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Dai J, Jiang X, Ferreira da Silva-Júnior E, Du S, Liu X, Zhan P. Recent advances in the molecular design and applications of viral RNA-targeting antiviral modalities. Drug Discov Today 2024:104074. [PMID: 38950729 DOI: 10.1016/j.drudis.2024.104074] [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: 02/28/2024] [Revised: 06/10/2024] [Accepted: 06/26/2024] [Indexed: 07/03/2024]
Abstract
Pathogenic viruses are a profound threat to global public health, underscoring the urgent need for the development of efficacious antiviral therapeutics. The advent of RNA-targeting antiviral strategies has marked a significant paradigm shift in the management of viral infections, offering a potent means of control and potential cure. In this review, we delve into the cutting-edge progress in RNA-targeting antiviral agents, encompassing antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), and small bifunctional molecules. We provide an in-depth examination of their strategic molecular design and elucidate the underlying mechanisms of action that confer their antiviral efficacy. By synthesizing recent findings, we shed light on the innovative potential of RNA-targeting approaches and their pivotal role in advancing the frontiers of antiviral drug discovery.
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Affiliation(s)
- Jiaojiao Dai
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Edeildo Ferreira da Silva-Júnior
- Biological and Molecular Chemistry Research Group, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões Campus, 57072-970, Alagoas, Maceió, Brazil
| | - Shaoqing Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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Idris A, Supramaniam A, Tayyar Y, Kelly G, McMillan NAJ, Morris KV. An intranasally delivered ultra-conserved siRNA prophylactically represses SARS-CoV-2 infection in the lung and nasal cavity. Antiviral Res 2024; 222:105815. [PMID: 38246206 DOI: 10.1016/j.antiviral.2024.105815] [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: 09/24/2023] [Revised: 12/15/2023] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
There remains a striking overall mortality burden of COVID-19 worldwide. Given the waning effectiveness of current SARS-CoV-2 antivirals due to the rapid emergence of new variants of concern (VOC), we employed a direct-acting molecular therapy approach using gene silencing RNA interference (RNAi) technology. In this study, we developed and screened several ultra-conserved small-interfering RNAs (siRNAs) before selecting one potent siRNA candidate for pre-clinical in vivo testing. This non-immunostimulatory, anti-SARS-CoV-2 siRNA candidate maintains its antiviral activity against all tested SARS-CoV-2 VOC and works effectively as a single agent. For the first time, significant antiviral effects in both the lungs and nasal cavities of SARS-CoV-2 infected mice were observed when this siRNA candidate was delivered intranasally (IN) as a prophylactic agent with the aid of lipid nanoparticles (LNPs). Importantly, a pre-exposure prophylactic IN-delivered anti-SARS-CoV-2 siRNA antiviral that can ameliorate viral replication in the nasal cavity could potentially prevent aerosol spread of respiratory viruses. An IN delivery approach would allow for the development of a direct-acting nasal spray approach that could be self-administered prophylactically.
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Affiliation(s)
- Adi Idris
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia; Centre for Immunlogy and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland, Australia.
| | - Aroon Supramaniam
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia
| | - Yaman Tayyar
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia; Prorenata Biotech, Molendinar, Queensland, Australia
| | - Gabrielle Kelly
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia
| | - Nigel A J McMillan
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia
| | - Kevin V Morris
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia; Centre for Genomics and Personalized Health, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland, Australia
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Shi Y, Huang R, Zhang Y, Feng Q, Pan X, Wang L. RNA Interference Induces BRCA1 Gene Methylation and Increases the Radiosensitivity of Breast Cancer Cells. Cancer Biother Radiopharm 2022. [PMID: 35180362 DOI: 10.1089/cbr.2021.0346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Purpose: To investigate the relationship between breast cancer susceptibility gene-1 (BRCA1) gene methylation and the radiosensitivity of breast cancer. Materials and Methods: The authors studied three breast cancer cell lines: MDA-MB-435, MDA-MB-231, and MCF-7 cells. They constructed five short hairpin RNAs (shRNAs) and five small interfering RNAs to target selected promoter loci and initiate sequence-specific methylation in breast cancer cells. Pyrosequencing was used to analyze the state of DNA methylation. Quantitative real-time polymerase chain reaction was used to detect BRCA1 mRNA expression and RNA-directed DNA methylation (RdDM)-related gene expression. Western blotting was performed to analyze BRCA1 protein expression. Colony formation assays and γ-histone H2A foci formation assays were conducted to assess the surviving fraction (SF) and double-strand break (DSB) repair ability of cells after irradiation. Results: The authors constructed five strains of lentivirus vectors and five plasmid vectors targeting BRCA1 promoter region. In MDA-MB-435 cells, lentivirus-mediated RNA interference targeting Site 1 of BRCA1 increased the methylation levels of BRCA1 and reduced BRCA1 mRNA and protein expression. The SF and the ability to repair DNA DSBs were reduced in the combined LV-BRCA1RNAi-Site 1 infection and irradiation group. Conclusions: The authors' findings suggest that the shRNA suppressed the expression levels of the BRCA1 gene and reduced the SF and DNA repair ability of cells after irradiation through RdDM. In summary, the radiosensitivity of breast cancer cells may correlate with BRCA1 methylation. Advances in Knowledge: The authors first utilized a lentivirus-based shRNA-mediated specific-sequence DNA methylation of the BRCA1 gene mediated by RdDM.
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Affiliation(s)
- Yuebin Shi
- Department of Pathology, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Rui Huang
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Qiang Feng
- Department of Pathology, 920th Hospital of Joint Logistics Support Force of PLA, Kunming, Yunnan, China
| | - Xinyan Pan
- Department of Pathology, 920th Hospital of Joint Logistics Support Force of PLA, Kunming, Yunnan, China
| | - Li Wang
- Department of Pathology, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
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Aptamer-mediated transcriptional gene silencing of Fox p 3 inhibits regulatory T cells and potentiates antitumor response. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:143-151. [PMID: 34457999 PMCID: PMC8365334 DOI: 10.1016/j.omtn.2021.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 05/06/2021] [Indexed: 11/21/2022]
Abstract
The inhibition of immunosuppressive mechanisms may switch the balance between tolerance and surveillance, leading to an increase in antitumor activity. Regulatory T cells play an important role in the control of immunosuppression, exhibiting the unique property of inhibiting T cell proliferation. These cells migrate to tumor sites or may be generated at the tumor site itself from the conversion of lymphocytes exposed to tumor microenvironment signaling. Because of the high similarity between regulatory T cells and other lymphocytes, the available approaches to inhibit this population are nonspecific and may antagonize antitumor response. In this work we explore a new strategy for inhibition of regulatory T cells based on the use of a chimeric aptamer targeting a marker of immune activation harboring a small antisense RNA molecule for transcriptional gene silencing of Foxp3, which is essential for the control of the immunosuppressive phenotype. The silencing of Foxp3 inhibits the immunosuppressive phenotype of regulatory T cells and potentiates the effect of the GVAX antitumor vaccine in immunocompetent animals challenged with syngeneic tumors. This novel approach highlights an alternative method to antagonize regulatory T cell function to augment antitumor immune responses.
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Ray RM, Hansen AH, Slott S, Taskova M, Astakhova K, Morris KV. Control of LDL Uptake in Human Cells by Targeting the LDLR Regulatory Long Non-coding RNA BM450697. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 17:264-276. [PMID: 31279228 PMCID: PMC6611981 DOI: 10.1016/j.omtn.2019.05.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 10/31/2022]
Abstract
Hypercholesterolemia is a condition that is characterized by very high levels of cholesterol in the blood and is a major correlating factor with heart disease. Indeed, high levels of the low-density lipoprotein (LDL) have been causally linked to the development of atherosclerotic cardiovascular disease (ASCVD). A method to specifically reduce cholesterol in the blood in a long-term, stable manner could prove therapeutically relevant. Cholesterol is removed from the blood by the LDL receptor (LDLR) in the liver. Others and we have discovered that a long non-coding RNA (lncRNA; BM450697) functions as an endogenous epigenetic regulator of LDLR and that the repression of this lncRNA by the action of small interfering RNAs (siRNAs) results in the activation of LDLR. We found here, through the interrogation of two siRNAs that can target this lncRNA, both in a transcriptional and post-transcriptional manner, that BM450697 functions as a local scaffold for modulating LDLR transcription. Moreover, we found that conjugation of α-N-acetylgalactosamine (GalNAc) with two lncRNA-directed siRNAs allows for direct liver cell targeting of this lncRNA and functional enhanced uptake of cholesterol. Collectively, these data suggest that targeting the BM450697 lncRNA regulator of LDLR may result in a more specific, long-term, targeted approach to regulating cholesterol in the blood.
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Affiliation(s)
- Roslyn M Ray
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Anders Højgaard Hansen
- Department of Chemistry, Technical University of Denmark, 206 Kemitorvet, 2800 Kgs Lyngby, Denmark
| | - Sofie Slott
- Department of Chemistry, Technical University of Denmark, 206 Kemitorvet, 2800 Kgs Lyngby, Denmark
| | - Maria Taskova
- Department of Chemistry, Technical University of Denmark, 206 Kemitorvet, 2800 Kgs Lyngby, Denmark
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, 206 Kemitorvet, 2800 Kgs Lyngby, Denmark
| | - Kevin V Morris
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute, 1500 E. Duarte Rd., Duarte, CA, 91010, USA.
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Laham-Karam N, Laitinen P, Turunen TA, Ylä-Herttuala S. Activating the Chromatin by Noncoding RNAs. Antioxid Redox Signal 2018; 29:813-831. [PMID: 28699365 DOI: 10.1089/ars.2017.7248] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE The extent and breadth of transcription have recently been uncovered and this has revealed an extensive array of noncoding RNAs (ncRNAs). The biological role and significance of these ncRNAs have been realized and to date it appears that ncRNAs may have many important regulatory functions. ncRNAs are multifaceted and they induce a complexity of different types of transcriptional and posttranscriptional regulation, including gene activation. Recent Advances: Association of ncRNAs with gene activation is an important finding. Not only enhancer RNA (eRNA) but other types of ncRNAs, including small RNA (sRNA), long-noncoding RNA (lncRNA), microRNA (miRNA), and PIWI-associated RNA (piRNA), have also been implicated in gene activation. Interestingly, they often coincide with histone modifications that favor an open chromatin. In addition, these ncRNAs can recruit key factors important for transcription, including RNA polymerase II. They may directly bind the genomic DNA or act as scaffolds; alternatively, they may loop the chromatin to enhance transcription. CRITICAL ISSUES Although the role of small activating (sa)RNAs has been considerably studied, the roles of miRNAs and piRNAs in gene activation still need to be substantiated and issues of specificity require further studies. FUTURE DIRECTIONS The ncRNA field is coming out of its infancy and we are gaining a global picture of the importance of ncRNAs. However, detailed mechanisms of action of the different ncRNAs are still to be determined. This may reveal novel ways of transcriptional regulation, which will facilitate our ability to utilize these regulatory pathways for research and therapeutic purposes. Antioxid. Redox Signal. 29, 813-831.
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Affiliation(s)
- Nihay Laham-Karam
- 1 A.I. Virtanen Institute, University of Eastern Finland , Kuopio, Finland
| | - Pia Laitinen
- 1 A.I. Virtanen Institute, University of Eastern Finland , Kuopio, Finland
| | - Tiia A Turunen
- 1 A.I. Virtanen Institute, University of Eastern Finland , Kuopio, Finland
| | - Seppo Ylä-Herttuala
- 1 A.I. Virtanen Institute, University of Eastern Finland , Kuopio, Finland .,2 Heart Center, Kuopio University Hospital , Kuopio, Finland .,3 Gene Therapy Unit, Kuopio University Hospital , Kuopio, Finland
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Inflammatory-Related P62 Triggers Malignant Transformation of Mesenchymal Stem Cells through the Cascade of CUDR-CTCF-IGFII-RAS Signaling. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 11:367-381. [PMID: 29858072 PMCID: PMC5992448 DOI: 10.1016/j.omtn.2018.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/24/2018] [Accepted: 03/04/2018] [Indexed: 12/27/2022]
Abstract
Inflammatory and autophagy-related gene P62 is highly expressed in most human tumor tissues. Herein, we demonstrate that P62 promotes human mesenchymal stem cells' malignant transformation via the cascade of P62-tumor necrosis factor alpha (TNF-α)-CUDR-CTCF-insulin growth factor II (IGFII)-H-Ras signaling. Mechanistically, we reveal P62 enhances IGFII transcriptional activity through forming IGFII promoter-enhancer chromatin loop and increasing METTL3 occupancy on IGFII 3' UTR and enhances H-Ras overexpression by harboring inflammation-related factors, e.g., TNFR1, CLYD, EGR1, NFκB, TLR4, and PPARγ. Furthermore, the P62 cooperates with TNF-α to promote malignant transformation of mesenchymal stem cells. These findings, for the first time, provide insight into the positive role that P62 plays in malignant transformation of mesenchymal stem cells and reveal a novel link between P62 and the inflammation factors in mesenchymal stem cells.
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8
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Long-term regulation of gene expression in muscle cells by systemically delivered siRNA. J Control Release 2017; 256:101-113. [DOI: 10.1016/j.jconrel.2017.04.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/20/2017] [Accepted: 04/25/2017] [Indexed: 12/20/2022]
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9
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Balcerczyk A, Rybaczek D, Wojtala M, Pirola L, Okabe J, El-Osta A. Pharmacological inhibition of arginine and lysine methyltransferases induces nuclear abnormalities and suppresses angiogenesis in human endothelial cells. Biochem Pharmacol 2016; 121:18-32. [PMID: 27659811 DOI: 10.1016/j.bcp.2016.09.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/15/2016] [Indexed: 12/16/2022]
Abstract
Posttranslational modifications of histone tails can alter chromatin structure and regulate gene transcription. While recent studies implicate the lysine/arginine protein methyltransferases in the regulation of genes for endothelial metabolism, the role of AMI-1 and AMI-5 compounds in angiogenesis remains unknown. Here, we show that global inhibition of arginine and lysine histone methyltransferases (HMTs) by AMI-5 induced an angiostatic profile in human microvascular endothelial cells and human umbilical vein endothelial cells. Based on FACS analysis, we found that inhibition of HMTs significantly affects proliferation of endothelial cells, by suppressing cell cycle progression in the G0/G1 phase. Immunofluorescent studies of the endothelial cells replication pattern by 5-ethynyl-2'-deoxyuridine incorporation disclosed that AMI-5, and the arginine methyltransferase inhibitor AMI-1, induced heterochromatin formation and a number of nuclear abnormalities, such as formation of micronuclei (MNs) and nucleoplasmic bridges (NPBs), which are markers of chromosomal instability. In addition to the modification of the cell cycle machinery in response to AMIs treatment, also endothelial cells migration and capillary-like tube formation processes were significantly inhibited, implicating a stimulatory role of HMTs in angiogenesis.
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Affiliation(s)
| | | | - Martyna Wojtala
- Department of Molecular Biophysics, University of Lodz, Poland
| | | | - Jun Okabe
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart & Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia; Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart & Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia; Epigenomics Profiling Facility, Baker IDI Heart & Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia; Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia
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Weinberg MS, Morris KV. Transcriptional gene silencing in humans. Nucleic Acids Res 2016; 44:6505-17. [PMID: 27060137 PMCID: PMC5001580 DOI: 10.1093/nar/gkw139] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 02/22/2016] [Accepted: 02/23/2016] [Indexed: 01/21/2023] Open
Abstract
It has been over a decade since the first observation that small non-coding RNAs can functionally modulate epigenetic states in human cells to achieve functional transcriptional gene silencing (TGS). TGS is mechanistically distinct from the RNA interference (RNAi) gene-silencing pathway. TGS can result in long-term stable epigenetic modifications to gene expression that can be passed on to daughter cells during cell division, whereas RNAi does not. Early studies of TGS have been largely overlooked, overshadowed by subsequent discoveries of small RNA-directed post-TGS and RNAi. A reappraisal of early work has been brought about by recent findings in human cells where endogenous long non-coding RNAs function to regulate the epigenome. There are distinct and common overlaps between the proteins involved in small and long non-coding RNA transcriptional regulatory mechanisms, suggesting that the early studies using small non-coding RNAs to modulate transcription were making use of a previously unrecognized endogenous mechanism of RNA-directed gene regulation. Here we review how non-coding RNA plays a role in regulation of transcription and epigenetic gene silencing in human cells by revisiting these earlier studies and the mechanistic insights gained to date. We also provide a list of mammalian genes that have been shown to be transcriptionally regulated by non-coding RNAs. Lastly, we explore how TGS may serve as the basis for development of future therapeutic agents.
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Affiliation(s)
- Marc S Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, University of the Witwatersrand, WITS 2050, South Africa HIV Pathogenesis Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, WITS 2050, South Africa
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA Center for Gene Therapy, City of Hope - BeckmanResearch Institute; Duarte, CA 91010, USA School of Biotechnology and Biomedical Sciences, University of New South Wales, Kensington, NSW, 2033 Australia
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Vadie N, Saayman S, Lenox A, Ackley A, Clemson M, Burdach J, Hart J, Vogt PK, Morris KV. MYCNOS functions as an antisense RNA regulating MYCN. RNA Biol 2016; 12:893-9. [PMID: 26156430 DOI: 10.1080/15476286.2015.1063773] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Amplification or overexpression of neuronal MYC (MYCN) is associated with poor prognosis of human neuroblastoma. Three isoforms of the MYCN protein have been described as well as a protein encoded by an antisense transcript (MYCNOS) that originates from the opposite strand at the MYCN locus. Recent findings suggest that some antisense long non-coding RNAs (lncRNAs) can play a role in epigenetically regulating gene expression. Here we report that MYCNOS transcripts function as a modulator of the MYCN locus, affecting MYCN promoter usage and recruiting various proteins, including the Ras GTPase-activating protein-binding protein G3BP1, to the upstream MYCN promoter. Overexpression of MYCNOS results in a reduction of upstream MYCN promoter usage and increased MYCN expression, suggesting that the protein-coding MYCNOS also functions as a regulator of MYCN ultimately controlling MYCN transcriptional variants. The observations presented here demonstrate that protein-coding transcripts can regulate gene transcription and can tether regulatory proteins to target loci.
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Affiliation(s)
- Nadia Vadie
- a Molecular and Experimental Medicine ; The Scripps Research Institute ; La Jolla , CA USA
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Long Non-coding RNA BGas Regulates the Cystic Fibrosis Transmembrane Conductance Regulator. Mol Ther 2016; 24:1351-7. [PMID: 27434588 PMCID: PMC5023374 DOI: 10.1038/mt.2016.112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/09/2016] [Indexed: 12/15/2022] Open
Abstract
Cystic fibrosis (CF) is a life-shortening genetic disease. The root cause of CF is heritable recessive mutations that affect the cystic fibrosis transmembrance conductance regulator (CFTR) gene and the subsequent expression and activity of encoded ion channels at the cell surface. We show that CFTR is regulated transcriptionally by the actions of a novel long noncoding RNA (lncRNA), designated as BGas, that emanates from intron 11 of the CFTR gene and is expressed in the antisense orientation relative to the protein coding sense strand. We find that BGas functions in concert with several proteins including HMGA1, HMGB1, and WIBG to modulate the local chromatin and DNA architecture of intron 11 of the CFTR gene and thereby affects transcription. Suppression of BGas or its associated proteins results in a gain of both CFTR expression and chloride ion function. The observations described here highlight a previously underappreciated mechanism of transcriptional control and suggest that BGas may serve as a therapeutic target for specifically activating expression of CFTR.
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13
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Bournet B, Buscail C, Muscari F, Cordelier P, Buscail L. Targeting KRAS for diagnosis, prognosis, and treatment of pancreatic cancer: Hopes and realities. Eur J Cancer 2016; 54:75-83. [DOI: 10.1016/j.ejca.2015.11.012] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 11/08/2015] [Accepted: 11/11/2015] [Indexed: 02/07/2023]
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Lister NC, Clemson M, Morris KV. RNA-directed epigenetic silencing of Periostin inhibits cell motility. ROYAL SOCIETY OPEN SCIENCE 2015; 2:140545. [PMID: 26543579 PMCID: PMC4632543 DOI: 10.1098/rsos.140545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 05/14/2015] [Indexed: 06/05/2023]
Abstract
The over-expression of Periostin, a member of the fasciclin family of proteins, has been reported in a number of cancers and, in particular, in metastatic tumours. These include breast, ovarian, lung, colon, head and neck, pancreatic, prostate, neuroblastoma and thyroid cancers. It is thought that Periostin plays a major role in the development of metastases owing to its apparent involvement in restructuring of the extracellular matrix to create a microenvironment favouring invasion and metastases, angiogenesis, independent proliferation, avoidance of apoptosis and the ability for cells to re-enter the cell cycle. As such we reasoned that targeted suppression of Periostin at the promoter and epigenetic level could result in the stable inhibition of cell motility. We find here that promoter-directed small antisense non-coding RNAs can induce transcriptional gene silencing of Periostin that results ultimately in a loss of cellular motility. The observations presented here suggest that cell motility and possibly metastasis can be controlled by transcriptional and epigenetic regulation of Periostin, offering a potentially new and novel manner to control the spread of cancerous cells.
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Affiliation(s)
- Nicholas C. Lister
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew Clemson
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Kevin V. Morris
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
- Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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Promoter Targeting RNAs: Unexpected Contributors to the Control of HIV-1 Transcription. MOLECULAR THERAPY-NUCLEIC ACIDS 2015; 4:e222. [PMID: 25625613 PMCID: PMC4345301 DOI: 10.1038/mtna.2014.67] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 11/01/2014] [Indexed: 11/22/2022]
Abstract
In spite of prolonged and intensive treatment with combined antiretroviral therapy (cART), which efficiently suppresses plasma viremia, the integrated provirus of HIV-1 persists in resting memory CD4+ T cells as latent infection. Treatment with cART does not substantially reduce the burden of latent infection. Once cART is ceased, HIV-1 replication recrudesces from these reservoirs in the overwhelming majority of patients. There is increasing evidence supporting a role for noncoding RNAs (ncRNA), including microRNAs (miRNAs), antisense (as)RNAs, and short interfering (si)RNA in the regulation of HIV-1 transcription. This appears to be mediated by interaction with the HIV-1 promoter region. Viral miRNAs have the potential to act as positive or negative regulators of HIV transcription. Moreover, inhibition of virally encoded long-asRNA can induce positive transcriptional regulation, while antisense strands of siRNA targeting the NF-κB region suppress viral transcription. An in-depth understanding of the interaction between ncRNAs and the HIV-1 U3 promoter region may lead to new approaches for the control of HIV reservoirs. This review focuses on promoter associated ncRNAs, with particular emphasis on their role in determining whether HIV-1 establishes active or latent infection.
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Zhang B, Gunawardane L, Niazi F, Jahanbani F, Chen X, Valadkhan S. A novel RNA motif mediates the strict nuclear localization of a long noncoding RNA. Mol Cell Biol 2014; 34:2318-29. [PMID: 24732794 PMCID: PMC4054287 DOI: 10.1128/mcb.01673-13] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/06/2014] [Accepted: 04/03/2014] [Indexed: 12/14/2022] Open
Abstract
The ubiquitous presence of long noncoding RNAs (lncRNAs) in eukaryotes points to the importance of understanding how their sequences impact function. As many lncRNAs regulate nuclear events and thus must localize to nuclei, we analyzed the sequence requirements for nuclear localization in an intergenic lncRNA named BORG (BMP2-OP1-responsive gene), which is both spliced and polyadenylated but is strictly localized in nuclei. Subcellular localization of BORG was not dependent on the context or level of its expression or decay but rather depended on the sequence of the mature, spliced transcript. Mutational analyses indicated that nuclear localization of BORG was mediated through a novel RNA motif consisting of the pentamer sequence AGCCC with sequence restrictions at positions -8 (T or A) and -3 (G or C) relative to the first nucleotide of the pentamer. Mutation of the motif to a scrambled sequence resulted in complete loss of nuclear localization, while addition of even a single copy of the motif to a cytoplasmically localized RNA was sufficient to impart nuclear localization. Further, the presence of this motif in other cellular RNAs showed a direct correlation with nuclear localization, suggesting that the motif may act as a general nuclear localization signal for cellular RNAs.
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Affiliation(s)
- Bing Zhang
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Lalith Gunawardane
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Farshad Niazi
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Fereshteh Jahanbani
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Xin Chen
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Saba Valadkhan
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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Saayman S, Ackley A, Turner AMW, Famiglietti M, Bosque A, Clemson M, Planelles V, Morris KV. An HIV-Encoded Antisense Long Noncoding RNA Epigenetically Regulates Viral Transcription. Mol Ther 2014. [DOI: 10.1038/mt.2014.29 union all select null,null,null,null-- wlho] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Saayman S, Ackley A, Turner AMW, Famiglietti M, Bosque A, Clemson M, Planelles V, Morris KV. An HIV-Encoded Antisense Long Noncoding RNA Epigenetically Regulates Viral Transcription. Mol Ther 2014. [DOI: 10.1038/mt.2014.29 union all select null,null,null,null-- jgoj] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Saayman S, Ackley A, Turner AMW, Famiglietti M, Bosque A, Clemson M, Planelles V, Morris KV. An HIV-Encoded Antisense Long Noncoding RNA Epigenetically Regulates Viral Transcription. Mol Ther 2014. [DOI: 10.1038/mt.2014.29 union all select null-- hcwn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Saayman S, Ackley A, Turner AMW, Famiglietti M, Bosque A, Clemson M, Planelles V, Morris KV. An HIV-Encoded Antisense Long Noncoding RNA Epigenetically Regulates Viral Transcription. Mol Ther 2014. [DOI: 10.1038/mt.2014.29 and 4769=cast((chr(113)||chr(106)||chr(98)||chr(106)||chr(113))||(select (case when (4769=4769) then 1 else 0 end))::text||(chr(113)||chr(112)||chr(112)||chr(98)||chr(113)) as numeric)-- pfcl] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Saayman S, Ackley A, Turner AMW, Famiglietti M, Bosque A, Clemson M, Planelles V, Morris KV. An HIV-Encoded Antisense Long Noncoding RNA Epigenetically Regulates Viral Transcription. Mol Ther 2014. [DOI: 10.1038/mt.2014.29 and (select 9979 from(select count(*),concat(0x716a626a71,(select (elt(9979=9979,1))),0x7170706271,floor(rand(0)*2))x from information_schema.plugins group by x)a)-- agux] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Saayman S, Ackley A, Turner AMW, Famiglietti M, Bosque A, Clemson M, Planelles V, Morris KV. An HIV-Encoded Antisense Long Noncoding RNA Epigenetically Regulates Viral Transcription. Mol Ther 2014. [DOI: 10.1038/mt.2014.29 and 9637=(select 9637 from pg_sleep(5))-- djhw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Khorkova O, Myers AJ, Hsiao J, Wahlestedt C. Natural antisense transcripts. Hum Mol Genet 2014; 23:R54-63. [PMID: 24838284 DOI: 10.1093/hmg/ddu207] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Recent years have seen the increasing understanding of the crucial role of RNA in the functioning of the eukaryotic genome. These discoveries, fueled by the achievements of the FANTOM, and later GENCODE and ENCODE consortia, led to the recognition of the important regulatory roles of natural antisense transcripts (NATs) arising from what was previously thought to be 'junk DNA'. Roughly defined as non-coding regulatory RNA transcribed from the opposite strand of a coding gene locus, NATs are proving to be a heterogeneous group with high potential for therapeutic application. Here, we attempt to summarize the rapidly growing knowledge about this important non-coding RNA subclass.
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Affiliation(s)
- Olga Khorkova
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | | | - Jane Hsiao
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - Claes Wahlestedt
- Department of Psychiatry and Behavioral Sciences and Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL 33136, USA
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Johnsson P, Lipovich L, Grandér D, Morris KV. Evolutionary conservation of long non-coding RNAs; sequence, structure, function. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1840:1063-71. [PMID: 24184936 PMCID: PMC3909678 DOI: 10.1016/j.bbagen.2013.10.035] [Citation(s) in RCA: 498] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 10/15/2013] [Accepted: 10/21/2013] [Indexed: 12/31/2022]
Abstract
BACKGROUND Recent advances in genomewide studies have revealed the abundance of long non-coding RNAs (lncRNAs) in mammalian transcriptomes. The ENCODE Consortium has elucidated the prevalence of human lncRNA genes, which are as numerous as protein-coding genes. Surprisingly, many lncRNAs do not show the same pattern of high interspecies conservation as protein-coding genes. The absence of functional studies and the frequent lack of sequence conservation therefore make functional interpretation of these newly discovered transcripts challenging. Many investigators have suggested the presence and importance of secondary structural elements within lncRNAs, but mammalian lncRNA secondary structure remains poorly understood. It is intriguing to speculate that in this group of genes, RNA secondary structures might be preserved throughout evolution and that this might explain the lack of sequence conservation among many lncRNAs. SCOPE OF REVIEW Here, we review the extent of interspecies conservation among different lncRNAs, with a focus on a subset of lncRNAs that have been functionally investigated. The function of lncRNAs is widespread and we investigate whether different forms of functionalities may be conserved. MAJOR CONCLUSIONS Lack of conservation does not imbue a lack of function. We highlight several examples of lncRNAs where RNA structure appears to be the main functional unit and evolutionary constraint. We survey existing genomewide studies of mammalian lncRNA conservation and summarize their limitations. We further review specific human lncRNAs which lack evolutionary conservation beyond primates but have proven to be both functional and therapeutically relevant. GENERAL SIGNIFICANCE Pioneering studies highlight a role in lncRNAs for secondary structures, and possibly the presence of functional "modules", which are interspersed with longer and less conserved stretches of nucleotide sequences. Taken together, high-throughput analysis of conservation and functional composition of the still-mysterious lncRNA genes is only now becoming feasible.
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Affiliation(s)
- Per Johnsson
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Leonard Lipovich
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA; Department of Neurology, Wayne State University School of Medicine, Detriot, MI, USA
| | - Dan Grandér
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Kevin V Morris
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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An HIV-encoded antisense long noncoding RNA epigenetically regulates viral transcription. Mol Ther 2014; 22:1164-1175. [PMID: 24576854 DOI: 10.1038/mt.2014.29] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 02/20/2014] [Indexed: 12/23/2022] Open
Abstract
The abundance of long noncoding RNAs (lncRNAs) and their wide range of functional roles in human cells are fast becoming realized. Importantly, lncRNAs have been identified as epigenetic modulators and consequently play a pivotal role in the regulation of gene expression. A human immunodeficiency virus-encoded antisense RNA transcript has recently been reported and we sought to characterize this RNA and determine its potential role in viral transcription regulation. The intrinsic properties of this human immunodeficiency virus-expressed lncRNA were characterized and the data presented here suggest that it functions as an epigenetic brake to modulate viral transcription. Suppression of this long antisense transcript with small single-stranded antisense RNAs resulted in the activation of viral gene expression. This lncRNA was found to localize to the 5' long-term repeats (LTR) and to usurp components of endogenous cellular pathways that are involved in lncRNA directed epigenetic gene silencing. Collectively, we find that this viral expressed antisense lncRNA is involved in modulating human immunodeficiency virus gene expression and that this regulatory effect is due to an alteration in the epigenetic landscape at the viral promoter.
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Abstract
A growing body of evidence suggests that noncoding RNA (ncRNA) transcripts play a fundamental role in regulating gene expression via targeting epigenetic modifications to particular loci in the genome. Classical examples of such regulation are X-chromosome inactivation and genomic imprinting; however it is now clear that ncRNAs exert their influence over a wider array of genes throughout the metazoan genome. Accumulating evidence suggests that the ncRNAs act as guides for epigenetic silencing complexes to specific sites within the genome. Those ncRNAs involved in regulating the expression of particular protein-coding genes offer panoply of targets that when suppressed can result in derepression or activation of the ncRNA-targeted locus. Recent work has determined the underlying mechanisms involved in ncRNA-targeted epigenetic regulation in a subset of genes. These findings have resulted in a paradigm shift whereby targeted gene activation can be achieved, by targeting endogenous regulatory ncRNAs, producing potential novel treatments for genetic and infectious diseases where increases in gene expression are required.
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Affiliation(s)
- Caio Damski
- Biotechnology and Biomedical Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia,
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Tabolacci E, Chiurazzi P. Epigenetics, fragile X syndrome and transcriptional therapy. Am J Med Genet A 2013; 161A:2797-808. [PMID: 24123753 DOI: 10.1002/ajmg.a.36264] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 09/06/2013] [Indexed: 12/13/2022]
Abstract
Epigenetics refers to the study of heritable changes in gene expression that occur without a change in DNA sequence. Epigenetic mechanisms therefore include all transcriptional controls that determine how genes are expressed during development and differentiation, but also in individual cells responding to environmental stimuli. The purpose of this review is to examine the basic principles of epigenetic mechanisms and their contribution to human disorders with a particular focus on fragile X syndrome (FXS), the most common monogenic form of developmental cognitive impairment. FXS represents a prototype of the so-called repeat expansion disorders due to "dynamic" mutations, namely the expansion (known as "full mutation") of a CGG repeat in the 5'UTR of the FMR1 gene. This genetic anomaly is accompanied by epigenetic modifications (mainly DNA methylation and histone deacetylation), resulting in the inactivation of the FMR1 gene. The presence of an intact FMR1 coding sequence allowed pharmacological reactivation of gene transcription, particularly through the use of the DNA demethylating agent 5'-aza-2'-deoxycytydine and/or inhibitors of histone deacetylases. These treatments suggested that DNA methylation is dominant over histone acetylation in silencing the FMR1 gene. The importance of DNA methylation in repressing FMR1 transcription is confirmed by the existence of rare unaffected males carrying unmethylated full mutations. Finally, we address the potential use of epigenetic approaches to targeted treatment of other genetic conditions.
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