent and RNA-independent mechanisms. Pseudouridylation impacts both the biochemical and biophysical properties of RNAs and thus influences RNA-mediated cellular processes. The investigation of nuclear-ncRNA pseudouridylation has demonstrated that it is critical for the proper control of multiple stages of gene expression regulation. Here, we review how nuclear-ncRNA pseudouridylation contributes to transcriptional regulation and pre-mRNA splicing.
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Affiliation(s)
- Yang Zhao
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University, Nashville, TN, United States
| | - William Dunker
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University, Nashville, TN, United States
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University, Nashville, TN, United States.,Vanderbilt-Ingram Cancer Center, Nashville, TN, United States
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9
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Neumann P, Jaé N, Knau A, Glaser SF, Fouani Y, Rossbach O, Krüger M, John D, Bindereif A, Grote P, Boon RA, Dimmeler S. The lncRNA GATA6-AS epigenetically regulates endothelial gene expression via interaction with LOXL2. Nat Commun 2018; 9:237. [PMID: 29339785 PMCID: PMC5770451 DOI: 10.1038/s41467-017-02431-1] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 11/30/2017] [Indexed: 12/21/2022] Open
Abstract
Impaired or excessive growth of endothelial cells contributes to several diseases. However, the functional involvement of regulatory long non-coding RNAs in these processes is not well defined. Here, we show that the long non-coding antisense transcript of GATA6 (GATA6-AS) interacts with the epigenetic regulator LOXL2 to regulate endothelial gene expression via changes in histone methylation. Using RNA deep sequencing, we find that GATA6-AS is upregulated in endothelial cells during hypoxia. Silencing of GATA6-AS diminishes TGF-β2-induced endothelial-mesenchymal transition in vitro and promotes formation of blood vessels in mice. We identify LOXL2, known to remove activating H3K4me3 chromatin marks, as a GATA6-AS-associated protein, and reveal a set of angiogenesis-related genes that are inversely regulated by LOXL2 and GATA6-AS silencing. As GATA6-AS silencing reduces H3K4me3 methylation of two of these genes, periostin and cyclooxygenase-2, we conclude that GATA6-AS acts as negative regulator of nuclear LOXL2 function.
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Affiliation(s)
- Philipp Neumann
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt am Main, 60590, Germany
| | - Nicolas Jaé
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt am Main, 60590, Germany
| | - Andrea Knau
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany
| | - Simone F Glaser
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt am Main, 60590, Germany
| | - Youssef Fouani
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Justus-Liebig-University, Heinrich-Buff-Ring 17, Giessen, 35392, Germany
| | - Marcus Krüger
- Max Planck Institute for Heart and Lung Research, Ludwigstraße 43, Bad Nauheim, 61231, Germany
| | - David John
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt am Main, 60590, Germany
| | - Albrecht Bindereif
- Institute of Biochemistry, Justus-Liebig-University, Heinrich-Buff-Ring 17, Giessen, 35392, Germany
| | - Phillip Grote
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt am Main, 60590, Germany
| | - Reinier A Boon
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt am Main, 60590, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany. .,German Center of Cardiovascular Research (DZHK), Frankfurt am Main, 60590, Germany.
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10
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Tarallo R, Giurato G, Bruno G, Ravo M, Rizzo F, Salvati A, Ricciardi L, Marchese G, Cordella A, Rocco T, Gigantino V, Pierri B, Cimmino G, Milanesi L, Ambrosino C, Nyman TA, Nassa G, Weisz A. The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading. Genome Biol 2017; 18:189. [PMID: 29017520 PMCID: PMC5634881 DOI: 10.1186/s13059-017-1321-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 09/20/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The RNA-binding protein Argonaute 2 (AGO2) is a key effector of RNA-silencing pathways It exerts a pivotal role in microRNA maturation and activity and can modulate chromatin remodeling, transcriptional gene regulation and RNA splicing. Estrogen receptor beta (ERβ) is endowed with oncosuppressive activities, antagonizing hormone-induced carcinogenesis and inhibiting growth and oncogenic functions in luminal-like breast cancers (BCs), where its expression correlates with a better prognosis of the disease. RESULTS Applying interaction proteomics coupled to mass spectrometry to characterize nuclear factors cooperating with ERβ in gene regulation, we identify AGO2 as a novel partner of ERβ in human BC cells. ERβ-AGO2 association was confirmed in vitro and in vivo in both the nucleus and cytoplasm and is shown to be RNA-mediated. ChIP-Seq demonstrates AGO2 association with a large number of ERβ binding sites, and total and nascent RNA-Seq in ERβ + vs ERβ - cells, and before and after AGO2 knock-down in ERβ + cells, reveals a widespread involvement of this factor in ERβ-mediated regulation of gene transcription rate and RNA splicing. Moreover, isolation and sequencing by RIP-Seq of ERβ-associated long and small RNAs in the cytoplasm suggests involvement of the nuclear receptor in RISC loading, indicating that it may also be able to directly control mRNA translation efficiency and stability. CONCLUSIONS These results demonstrate that AGO2 can act as a pleiotropic functional partner of ERβ, indicating that both factors are endowed with multiple roles in the control of key cellular functions.
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Affiliation(s)
- Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Giuseppina Bruno
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Maria Ravo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Luca Ricciardi
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Giovanna Marchese
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | | | - Teresa Rocco
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Valerio Gigantino
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Biancamaria Pierri
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Giovanni Cimmino
- Department of Cardiothoracic and Respiratory Sciences, University of Campania'L. Vanvitelli', Naples, Italy
| | - Luciano Milanesi
- Institute of Biomedical Technologies, National Research Council, Segregate, MI, Italy
| | - Concetta Ambrosino
- Department of Science and Technology, University of Sannio, Benevento, Italy
- IRGS Biogem, Ariano Irpino, AV, Italy
| | - Tuula A Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo, Oslo, Norway
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy.
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy.
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11
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Steroid receptor RNA activator: Biologic function and role in disease. Clin Chim Acta 2016; 459:137-146. [DOI: 10.1016/j.cca.2016.06.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 06/05/2016] [Accepted: 06/05/2016] [Indexed: 12/25/2022]
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12
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Jung E, Jang S, Lee J, Kim Y, Shin H, Park HS, Lee Y. Truncated SRA RNA derivatives inhibit estrogen receptor-α-mediated transcription. Mol Biol Rep 2016; 43:1019-25. [PMID: 27406387 DOI: 10.1007/s11033-016-4039-2] [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: 04/27/2016] [Accepted: 07/06/2016] [Indexed: 10/21/2022]
Abstract
The steroid receptor RNA activator (SRA) is a long non-coding RNA (lncRNA) that acts as a putative coactivator for steroid receptor-mediated transcription. A recent study showed that SRA RNA can be structurally dissected into four domains comprising various secondary structures, but the contribution of each domain to the coactivation ability of SRA RNA was previously unknown. Here, we assessed the functional contributions of the various domains of SRA. We examined the effects of each domain on the coactivation of estrogen receptor-α (ERα)-mediated transcription of a luciferase reporter gene in HeLa cells. Then the detailed domain analysis was focused on domain III (D3) not only with the reporter gene in HeLa cells, but also with ERα-responsive genes in MCF7 breast cancer cells. Domain deletion analysis showed that the deletion of any domain decreased the luciferase activity, and that deletion of D3 caused the largest decrease. This D3 deletion effect was not recovered by co-expression of D3 alone; moreover, the expression of D3 fragments (particularly helices H15-H18, which are highly conserved across vertebrates) inhibited luciferase expression in HeLa cells. Moreover, a fragment containing helices H15-H18 reduced ERα-responsive gene expression in MCF7 breast cancer cells. Our findings indicate that D3 inhibited ERα-mediated transcription of a reporter gene in HeLa cells and that helices H15-H18, as a core element responsible for the D3-driven inhibition, reduced expression of ERα-responsive genes in breast cancer cells.
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Affiliation(s)
- Euihan Jung
- Department of Chemistry, KAIST, Daejeon, 305-701, Korea
| | - Seonghui Jang
- Department of Chemistry, KAIST, Daejeon, 305-701, Korea
| | - Jungmin Lee
- Department of Chemistry, KAIST, Daejeon, 305-701, Korea
| | - Youngmi Kim
- Department of Chemistry, KAIST, Daejeon, 305-701, Korea
| | - Heegwon Shin
- Department of Chemistry, KAIST, Daejeon, 305-701, Korea
| | - Hee-Sung Park
- Department of Chemistry, KAIST, Daejeon, 305-701, Korea
| | - Younghoon Lee
- Department of Chemistry, KAIST, Daejeon, 305-701, Korea.
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Li X, Ma S, Yi C. Pseudouridine: the fifth RNA nucleotide with renewed interests. Curr Opin Chem Biol 2016; 33:108-16. [PMID: 27348156 DOI: 10.1016/j.cbpa.2016.06.014] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 06/10/2016] [Accepted: 06/10/2016] [Indexed: 12/23/2022]
Abstract
More than 100 different types of chemical modifications to RNA have been documented so far. Historically, most of these modifications were found in rRNA, tRNA and snRNA; recently, new methods aided by high-throughput sequencing have enabled identification of chemical modifications to mRNA, leading to the emerging field of 'RNA epigenetics'. One such example is pseudouridine, which has long been known as a RNA modification in abundant non-coding RNA (ncRNA) and has recently been found to be present in mRNAas well. This review first summarizes biogenesis and known functions of pseudouridine in ncRNAs. We then focus on progress in pseudouridine detection, especially the chemical-assisted, transcriptome-wide sequencing tools that revealed the dynamic nature of mRNA pseudouridylation. Such enabling tools are expected to facilitate future functional studies of pseudouridine.
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Affiliation(s)
- Xiaoyu Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shiqing Ma
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, PR China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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Pseudouridine synthase 1 deficient mice, a model for Mitochondrial Myopathy with Sideroblastic Anemia, exhibit muscle morphology and physiology alterations. Sci Rep 2016; 6:26202. [PMID: 27197761 PMCID: PMC4873756 DOI: 10.1038/srep26202] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 04/28/2016] [Indexed: 01/02/2023] Open
Abstract
Mitochondrial myopathy with lactic acidosis and sideroblastic anemia (MLASA) is an oxidative phosphorylation disorder, with primary clinical manifestations of myopathic exercise intolerance and a macrocytic sideroblastic anemia. One cause of MLASA is recessive mutations in PUS1, which encodes pseudouridine (Ψ) synthase 1 (Pus1p). Here we describe a mouse model of MLASA due to mutations in PUS1. As expected, certain Ψ modifications were missing in cytoplasmic and mitochondrial tRNAs from Pus1−/− animals. Pus1−/− mice were born at the expected Mendelian frequency and were non-dysmorphic. At 14 weeks the mutants displayed reduced exercise capacity. Examination of tibialis anterior (TA) muscle morphology and histochemistry demonstrated an increase in the cross sectional area and proportion of myosin heavy chain (MHC) IIB and low succinate dehydrogenase (SDH) expressing myofibers, without a change in the size of MHC IIA positive or high SDH myofibers. Cytochrome c oxidase activity was significantly reduced in extracts from red gastrocnemius muscle from Pus1−/− mice. Transmission electron microscopy on red gastrocnemius muscle demonstrated that Pus1−/− mice also had lower intermyofibrillar mitochondrial density and smaller mitochondria. Collectively, these results suggest that alterations in muscle metabolism related to mitochondrial content and oxidative capacity may account for the reduced exercise capacity in Pus1−/− mice.
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Shafik A, Schumann U, Evers M, Sibbritt T, Preiss T. The emerging epitranscriptomics of long noncoding RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:59-70. [PMID: 26541084 DOI: 10.1016/j.bbagrm.2015.10.019] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 10/15/2015] [Accepted: 10/28/2015] [Indexed: 01/08/2023]
Abstract
The pervasive transcription of genomes into long noncoding RNAs has been amply demonstrated in recent years and garnered much attention. Similarly, emerging 'epitranscriptomics' research has shown that chemically modified nucleosides, thought to be largely the domain of tRNAs and other infrastructural RNAs, are far more widespread and can exert unexpected influence on RNA utilization. Both areas are characterized by the often-ephemeral nature of the subject matter in that few individual examples have been fully assessed for their molecular or cellular function, and effects might often be subtle and cumulative. Here we review available information at the intersection of these two exciting areas of biology, by focusing on four RNA modifications that have been mapped transcriptome-wide: 5-methylcytidine, N6-methyladenosine, pseudouridine as well as adenosine to inosine (A-to-I) editing, and their incidence and function in long noncoding RNAs. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Andrew Shafik
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Ulrike Schumann
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Maurits Evers
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Tennille Sibbritt
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia; Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst (Sydney), New South Wales 2010, Australia.
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Association of the Long Non-coding RNA Steroid Receptor RNA Activator (SRA) with TrxG and PRC2 Complexes. PLoS Genet 2015; 11:e1005615. [PMID: 26496121 PMCID: PMC4619771 DOI: 10.1371/journal.pgen.1005615] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 09/28/2015] [Indexed: 01/09/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been recognized as key players in transcriptional regulation. We show that the lncRNA steroid receptor RNA activator (SRA) participates in regulation through complex formation with trithorax group (TrxG) and polycomb repressive complex 2 (PRC2) complexes. Binding of the SRA-associated RNA helicase p68 preferentially stabilizes complex formation between SRA and a TrxG complex but not PRC2. In human pluripotent stem cells NTERA2, SRA binding sites that are also occupied by p68 are significantly enriched for H3K4 trimethylation. Consistent with its ability to interact with TrxG and PRC2 complexes, some SRA binding sites in human pluripotent stem cells overlap with bivalent domains. CTCF sites associated with SRA appear also to be enriched for bivalent modifications. We identify NANOG as a transcription factor directly interacting with SRA and co-localizing with it genome-wide in NTERA2. Further, we show that SRA is important for maintaining the stem cell state and for reprogramming of human fibroblasts to achieve the pluripotent state. Our results suggest a mechanism whereby the lncRNA SRA interacts with either TrxG or PRC2. These complexes may then be recruited by various DNA binding factors to deliver either activating or silencing signals, or both, to establish bivalent domains.
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Huet T, Miannay FA, Patton JR, Thore S. Steroid receptor RNA activator (SRA) modification by the human pseudouridine synthase 1 (hPus1p): RNA binding, activity, and atomic model. PLoS One 2014; 9:e94610. [PMID: 24722331 PMCID: PMC3983220 DOI: 10.1371/journal.pone.0094610] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 03/18/2014] [Indexed: 11/23/2022] Open
Abstract
The most abundant of the modified nucleosides, and once considered as the “fifth” nucleotide in RNA, is pseudouridine, which results from the action of pseudouridine synthases. Recently, the mammalian pseudouridine synthase 1 (hPus1p) has been reported to modulate class I and class II nuclear receptor responses through its ability to modify the Steroid receptor RNA Activator (SRA). These findings highlight a new level of regulation in nuclear receptor (NR)-mediated transcriptional responses. We have characterised the RNA association and activity of the human Pus1p enzyme with its unusual SRA substrate. We validate that the minimal RNA fragment within SRA, named H7, is necessary for both the association and modification by hPus1p. Furthermore, we have determined the crystal structure of the catalytic domain of hPus1p at 2.0 Å resolution, alone and in a complex with several molecules present during crystallisation. This model shows an extended C-terminal helix specifically found in the eukaryotic protein, which may prevent the enzyme from forming a homodimer, both in the crystal lattice and in solution. Our biochemical and structural data help to understand the hPus1p active site architecture, and detail its particular requirements with regard to one of its nuclear substrates, the non-coding RNA SRA.
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Affiliation(s)
- Tiphaine Huet
- Department of Molecular Biology, University of Geneva, Sciences III, Geneva, Switzerland
| | | | - Jeffrey R. Patton
- Department of Pathology, Microbiology and Immunology, University of South Carolina, School of Medicine, Columbia, South Carolina, United States of America
| | - Stéphane Thore
- Department of Molecular Biology, University of Geneva, Sciences III, Geneva, Switzerland
- * E-mail:
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Novikova IV, Hennelly SP, Sanbonmatsu KY. Tackling structures of long noncoding RNAs. Int J Mol Sci 2013; 14:23672-84. [PMID: 24304541 PMCID: PMC3876070 DOI: 10.3390/ijms141223672] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 11/15/2013] [Accepted: 11/25/2013] [Indexed: 11/16/2022] Open
Abstract
RNAs are important catalytic machines and regulators at every level of gene expression. A new class of RNAs has emerged called long non-coding RNAs, providing new insights into evolution, development and disease. Long non-coding RNAs (lncRNAs) predominantly found in higher eukaryotes, have been implicated in the regulation of transcription factors, chromatin-remodeling, hormone receptors and many other processes. The structural versatility of RNA allows it to perform various functions, ranging from precise protein recognition to catalysis and metabolite sensing. While major housekeeping RNA molecules have long been the focus of structural studies, lncRNAs remain the least characterized class, both structurally and functionally. Here, we review common methodologies used to tackle RNA structure, emphasizing their potential application to lncRNAs. When considering the complexity of lncRNAs and lack of knowledge of their structure, chemical probing appears to be an indispensable tool, with few restrictions in terms of size, quantity and heterogeneity of the RNA molecule. Probing is not constrained to in vitro analysis and can be adapted to high-throughput sequencing platforms. Significant efforts have been applied to develop new in vivo chemical probing reagents, new library construction protocols for sequencing platforms and improved RNA prediction software based on the experimental evidence.
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Novikova IV, Hennelly SP, Tung CS, Sanbonmatsu KY. Rise of the RNA machines: exploring the structure of long non-coding RNAs. J Mol Biol 2013; 425:3731-46. [PMID: 23467124 DOI: 10.1016/j.jmb.2013.02.030] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/21/2013] [Accepted: 02/25/2013] [Indexed: 01/19/2023]
Abstract
Novel, profound and unexpected roles of long non-coding RNAs (lncRNAs) are emerging in critical aspects of gene regulation. Thousands of lncRNAs have been recently discovered in a wide range of mammalian systems, related to development, epigenetics, cancer, brain function and hereditary disease. The structural biology of these lncRNAs presents a brave new RNA world, which may contain a diverse zoo of new architectures and mechanisms. While structural studies of lncRNAs are in their infancy, we describe existing structural data for lncRNAs, as well as crystallographic studies of other RNA machines and their implications for lncRNAs. We also discuss the importance of dynamics in RNA machine mechanism. Determining commonalities between lncRNA systems will help elucidate the evolution and mechanistic role of lncRNAs in disease, creating a structural framework necessary to pursue lncRNA-based therapeutics.
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