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Koopmans PJ, Ismaeel A, Goljanek-Whysall K, Murach KA. The roles of miRNAs in adult skeletal muscle satellite cells. Free Radic Biol Med 2023; 209:228-238. [PMID: 37879420 PMCID: PMC10911817 DOI: 10.1016/j.freeradbiomed.2023.10.403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/16/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023]
Abstract
Satellite cells are bona fide muscle stem cells that are indispensable for successful post-natal muscle growth and regeneration after severe injury. These cells also participate in adult muscle adaptation in several capacities. MicroRNAs (miRNAs) are post-transcriptional regulators of mRNA that are implicated in several aspects of stem cell function. There is evidence to suggest that miRNAs affect satellite cell behavior in vivo during development and myogenic progenitor behavior in vitro, but the role of miRNAs in adult skeletal muscle satellite cells is less studied. In this review, we provide evidence for how miRNAs control satellite cell function with emphasis on satellite cells of adult skeletal muscle in vivo. We first outline how miRNAs are indispensable for satellite cell viability and control the phases of myogenesis. Next, we discuss the interplay between miRNAs and myogenic cell redox status, senescence, and communication to other muscle-resident cells during muscle adaptation. Results from recent satellite cell miRNA profiling studies are also summarized. In vitro experiments in primary myogenic cells and cell lines have been invaluable for exploring the influence of miRNAs, but we identify a need for novel genetic tools to further interrogate how miRNAs control satellite cell behavior in adult skeletal muscle in vivo.
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Affiliation(s)
- Pieter Jan Koopmans
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, 72701, USA; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Ahmed Ismaeel
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, 40506, USA
| | - Katarzyna Goljanek-Whysall
- School of Medicine, College of Medicine, Nursing, and Health Sciences, University of Galway, Galway, Ireland
| | - Kevin A Murach
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, 72701, USA; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA.
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2
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Luo J, Ji Y, Chen N, Song G, Zhou S, Niu X, Yu D. Nuclear miR-150 enhances hepatic lipid accumulation by targeting RNA transcripts overlapping the PLIN2 promoter. iScience 2023; 26:107837. [PMID: 37736048 PMCID: PMC10509351 DOI: 10.1016/j.isci.2023.107837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/09/2023] [Accepted: 09/02/2023] [Indexed: 09/23/2023] Open
Abstract
Alcohol-associated liver disease is a prevalent chronic liver disease caused by excessive ethanol consumption. This study aims to investigate the role of miR-150 in regulating hepatic lipid homeostasis in alcoholic fatty liver (AFL). miR-150 was mainly distributed in the nucleus of hepatocytes and correlated with the degree of liver injury. The decreased expression of miR-150 observed in AFL was a compensatory response to ethanol-induced hepatic steatosis. Overexpression of miR-150 facilitated hepatic lipid accumulation in cellulo and exacerbated ethanol-induced liver steatosis in vivo. In silico analysis identified perilipin-2 (PLIN2) as a potential target gene of miR-150. miR-150 activated PLIN2 transcription by directly binding the RNA transcripts overlapping PLIN2 promoter and facilitating the recruitment of DNA helicase DHX9 and RNA polymeraseⅡ. Overall, our study provides fresh insights into the homeostasis regulation of hepatic steatosis induced by ethanol and identifies miR-150 as a pro-steatosis effector driving transcriptional PLIN2 gene activation.
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Affiliation(s)
- Jiao Luo
- School of Public Health, Qingdao University, Qingdao, China
| | - Yanan Ji
- School of Public Health, Qingdao University, Qingdao, China
| | - Ningning Chen
- School of Public Health, Qingdao University, Qingdao, China
| | - Ge Song
- School of Public Health, Qingdao University, Qingdao, China
| | - Shuyue Zhou
- School of Public Health, Qingdao University, Qingdao, China
| | - Xuan Niu
- School of Public Health, Qingdao University, Qingdao, China
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao, China
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3
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Tedford E, Badya NB, Laing C, Asaoka N, Kaneko S, Filippi BM, McConkey GA. Infection-induced extracellular vesicles evoke neuronal transcriptional and epigenetic changes. Sci Rep 2023; 13:6913. [PMID: 37106020 PMCID: PMC10140046 DOI: 10.1038/s41598-023-34074-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/24/2023] [Indexed: 04/29/2023] Open
Abstract
Infection with the protozoan Toxoplasma gondii induces changes in neurotransmission, neuroinflammation, and behavior, yet it remains elusive how these changes come about. In this study we investigated how norepinephrine levels are altered by infection. TINEV (Toxoplasma-induced neuronal extracellular vesicles) isolated from infected noradrenergic cells down-regulated dopamine ß-hydroxylase (DBH) gene expression in human and rodent cells. Here we report that intracerebral injection of TINEVs into the brain is sufficient to induce DBH down-regulation and distrupt catecholaminergic signalling. Further, TINEV treatment induced hypermethylation upstream of the DBH gene. An antisense lncRNA to DBH was found in purified TINEV preparations. Paracrine signalling to induce transcriptional gene silencing and DNA methylation may be a common mode to regulate neurologic function.
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Affiliation(s)
- Ellen Tedford
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Norhidayah Binti Badya
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Conor Laing
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Nozomi Asaoka
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-Cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shuji Kaneko
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-Cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Beatrice Maria Filippi
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Glenn Alan McConkey
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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4
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Alvanou M, Lysandrou M, Christophi P, Psatha N, Spyridonidis A, Papadopoulou A, Yannaki E. Empowering the Potential of CAR-T Cell Immunotherapies by Epigenetic Reprogramming. Cancers (Basel) 2023; 15:cancers15071935. [PMID: 37046597 PMCID: PMC10093039 DOI: 10.3390/cancers15071935] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
T-cell-based, personalized immunotherapy can nowadays be considered the mainstream treatment for certain blood cancers, with a high potential for expanding indications. Chimeric antigen receptor T cells (CAR-Ts), an ex vivo genetically modified T-cell therapy product redirected to target an antigen of interest, have achieved unforeseen successes in patients with B-cell hematologic malignancies. Frequently, however, CAR-T cell therapies fail to provide durable responses while they have met with only limited success in treating solid cancers because unique, unaddressed challenges, including poor persistence, impaired trafficking to the tumor, and site penetration through a hostile microenvironment, impede their efficacy. Increasing evidence suggests that CAR-Ts' in vivo performance is associated with T-cell intrinsic features that may be epigenetically altered or dysregulated. In this review, we focus on the impact of epigenetic regulation on T-cell differentiation, exhaustion, and tumor infiltration and discuss how epigenetic reprogramming may enhance CAR-Ts' memory phenotype, trafficking, and fitness, contributing to the development of a new generation of potent CAR-T immunotherapies.
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Affiliation(s)
- Maria Alvanou
- Hematology Department-Hematopoietic Cell Transplantation Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, 570 10 Thessaloniki, Greece
- Bone Marrow Transplantation Unit, Institute of Cell Therapy, University of Patras, 265 04 Rio, Greece
| | - Memnon Lysandrou
- Bone Marrow Transplantation Unit, Institute of Cell Therapy, University of Patras, 265 04 Rio, Greece
| | - Panayota Christophi
- Hematology Department-Hematopoietic Cell Transplantation Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, 570 10 Thessaloniki, Greece
- Bone Marrow Transplantation Unit, Institute of Cell Therapy, University of Patras, 265 04 Rio, Greece
| | - Nikoleta Psatha
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 570 10 Thessaloniki, Greece
| | - Alexandros Spyridonidis
- Bone Marrow Transplantation Unit, Institute of Cell Therapy, University of Patras, 265 04 Rio, Greece
| | - Anastasia Papadopoulou
- Hematology Department-Hematopoietic Cell Transplantation Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, 570 10 Thessaloniki, Greece
| | - Evangelia Yannaki
- Hematology Department-Hematopoietic Cell Transplantation Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, 570 10 Thessaloniki, Greece
- Department of Medicine, University of Washington, Seattle, WA 98195-2100, USA
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5
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Singh S, Chaurasia S. Recent and Evolving Therapies in the Management of Endothelial Diseases. Semin Ophthalmol 2023; 38:207-215. [PMID: 36582139 DOI: 10.1080/08820538.2022.2152717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Corneal endothelium is the innermost layer of the cornea which has both barrier and pump function and very important to maintain cornea clarity. Unlike epithelium, endothelium does not have regenerative potential; hence, endothelial damage or dysfunction could lead to corneal edema and visual impairment. Advanced corneal transplantation which involves selective replacement of dysfunctional endothelium has led to improved and faster visual rehabilitation. But in recent times, alternative therapies in the management of corneal edema and endothelial diseases have been reported. In this review, we aim to give a comprehensive review of various strategies for the management of corneal endothelial dysfunction in order to give treatment which is precisely tailored for each individual patient. A review of all peer-reviewed publications on novel strategies for the management of endothelial dysfunction was performed. The various approaches to the management of endothelial dysfunction are compared and discussed. Shortage of human donor corneas globally is fuelling the search for keratoplasty alternatives. Corneal endothelial dysfunction can be caused following surgery, laser or corneal endothelial dystrophies which could be amenable to treatment with pharmacological, biological intervention and reverse the endothelial dysfunction in the early stages of endothelial failure. Pharmacological and surgical intervention are helpful in cases of good peripheral endothelial cell reserve, and advanced cases of endothelial cell dysfunction can be targeted with cell culture therapies, gene therapy and artificial implant. Treatment strategies which target endothelial dysfunction, especially FECD in its early stages, and gene therapy are rapidly evolving. Therapies which delay endothelial keratoplasty also are evolving like DSO and need more studies of long-term follow-up and patient selection criteria.
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Affiliation(s)
- Shalini Singh
- Academy of Eye Care Education, L V Prasad Eye Institute, Hyderabad, India.,The Cornea Institute, L V Prasad Eye Institute, Hyderabad, India
| | - Sunita Chaurasia
- The Cornea Institute, L V Prasad Eye Institute, Hyderabad, India
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6
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Small Interfering RNAs Targeting a Chromatin-Associated RNA Induce Its Transcriptional Silencing in Human Cells. Mol Cell Biol 2022; 42:e0027122. [PMID: 36445136 PMCID: PMC9753735 DOI: 10.1128/mcb.00271-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Transcriptional gene silencing by small interfering RNAs (siRNAs) has been widely described in various species, including plants and yeast. In mammals, its extent remains somewhat debated. Previous studies showed that siRNAs targeting gene promoters could induce the silencing of the targeted promoter, although the involvement of off-target mechanisms was also suggested. Here, by using nascent RNA capture and RNA polymerase II chromatin immunoprecipitation, we show that siRNAs targeting a chromatin-associated noncoding RNA induced its transcriptional silencing. Deletion of the sequence targeted by one of these siRNAs on the two alleles by genome editing further showed that this silencing was due to base-pairing of the siRNA to the target. Moreover, by using cells with heterozygous deletion of the target sequence, we showed that only the wild-type allele, but not the deleted allele, was silenced by the siRNA, indicating that transcriptional silencing occurred only in cis. Finally, we demonstrated that both Ago1 and Ago2 are involved in this transcriptional silencing. Altogether, our data demonstrate that siRNAs targeting a chromatin-associated RNA at a distance from its promoter induce its transcriptional silencing. Our results thus extend the possible repertoire of endogenous or exogenous interfering RNAs.
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7
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Rodriguez FD. Targeting Epigenetic Mechanisms to Treat Alcohol Use Disorders (AUD). Curr Pharm Des 2021; 27:3252-3272. [PMID: 33535943 PMCID: PMC8778698 DOI: 10.2174/1381612827666210203142539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/08/2020] [Indexed: 12/04/2022]
Abstract
BACKGROUND The impact of abusive alcohol consumption on human health is remarkable. According to the World Health Organization (WHO), approximately 3.3 million people die annually because of harmful alcohol consumption (the figure represents around 5.9% of global deaths). Alcohol Use Disorder (AUD) is a chronic disease where individuals exhibit compulsive alcohol drinking and present negative emotional states when they do not drink. In the most severe manifestations of AUD, the individuals lose control over intake despite a decided will to stop drinking. Given the multiple faces and the specific forms of this disease, the term AUD often appears in the plural (AUDs). Since only a few approved pharmacological treatments are available to treat AUD and they do not apply to all individuals or AUD forms, the search for compounds that may help to eliminate the burden of the disease and complement other therapeutical approaches is necessary. METHODS This work reviews recent research focused on the involvement of epigenetic mechanisms in the pathophysiology of AUD. Excessive drinking leads to chronic and compulsive consumption that eventually damages the organism. The central nervous system is a key target and is the focus of this study. The search for the genetic and epigenetic mechanisms behind the intricated dysregulation induced by ethanol will aid researchers in establishing new therapy approaches. CONCLUSION Recent findings in the field of epigenetics are essential and offer new windows for observation and research. The study of small molecules that inhibit key epienzymes involved in nucleosome architecture dynamics is necessary in order to prove their action and specificity in the laboratory and to test their effectivity and safety in clinical trials with selected patients bearing defined alterations caused by ethanol.
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Affiliation(s)
- F. David Rodriguez
- Department of Biochemistry and Molecular Biology, Faculty of Chemistry, University of Salamanca and Group GIR BMD (Bases Moleculares del Desarrollo), University of Salamanca, Salamanca, Spain
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8
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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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9
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Korpela H, Järveläinen N, Siimes S, Lampela J, Airaksinen J, Valli K, Turunen M, Pajula J, Nurro J, Ylä-Herttuala S. Gene therapy for ischaemic heart disease and heart failure. J Intern Med 2021; 290:567-582. [PMID: 34033164 DOI: 10.1111/joim.13308] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/27/2022]
Abstract
Gene therapy has been expected to become a novel treatment method since the structure of DNA was discovered in 1953. The morbidity from cardiovascular diseases remains remarkable despite the improvement of percutaneous interventions and pharmacological treatment, underlining the need for novel therapeutics. Gene therapy-mediated therapeutic angiogenesis could help those who have not gained sufficient symptom relief with traditional treatment methods. Especially patients with severe coronary artery disease and heart failure could benefit from gene therapy. Some clinical trials have reported improved myocardial perfusion and symptom relief in CAD patients, but few trials have come up with disappointing negative results. Translating preclinical success into clinical applications has encountered difficulties in successful transduction, study design, endpoint selection, and patient selection and recruitment. However, promising new methods for transducing the cells, such as retrograde delivery and cardiac-specific AAV vectors, hold great promise for myocardial gene therapy. This review introduces gene therapy for ischaemic heart disease and heart failure and discusses the current status and future developments in this field.
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Affiliation(s)
- H Korpela
- From the, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - N Järveläinen
- From the, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - S Siimes
- From the, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - J Lampela
- From the, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - J Airaksinen
- From the, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - K Valli
- From the, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - M Turunen
- From the, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - J Pajula
- From the, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - J Nurro
- From the, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - S Ylä-Herttuala
- From the, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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10
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Akbari B, Ghahri-Saremi N, Soltantoyeh T, Hadjati J, Ghassemi S, Mirzaei HR. Epigenetic strategies to boost CAR T cell therapy. Mol Ther 2021; 29:2640-2659. [PMID: 34365035 DOI: 10.1016/j.ymthe.2021.08.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/19/2021] [Accepted: 07/31/2021] [Indexed: 02/08/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy has led to a paradigm shift in cancer immunotherapy, but still several obstacles limit CAR T cell efficacy in cancers. Advances in high-throughput technologies revealed new insights into the role that epigenetic reprogramming plays in T cells. Mechanistic studies as well as comprehensive epigenome maps revealed an important role for epigenetic remodeling in T cell differentiation. These modifications shape the overall immune response through alterations in T cell phenotype and function. Here, we outline how epigenetic modifications in CAR T cells can overcome barriers limiting CAR T cell effectiveness, particularly in immunosuppressive tumor microenvironments. We also offer our perspective on how selected epigenetic modifications can boost CAR T cells to ultimately improve the efficacy of CAR T cell therapy.
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Affiliation(s)
- Behnia Akbari
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Navid Ghahri-Saremi
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Tahereh Soltantoyeh
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Jamshid Hadjati
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Saba Ghassemi
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran.
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Nowak I, Sarshad AA. Argonaute Proteins Take Center Stage in Cancers. Cancers (Basel) 2021; 13:cancers13040788. [PMID: 33668654 PMCID: PMC7918559 DOI: 10.3390/cancers13040788] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary The dysregulation of RNA interference (RNAi) has often been observed in cancers, where the main focus of research has been on the small RNA molecules directing RNAi. In this review, we focus on the activity of Argonaute proteins, central components of RNAi, in tumorigenesis, and also highlight their potential applications in grading tumors and anti-cancer therapies. Abstract Argonaute proteins (AGOs) play crucial roles in RNA-induced silencing complex (RISC) formation and activity. AGOs loaded with small RNA molecules (miRNA or siRNA) either catalyze endoribonucleolytic cleavage of target RNAs or recruit factors responsible for translational silencing and target destabilization. miRNAs are well characterized and broadly studied in tumorigenesis; nevertheless, the functions of the AGOs in cancers have lagged behind. Here, we discuss the current state of knowledge on the role of AGOs in tumorigenesis, highlighting canonical and non-canonical functions of AGOs in cancer cells, as well as the biomarker potential of AGO expression in different of tumor types. Furthermore, we point to the possible application of the AGOs in development of novel therapeutic approaches.
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Affiliation(s)
- Iwona Nowak
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Aishe A. Sarshad
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
- Correspondence:
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Zhang B, Han X, Gao Q, Liu J, Li S, Zha W, Wang X, Guo X, Gao D. Enhancer II-targeted dsRNA decreases GDNF expression via histone H3K9 trimethylation to inhibit glioblastoma progression. Brain Res Bull 2020; 167:22-32. [PMID: 33278485 DOI: 10.1016/j.brainresbull.2020.11.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/01/2020] [Accepted: 11/30/2020] [Indexed: 11/18/2022]
Abstract
BACKGROUND Glial cell line-derived neurotrophic factor (GDNF) is expressed in both astrocytes and glioblastoma (GBM) cells. GDNF expression is significantly increased in GBM, and inhibiting its expression can retard GBM progression. However, there is no known method for specific inhibition of GDNF in GBM cells. METHODS Promoter-targeted dsRNA-induced transcriptional gene silencing or activation was recently achieved in human cells. This approach has the potential to specifically regulate gene transcription via epigenetic modifications. In this study, we designed six candidate dsRNAs targeting the enhancer or silencer in GDNF gene promoter II to check their effects on GDNF transcription and GBM progression. RESULTS Among these dsRNAs, enhancer II-targeted dsRNA significantly inhibited U251 GBM progression by downregulating GDNF (P < 0.05), while silencer II-targeted dsRNA exerted an opposite effect. Moreover, enhancer II-targeted dsRNA did not significantly change GDNF expression in human astrocytes (HA) and the proliferation and migration of HA cells (P > 0.05). Bisulfate PCR and chromatin immunoprecipitation analyses revealed that both DNA methylation and trimethylation of histone 3 at lysine 9 (H3K9me3) at silencer II-targeted region significantly increased, and H3K9me3 at enhancer II-targeted region significantly decreased, in U251 cells compared with HA cells in non-intervention condition (P < 0.05). Both enhancer II- and silencer II-targeted dsRNA significantly increased H3K9me3 methylation rather than DNA at the targeted site in U251 cells (P < 0.05). The expression and activity of histone methyltransferase SETDB1 increased dramatically in U251 cells compared with HA cells, and it was recruited to enhancer II targeting region after enhancer II-targeted dsRNA treatment in U251 cells (P < 0.05). CONCLUSIONS Our results demonstrate that a promoter-targeted dsRNA can silence or promote gene transcription depending on its targeted site in different cis-acting elements in the gene promoter. Targeted inhibition of GDNF by enhancer II-targeted dsRNA may be explored as a novel treatment for GBM.
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Affiliation(s)
- Baole Zhang
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu Province, China.
| | - Xiao Han
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu Province, China
| | - Qing Gao
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu Province, China
| | - Jie Liu
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu Province, China
| | - Saisai Li
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu Province, China
| | - Wei Zha
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu Province, China
| | - Xiaoyu Wang
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu Province, China
| | - Xiaoxiao Guo
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu Province, China
| | - Dianshuai Gao
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu Province, China.
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13
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Natural antisense transcripts in the biological hallmarks of cancer: powerful regulators hidden in the dark. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:187. [PMID: 32928281 PMCID: PMC7490906 DOI: 10.1186/s13046-020-01700-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/04/2020] [Indexed: 02/06/2023]
Abstract
Natural antisense transcripts (NATs), which are transcribed from opposite strands of DNA with partial or complete overlap, affect multiple stages of gene expression, from epigenetic to post-translational modifications. NATs are dysregulated in various types of cancer, and an increasing number of studies focusing on NATs as pivotal regulators of the hallmarks of cancer and as promising candidates for cancer therapy are just beginning to unravel the mystery. Here, we summarize the existing knowledge on NATs to highlight their underlying mechanisms of functions in cancer biology, discuss their potential roles in therapeutic application, and explore future research directions.
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14
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Li X, Wang X, Cheng Z, Zhu Q. AGO2 and its partners: a silencing complex, a chromatin modulator, and new features. Crit Rev Biochem Mol Biol 2020; 55:33-53. [DOI: 10.1080/10409238.2020.1738331] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Xiaojing Li
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Xueying Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Zeneng Cheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
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Abstract
Non-communicable diseases (NCD) such as type-2 diabetes and CVD are now highly prevalent in both developed and developing countries. Evidence from both human and animal studies shows that early-life nutrition is an important determinant of NCD risk in later life. The mechanism by which the early-life environment influences future disease risk has been suggested to include the altered epigenetic regulation of gene expression. Epigenetic processes regulate the accessibility of genes to the cellular proteins that control gene transcription, determining where and when a gene is switched on and its level of activity. Epigenetic processes not only play a central role in regulating gene expression but also allow an organism to adapt to the environment. In this review, we will focus on how both maternal and paternal nutrition can alter the epigenome and the evidence that these changes are causally involved in determining future disease risk.
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Affiliation(s)
- Mark A Burton
- Academic Unit of Human Development and Health, Faculty of Medicine,University of Southampton,Southampton,UK
| | - Karen A Lillycrop
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences,University of Southampton,Southampton,UK
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16
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Ren X, Yu Y, Li H, Huang J, Zhou A, Liu S, Hu P, Li B, Qi W, Liao M. Avian Influenza A Virus Polymerase Recruits Cellular RNA Helicase eIF4A3 to Promote Viral mRNA Splicing and Spliced mRNA Nuclear Export. Front Microbiol 2019; 10:1625. [PMID: 31379779 PMCID: PMC6646474 DOI: 10.3389/fmicb.2019.01625] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/01/2019] [Indexed: 01/16/2023] Open
Abstract
The influenza A virus replicates in a broad range of avian and mammalian species by hijacking cellular factors and processes. Avian influenza A viruses (AIVs) generally propagated poorly in mammalian cells, but some mutants of virus-encoded RNA polymerase components, especially PB2 subunit, can overcome host restriction. Host factors associated with PB2 may be essential for efficient AIV replication in mammalian cells. Here, we infected human cells with the PB2 Flag-tagged replication-competent recombinant AIV and identified cellular proteins that coprecipitate with PB2 protein by mass spectrometry. We confirmed one of the coprecipitating host factors, DEAD-box protein eIF4A3, that interacts with viral PB2, PB1, and NP proteins. Depletion of endogenous eIF4A3 significantly reduced virus replication. Later studies showed that eIF4A3 is essential for viral RNA polymerase activity and viral RNAs synthesis. Upon systematic dissection of the influenza virus progeny mRNA generation, from pre-mRNA processing to nuclear export, we found that the depletion of eIF4A3 resulted in significant defects in the ratio of M2 to M1 and NS2 to NS1, and the proportion of viral spliced mRNA in the nucleus increased, indicating that eIF4A3 plays a significant function in viral nascent intron mRNA splicing and spliced mRNA (M2 and NS2) nuclear export. Additionally, we confirmed that in specific deletion of eIF4A3, the synthesis of reduced NS2 can significantly impair neo-synthetized viral ribonucleoprotein (vRNP) nuclear export. Taken together, our findings revealed that eIF4A3 is a key mediator of AIV polymerase activity, mRNA splicing, and spliced mRNA nuclear export.
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Affiliation(s)
- Xingxing Ren
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yuandi Yu
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Huanan Li
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jinyu Huang
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Aobaixue Zhou
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Shukai Liu
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Pingsheng Hu
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Bo Li
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wenbao Qi
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Ming Liao
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
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17
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Abstract
Small RNAs govern almost every biological process in eukaryotes associating with the Argonaute (AGO) proteins to form the RNA-induced silencing complex (mRISC). AGO proteins constitute the core of RISCs with different members having variety of protein-binding partners and biochemical properties. This review focuses on the AGO subfamily of the AGOs that are ubiquitously expressed and are associated with small RNAs. The structure, function and role of the AGO proteins in the cell is discussed in detail.
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Affiliation(s)
- Saife Niaz
- Department of Biotechnology, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
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18
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Baltusnikas J, Satkauskas S, Lundstrom K. Constructing RNA Viruses for Long-Term Transcriptional Gene Silencing. Trends Biotechnol 2019; 37:20-28. [DOI: 10.1016/j.tibtech.2018.07.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 10/28/2022]
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19
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Fan B, Luk AOY, Chan JCN, Ma RCW. MicroRNA and Diabetic Complications: A Clinical Perspective. Antioxid Redox Signal 2018; 29:1041-1063. [PMID: 28950710 DOI: 10.1089/ars.2017.7318] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SIGNIFICANCE The rising global prevalence of diabetes and its debilitating complications give rise to significant disability and premature mortality. Due to the silent nature of diabetes and its vascular complications, and limitations in current methods for detection, there is a need for novel biomarkers for early detection and prognosis. Recent Advances: Metabolic memory and epigenetic factors are important in the pathogenesis of diabetic complications and interact with genetic variants, metabolic factors, and clinical risk factors. Micro(mi)RNAs interact with epigenetic mechanisms and pleiotropically mediate the effects of hyperglycemia on the vasculature. Utilizing mature profiling techniques and platforms, an increasing number of miRNA signatures and interaction networks have been identified for diabetes and its related cardiorenal complications. As a result, these short, single-stranded molecules are emerging as potential diagnostic and predictive tools in human studies, and may function as disease biomarkers, as well as treatment targets. CRITICAL ISSUES However, there is complex interaction between the genome and epigenome. The regulation of miRNAs may differ across species and tissues. Most profiling studies to date lack validation, often requiring large, well-characterized cohorts and reliable normalization strategies. Furthermore, the incremental benefits of miRNAs as biomarkers, beyond prediction provided by traditional risk factors, are critical issues to consider, yet often neglected in published studies. FUTURE DIRECTIONS All in all, the future for miRNA-based diagnostics and therapeutics for diabetic complications appears promising. Improved understanding of the complex mechanisms underlying miRNA dysregulation, and more well-designed studies utilizing prospective samples would facilitate the translation to clinical use.
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Affiliation(s)
- Baoqi Fan
- 1 Department of Medicine and Therapeutics, The Chinese University of Hong Kong , Shatin, China
| | - Andrea On Yan Luk
- 1 Department of Medicine and Therapeutics, The Chinese University of Hong Kong , Shatin, China .,2 Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong , Shatin, China
| | - Juliana Chung Ngor Chan
- 1 Department of Medicine and Therapeutics, The Chinese University of Hong Kong , Shatin, China .,2 Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong , Shatin, China .,3 Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong , Prince of Wales Hospital, Shatin, China .,4 The Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine , Shatin, China
| | - Ronald Ching Wan Ma
- 1 Department of Medicine and Therapeutics, The Chinese University of Hong Kong , Shatin, China .,2 Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong , Shatin, China .,3 Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong , Prince of Wales Hospital, Shatin, China .,4 The Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine , Shatin, China
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20
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Ma XX, Ma Z, Pan Q. The Challenges of Long-Term Transcriptional Gene Silencing by RNA Viruses. Trends Biochem Sci 2018; 43:649-650. [PMID: 30041840 DOI: 10.1016/j.tibs.2018.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/13/2018] [Accepted: 06/29/2018] [Indexed: 11/25/2022]
Abstract
Since the past few decades, the small RNA (sRNA) technologies including small interfering RNA and miRNA have been widely explored for therapeutic development. Classically, these sRNAs target the coding regions of mRNA to exert temporal gene silencing in a post-transcriptional manner. Interestingly, sRNAs targeting gene promoters have been recently described to mediate long-term transcriptional gene silencing (TGS) by epigenetic modifications. This has further harnessed the potential applications in gene therapy. However, efficient delivery is a common hurdle for almost any types of gene therapy approaches. In a recent issue of Trends in Biochemical Sciences, Baltusnikas et al. have proposed to use RNA viruses to deliver sRNA for long-term TGS, suggesting long-term therapy by a single administration approach for various diseases, including chronic, incurable, and fatal illnesses. Being a novel and ambitious gene therapy strategy, we hereby would like to emphasize three major challenges and propose potential solutions.
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Affiliation(s)
- Xiao-Xia Ma
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China; Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Zhongren Ma
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Qiuwei Pan
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China; Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands.
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21
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Costello KR, Schones DE. Chromatin modifications in metabolic disease: Potential mediators of long-term disease risk. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2018; 10:e1416. [PMID: 29369528 PMCID: PMC6002879 DOI: 10.1002/wsbm.1416] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/30/2017] [Accepted: 12/08/2017] [Indexed: 12/29/2022]
Abstract
Metabolic diseases such as obesity and diabetes are complex diseases resulting from multiple genetic and environmental factors, such as diet and activity levels. These factors are well known contributors to the development of metabolic diseases. One manner by which environmental factors can influence metabolic disease progression is through modifications to chromatin. These modifications can lead to altered gene regulatory programs, which alters disease risk. Furthermore, there is evidence that parents exposed to environmental factors can influence the metabolic health of offspring, especially if exposures are during intrauterine growth periods. In this review, we outline the evidence that chromatin modifications are associated with metabolic diseases, including diabetes and obesity. We also consider evidence that these chromatin modifications can lead to long-term disease risk and contribute to disease risk for future generations. This article is categorized under: Biological Mechanisms > Metabolism Developmental Biology > Developmental Processes in Health and Disease Physiology > Organismal Responses to Environment.
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Affiliation(s)
- Kevin R. Costello
- Department of Diabetes Complications and MetabolismIrell & Manella Graduate School, City of HopeDuarteCalifornia
| | - Dustin E. Schones
- Department of Diabetes Complications and MetabolismIrell & Manella Graduate School, City of HopeDuarteCalifornia
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22
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Long-Term Transcriptional Gene Silencing by RNA Viruses. Trends Biochem Sci 2018; 43:397-401. [DOI: 10.1016/j.tibs.2018.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 03/09/2018] [Accepted: 03/12/2018] [Indexed: 01/16/2023]
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23
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Yu D, Ma X, Zuo Z, Wang H, Meng Y. Classification of Transcription Boundary-Associated RNAs (TBARs) in Animals and Plants. Front Genet 2018; 9:168. [PMID: 29868116 PMCID: PMC5960741 DOI: 10.3389/fgene.2018.00168] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/26/2018] [Indexed: 11/13/2022] Open
Abstract
There is increasing evidence suggesting the contribution of non-coding RNAs (ncRNAs) to the phenotypic and physiological complexity of organisms. A novel ncRNA species has been identified near the transcription boundaries of protein-coding genes in eukaryotes, bacteria, and archaea. This review provides a detailed description of these transcription boundary-associated RNAs (TBARs), including their classification. Based on their genomic distribution, TBARs are divided into two major groups: promoter-associated RNAs (PARs) and terminus-associated RNAs (TARs). Depending on the sequence length, each group is further classified into long RNA species (>200 nt) and small RNA species (<200 nt). According to these rules of TBAR classification, divergent ncRNAs with confusing nomenclatures, such as promoter upstream transcripts (PROMPTs), upstream antisense RNAs (uaRNAs), stable unannotated transcripts (SUTs), cryptic unstable transcripts (CUTs), upstream non-coding transcripts (UNTs), transcription start site-associated RNAs (TSSaRNAs), transcription initiation RNAs (tiRNAs), and transcription termination site-associated RNAs (TTSaRNAs), were assigned to specific classes. Although the biogenesis pathways of PARs and TARs have not yet been clearly elucidated, previous studies indicate that some of the PARs have originated either through divergent transcription or via RNA polymerase pausing. Intriguing findings regarding the functional implications of the TBARs such as the long-range “gene looping” model, which explains their role in the transcriptional regulation of protein-coding genes, are also discussed. Altogether, this review provides a comprehensive overview of the current research status of TBARs, which will promote further investigations in this research area.
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Affiliation(s)
- Dongliang Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaoxia Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Ziwei Zuo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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24
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Cheng Y, Monteiro C, Matos A, You J, Fraga A, Pereira C, Catalán V, Rodríguez A, Gómez-Ambrosi J, Frühbeck G, Ribeiro R, Hu P. Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity-a pilot study. Clin Epigenetics 2018; 10:54. [PMID: 29692867 PMCID: PMC5904983 DOI: 10.1186/s13148-018-0490-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/05/2018] [Indexed: 12/12/2022] Open
Abstract
Background Periprostatic adipose tissue (PPAT) has been recognized to associate with prostate cancer (PCa) aggressiveness and progression. Here, we sought to investigate whether excess adiposity modulates the methylome of PPAT in PCa patients. DNA methylation profiling was performed in PPAT from obese/overweight (OB/OW, BMI > 25 kg m−2) and normal weight (NW, BMI < 25 kg m−2) PCa patients. Significant differences in methylated CpGs between OB/OW and NW groups were inferred by statistical modeling. Results Five thousand five hundred twenty-six differentially methylated CpGs were identified between OB/OW and NW PCa patients with 90.2% hypermethylated. Four hundred eighty-three of these CpGs were found to be located at both promoters and CpG islands, whereas the representing 412 genes were found to be involved in pluripotency of stem cells, fatty acid metabolism, and many other biological processes; 14 of these genes, particularly FADS1, MOGAT1, and PCYT2, with promoter hypermethylation presented with significantly decreased gene expression in matched samples. Additionally, 38 genes were correlated with antigen processing and presentation of endogenous antigen via MHC class I, which might result in fatty acid accumulation in PPAT and tumor immune evasion. Conclusions Results showed that the whole epigenome methylation profiles of PPAT were significantly different in OB/OW compared to normal weight PCa patients. The epigenetic variation associated with excess adiposity likely resulted in altered lipid metabolism and immune dysregulation, contributing towards unfavorable PCa microenvironment, thus warranting further validation studies in larger samples. Electronic supplementary material The online version of this article (10.1186/s13148-018-0490-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Cheng
- 1Department of Biochemistry and Medical Genetics & Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada.,2Experimental Center, Northwest University for Nationalities, Lanzhou, People's Republic of China
| | - Cátia Monteiro
- 3Molecular Oncology Group, Portuguese Institute of Oncology, Porto, Portugal.,Research Department, Portuguese League Against Cancer-North, Porto, Portugal
| | - Andreia Matos
- 5Laboratory of Genetics and Environmental Health Institute, Faculty of Medicine, University of Lisboa, Lisbon, Portugal.,6Tumor & Microenvironment Interactions, i3S/INEB, Institute for Research and Innovation in Health, and Institute of Biomedical Engineering, University of Porto, Porto, Portugal
| | - Jiaying You
- 1Department of Biochemistry and Medical Genetics & Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada
| | - Avelino Fraga
- 6Tumor & Microenvironment Interactions, i3S/INEB, Institute for Research and Innovation in Health, and Institute of Biomedical Engineering, University of Porto, Porto, Portugal.,7Department of Urology, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Carina Pereira
- 3Molecular Oncology Group, Portuguese Institute of Oncology, Porto, Portugal.,8CINTESIS, Center for Health Technology and Services Research, Faculty of Medicine, e, University of Porto, Porto, Portugal
| | - Victoria Catalán
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain
| | - Amaia Rodríguez
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Gómez-Ambrosi
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain
| | - Gema Frühbeck
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain.,11Department of Endocrinology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ricardo Ribeiro
- 3Molecular Oncology Group, Portuguese Institute of Oncology, Porto, Portugal.,5Laboratory of Genetics and Environmental Health Institute, Faculty of Medicine, University of Lisboa, Lisbon, Portugal.,6Tumor & Microenvironment Interactions, i3S/INEB, Institute for Research and Innovation in Health, and Institute of Biomedical Engineering, University of Porto, Porto, Portugal.,12Department of Clinical Pathology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,13i3S/INEB, Instituto de Investigação e Inovação em Saúde/Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Tumor & Microenvironment Interactions, Rua Alfredo Allen, 208 4200-135 Porto, Portugal
| | - Pingzhao Hu
- 1Department of Biochemistry and Medical Genetics & Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada
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Zhou J, Lazar D, Li H, Xia X, Satheesan S, Charlins P, O'Mealy D, Akkina R, Saayman S, Weinberg MS, Rossi JJ, Morris KV. Receptor-targeted aptamer-siRNA conjugate-directed transcriptional regulation of HIV-1. Am J Cancer Res 2018; 8:1575-1590. [PMID: 29556342 PMCID: PMC5858168 DOI: 10.7150/thno.23085] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/09/2017] [Indexed: 12/16/2022] Open
Abstract
Gene-based therapies represent a promising therapeutic paradigm for the treatment of HIV-1, as they have the potential to maintain sustained viral inhibition with reduced treatment interventions. Such an option may represent a long-term treatment alternative to highly active antiretroviral therapy. Methods: We previously described a therapeutic approach, referred to as transcriptional gene silencing (TGS), whereby small noncoding RNAs directly inhibit the transcriptional activity of HIV-1 by targeting sites within the viral promoter, specifically the 5' long terminal repeat (LTR). TGS differs from traditional RNA interference (RNAi) in that it is characterized by concomitant silent-state epigenetic marks on histones and DNA. To deliver TGS-inducing RNAs, we developed functional RNA conjugates based on the previously reported dual function of the gp120 (A-1) aptamer conjugated to 27-mer Dicer-substrate anti-HIV-1 siRNA (dsiRNA), LTR-362. Results: We demonstrate here that high levels of processed guide RNAs localize to the nucleus in infected T lymphoblastoid CEM cell line and primary human CD4+ T-cells. Treatment of the aptamer-siRNA conjugates induced TGS with an ~10-fold suppression of viral p24 levels as measured at day 12 post infection. To explore the silencing efficacy of aptamer-siRNA conjugates in vivo, HIV-1-infected humanized NOD/SCID/IL2 rγnull mice (hu-NSG) were treated with the aptamer-siRNA conjugates. Systemic delivery of the A-1-stick-LTR-362 27-mer siRNA conjugates suppressed HIV-1 infection and protected CD4+ T cell levels in viremia hu-NSG mice. Principle conclusions: Collectively these data suggest that the gp120 aptamer-dsiRNA conjugate design is suitable for systemic delivery of small RNAs that can be used to suppress HIV-1.
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Epigenetic modifications in hyperhomocysteinemia: potential role in diabetic retinopathy and age-related macular degeneration. Oncotarget 2018; 9:12562-12590. [PMID: 29560091 PMCID: PMC5849155 DOI: 10.18632/oncotarget.24333] [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: 08/06/2017] [Accepted: 01/24/2018] [Indexed: 02/03/2023] Open
Abstract
To study Hyperhomocysteinemia (HHcy)-induced epigenetic modifications as potential mechanisms of blood retinal barrier (BRB) dysfunction, retinas isolated from three- week-old mice with elevated level of Homocysteine (Hcy) due to lack of the enzyme cystathionine β-synthase (cbs-/- , cbs+/- and cbs+/+ ), human retinal endothelial cells (HRECs), and human retinal pigmented epithelial cells (ARPE-19) treated with or without Hcy were evaluated for (1) histone deacetylases (HDAC), (2) DNA methylation (DNMT), and (3) miRNA analysis. Differentially expressed miRNAs in mice with HHcy were further compared with miRNA analysis of diabetic mice retinas (STZ) and miRNAs within the exosomes released from Hcy-treated RPEs. Differentially expressed miRNAs were further evaluated for predicted target genes and associated pathways using Ingenuity Pathway Analysis. HHcy significantly increased HDAC and DNMT activity in HRECs, ARPE-19, and cbs mice retinas, whereas inhibition of HDAC and DNMT decreased Hcy-induced BRB dysfunction. MiRNA profiling detected 127 miRNAs in cbs+/- and 39 miRNAs in cbs-/- mice retinas, which were significantly differentially expressed compared to cbs+/+ . MiRNA pathway analysis showed their involvement in HDAC and DNMT activation, endoplasmic reticulum (ER), and oxidative stresses, inflammation, hypoxia, and angiogenesis pathways. Hcy-induced epigenetic modifications may be involved in retinopathies associated with HHcy, such as age-related macular degeneration and diabetic retinopathy.
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Abstract
Fuchs' endothelial dystrophy (FED) is characterized by corneal endothelial dysfunction and guttate excrescences on the posterior corneal surface, and is the leading indication for corneal transplantation in developed countries. In severe cases, keratoplasty is considered as the gold standard of treatment. However, there have been significant developments in our understanding of FED over the past decade. Attempts have been made to treat this disease with regenerative therapy techniques such as primary descemetorhexis without an endothelial graft or with a tissue-engineering approach. The discovery of a strong association between the CTG18.1 trinucleotide repeat expansion sequence and FED may pave the way for gene therapy strategies in the future. In this review, we evaluate these novel therapeutic modalities as possible alternatives to keratoplasty as the standard of care for FED.
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Affiliation(s)
- Yu Qiang Soh
- Tissue Engineering & Stem Cell Group, Singapore Eye Research Institute, 168751, Singapore.,Department of Corneal & External Eye Disease, Singapore National Eye Centre, 168751, Singapore
| | - Gary Sl Peh
- Tissue Engineering & Stem Cell Group, Singapore Eye Research Institute, 168751, Singapore.,Ophthalmology Academic Clinical Program, Duke-NUS Graduate Medical School, 169857, Singapore
| | - Jodhbir S Mehta
- Tissue Engineering & Stem Cell Group, Singapore Eye Research Institute, 168751, Singapore.,Department of Corneal & External Eye Disease, Singapore National Eye Centre, 168751, Singapore.,Ophthalmology Academic Clinical Program, Duke-NUS Graduate Medical School, 169857, Singapore.,Department of Clinical Sciences, Duke-NUS Graduate Medical School, 169857, Singapore
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28
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Avivi S, Mor A, Dotan I, Tzadok S, Kanter I, Kinor N, Canaani D, Shav-Tal Y. Visualizing nuclear RNAi activity in single living human cells. Proc Natl Acad Sci U S A 2017; 114:E8837-E8846. [PMID: 29073029 PMCID: PMC5651755 DOI: 10.1073/pnas.1707440114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Nuclear RNA interference (RNAi) is mediated by the canonical RNAi machinery and can lead to transcriptional silencing, transcriptional activation, or modulation of alternative splicing patterns. These effects transpire through changes in histone and DNA modifications via RNAi-mediated recruitment of chromatin-modifying enzymes. To prove that nuclear RNAi occurs and modulates transcription in human cells, we used live-cell imaging to detect and track nuclear RNAi transcriptional repression in single living human cells. While employing reporter genes constructed with inducible promoters and cognate-inducible short hairpin RNA (shRNA) targeted against the reporter coding region, we have characterized the dynamics of the nuclear RNAi process in living human cells. We show that the silencing effect is mediated through the nascent mRNA, followed by activity of histone methylating enzymes, but not through DNA methylation.
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Affiliation(s)
- Shira Avivi
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Amir Mor
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Iris Dotan
- Department of Biochemistry & Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Sivan Tzadok
- Department of Biochemistry & Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Itamar Kanter
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Noa Kinor
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dan Canaani
- Department of Biochemistry & Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
- Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
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29
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The molecular dynamics of long noncoding RNA control of transcription in PTEN and its pseudogene. Proc Natl Acad Sci U S A 2017; 114:9942-9947. [PMID: 28847966 DOI: 10.1073/pnas.1621490114] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA has been found to interact with chromatin and modulate gene transcription. In human cells, little is known about how long noncoding RNAs (lncRNAs) interact with target loci in the context of chromatin. We find here, using the phosphatase and tensin homolog (PTEN) pseudogene as a model system, that antisense lncRNAs interact first with a 5' UTR-containing promoter-spanning transcript, which is then followed by the recruitment of DNA methyltransferase 3a (DNMT3a), ultimately resulting in the transcriptional and epigenetic control of gene expression. Moreover, we find that the lncRNA and promoter-spanning transcript interaction are based on a combination of structural and sequence components of the antisense lncRNA. These observations suggest, on the basis of this one example, that evolutionary pressures may be placed on RNA structure more so than sequence conservation. Collectively, the observations presented here suggest a much more complex and vibrant RNA regulatory world may be operative in the regulation of gene expression.
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30
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Reactivity of human AGO2 monoclonal antibody 11A9 with the SWI/SNF complex: A case study for rigorously defining antibody selectivity. Sci Rep 2017; 7:7278. [PMID: 28779093 PMCID: PMC5544689 DOI: 10.1038/s41598-017-07539-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/29/2017] [Indexed: 12/12/2022] Open
Abstract
In this study, we originally aimed to characterize the potential role of Argonaute 2 (AGO2) in the nucleus, a key protein of the miRNA machinery. We combined Chromatin Immunoprecipitation (ChIP) with high throughput sequencing (ChIP-seq) and quantitative mass spectrometry (ChIP-MS) using the broadly used AGO2 11A9 antibody to determine interactions with chromatin and nuclear proteins. We found a previously described interaction between AGO2 and SWI/SNF on chromatin with ChIP-MS and observed enrichment at enhancers and transcription start sites using ChIP-seq. However, antibody specificity issues can produce misleading results for ChIP, RNA-seq and Mass spectrometry. Therefore, we developed a CRISPR/Cas9 engineered AGO2−/− HEK293T cell line to validate our findings. ChIP-qPCR and immunoprecipitation combined with MS (IP-MS) showed that the 11A9 antibody associates with chromatin and SWI/SNF in the absence of AGO2. Furthermore, stoichiometry, IP-MS and co-IP analysis suggests a direct interaction of this antibody with SMARCC1, a component of the SWI/SNF complex. For this reason, particular care should be taken in performing and interpreting experiments in which the 11A9 antibody is used to study a nuclear role of AGO2.
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31
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Kim JH, Lee JH, Lee IS, Lee SB, Cho KS. Histone Lysine Methylation and Neurodevelopmental Disorders. Int J Mol Sci 2017; 18:ijms18071404. [PMID: 28665350 PMCID: PMC5535897 DOI: 10.3390/ijms18071404] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 06/25/2017] [Accepted: 06/27/2017] [Indexed: 02/08/2023] Open
Abstract
Methylation of several lysine residues of histones is a crucial mechanism for relatively long-term regulation of genomic activity. Recent molecular biological studies have demonstrated that the function of histone methylation is more diverse and complex than previously thought. Moreover, studies using newly available genomics techniques, such as exome sequencing, have identified an increasing number of histone lysine methylation-related genes as intellectual disability-associated genes, which highlights the importance of accurate control of histone methylation during neurogenesis. However, given the functional diversity and complexity of histone methylation within the cell, the study of the molecular basis of histone methylation-related neurodevelopmental disorders is currently still in its infancy. Here, we review the latest studies that revealed the pathological implications of alterations in histone methylation status in the context of various neurodevelopmental disorders and propose possible therapeutic application of epigenetic compounds regulating histone methylation status for the treatment of these diseases.
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Affiliation(s)
- Jeong-Hoon Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.
- Department of Functional Genomics, University of Science and Technology, Daejeon 34113, Korea.
| | - Jang Ho Lee
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea.
| | - Im-Soon Lee
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea.
| | - Sung Bae Lee
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Korea.
| | - Kyoung Sang Cho
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea.
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32
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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33
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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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34
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Capozzo I, Iannelli F, Francia S, d'Adda di Fagagna F. Express or repress? The transcriptional dilemma of damaged chromatin. FEBS J 2017; 284:2133-2147. [PMID: 28231404 DOI: 10.1111/febs.14048] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/23/2017] [Accepted: 02/20/2017] [Indexed: 01/06/2023]
Abstract
The fine modulation of transcriptional activity around DNA lesions is essential to carefully regulate the crosstalk between the activation of the DNA damage response, DNA repair and transcription, particularly when the lesion occurs next to actively transcribed genes. Recently, several studies have been carried out to investigate how DNA lesions impact on local transcription, but the emerging model remains incomplete. Transcription of genes around damaged DNA is actively downregulated by the DNA damage response through different mechanisms, which appear specific to the chromatin context, the type of DNA damage or its complexity. Intriguingly, emerging evidence also indicates that transcription of noncoding RNAs (ncRNAs) is induced at sites of DNA damage, producing small ncRNAs that are, in turn, required for a full DNA damage response activation. We discuss here these recent findings, highlighting the major unresolved questions in the field, and propose ways to reconcile these apparently contradictory observations.
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Affiliation(s)
- Ilaria Capozzo
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia, Italy.,Scuola Universitaria Superiore IUSS Pavia, Italy
| | - Fabio Iannelli
- IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| | - Sofia Francia
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia, Italy.,IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia, Italy.,IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, Milan, Italy
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35
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Noncoding RNAs in the development, diagnosis, and prognosis of colorectal cancer. Transl Res 2017; 181:108-120. [PMID: 27810413 DOI: 10.1016/j.trsl.2016.10.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 09/29/2016] [Accepted: 10/06/2016] [Indexed: 12/17/2022]
Abstract
More than 90% of the human genome is actively transcribed, but less than 2% of the total genome encodes protein-coding RNA, and thus, noncoding RNA (ncRNA) is a major component of the human transcriptome. Recently, ncRNA was demonstrated to play important roles in multiple biological processes by directly or indirectly interfering with gene expression, and the dysregulation of ncRNA is associated with a variety of diseases, including cancer. In this review, we summarize the function and mechanism of miRNA, long intergenic ncRNA, and some other types of ncRNAs, such as small nucleolar RNA, circular ncRNA, pseudogene RNA, and even protein-coding mRNA, in the progression of colorectal cancer (CRC). We also presented their clinical application in the diagnosis and prognosis of CRC. The summary of the current state of ncRNA in CRC will contribute to our understanding of the complex processes of CRC initiation and development and will help in the discovery of novel biomarkers and therapeutic targets for CRC diagnosis and treatment.
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36
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DeWitt JJ, Hecht PM, Grepo N, Wilkinson B, Evgrafov OV, Morris KV, Knowles JA, Campbell DB. Transcriptional Gene Silencing of the Autism-Associated Long Noncoding RNA MSNP1AS in Human Neural Progenitor Cells. Dev Neurosci 2016; 38:375-383. [PMID: 28030860 DOI: 10.1159/000453258] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/08/2016] [Indexed: 12/21/2022] Open
Abstract
The long noncoding RNA MSNP1AS (moesin pseudogene 1, antisense) is a functional element that was previously associated with autism spectrum disorder (ASD) with genome-wide significance. Expression of MSNP1AS was increased 12-fold in the cerebral cortex of individuals with ASD and 22-fold in individuals with a genome-wide significantly associated ASD genetic marker on chromosome 5p14.1. Overexpression of MSNP1AS in human neuronal cells caused decreased expression of moesin protein, which is involved in neuronal process stability. In this study, we hypothesize that MSNP1AS knockdown impacts global transcriptome levels. We transfected the human neural progenitor cell line SK- N-SH with constructs that caused a 50% suppression of MSNP1AS expression. After 24 h, cells were harvested for total RNA isolation. Strand-specific RNA sequencing analysis indicated altered expression of 1,352 genes, including altered expression of 318 genes following correction for multiple comparisons. Expression of the OAS2 gene was increased >150-fold, a result that was validated by quantitative PCR. Gene ontology analysis of the 318 genes with altered expression following correction for multiple comparisons indicated that upregulated genes were significantly enriched for genes involved in immune response, and downregulated genes were significantly enriched for genes involved in chromatin remodeling. These data indicate multiple transcriptional and translational functions of MSNP1AS that impact ASD-relevant biological processes. Chromatin remodeling and immune response are biological processes implicated by genes with rare mutations associated with ASD. Our data suggest that the functional elements implicated by association of common genetic variants impact the same biological processes, suggesting a possible shared common molecular pathway of ASD.
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Affiliation(s)
- Jessica J DeWitt
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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37
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Wu HL, Li SM, Hu J, Yu X, Xu H, Chen Z, Ye ZQ. Demystifying the mechanistic and functional aspects of p21 gene activation with double-stranded RNAs in human cancer cells. J Exp Clin Cancer Res 2016; 35:145. [PMID: 27639690 PMCID: PMC5027115 DOI: 10.1186/s13046-016-0423-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 09/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The recently identified phenomenon of double-stranded RNA (dsRNA)-mediated gene activation (RNAa) has been studied extensively, as it is present in humans, mice, and Caenorhabditis elegans, suggesting that dsRNA-mediated RNAa is an evolutionarily conserved mechanism. Previous studies have shown that dsP21-322 can induce tumor suppressor gene p21 expression in several human cancer cells. Nonetheless, the role of dsRNAs in the activation of gene expression, including their target molecules and associated key factors, remains poorly understood. METHODS Oligonucleotides were used to overexpress dsRNAs and dsControl. Real-time PCR and Western blotting were used to detect corresponding mRNA and protein expression, respectively. Fluorescence microscopy was used to examine the kinetics of dsRNA subcellular distribution. Luciferase reporter assays were performed to verify dsRNA target molecules. Chromatin immunoprecipitation (ChIP) assays were carried out to determine whether histone modification and other associated key factors are involved in saRNA-mediated p21 expression. RESULTS We demonstrated that dsRNA-mediated p21 induction in human cell lines is a common phenomenon. This process occurs at the transcriptional level, and the complementary p21 promoter is the intended dsRNA target. Additionally, ChIP assays indicated that p21 activation was accompanied by an increased enrichment of AGO1 and the trimethylation of histone H3K4 at dsRNA-targeted genomic sites. CONCLUSION These data systematically reveal the mechanistic and functional aspects of ncRNA-mediated p21 activation in human cancer cells, which may be a useful tool to analyze gene function and aid in the development of novel drug targets for cancer therapeutics.
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Affiliation(s)
- Huan-Lei Wu
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Sen-Mao Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Liberalization Avenue, No. 1095, Wuhan, 430030, People's Republic of China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Jia Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Liberalization Avenue, No. 1095, Wuhan, 430030, People's Republic of China. .,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China.
| | - Xiao Yu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Liberalization Avenue, No. 1095, Wuhan, 430030, People's Republic of China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Liberalization Avenue, No. 1095, Wuhan, 430030, People's Republic of China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Zhong Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Liberalization Avenue, No. 1095, Wuhan, 430030, People's Republic of China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Zhang-Qun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Liberalization Avenue, No. 1095, Wuhan, 430030, People's Republic of China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
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38
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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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39
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Promoter-Associated RNAs Regulate HSPC152 Gene Expression in Malignant Melanoma. Noncoding RNA 2016; 2:ncrna2030007. [PMID: 29657265 PMCID: PMC5831909 DOI: 10.3390/ncrna2030007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 06/13/2016] [Accepted: 06/19/2016] [Indexed: 01/02/2023] Open
Abstract
The threshold of 200 nucleotides (nt) conventionally divides non-coding RNAs (ncRNA) into long ncRNA (lincRNA, that have more than 200 nt in length) and the remaining ones which are grouped as "small" RNAs (microRNAs, small nucleolar RNAs and piwiRNAs). Promoter-associated RNAs (paRNAs) are generally 200-500 nt long and are transcribed from sequences positioned in the promoter regions of genes. Growing evidence suggests that paRNAs play a crucial role in controlling gene transcription. Here, we used deep sequencing to identify paRNA sequences that show altered expression in a melanoma cell line compared to normal melanocytes. Thousands of reads were mapped to transcription start site (TSS) regions. We limited our search to paRNAs adjacent to genes with an expression that differed between melanoma and normal melanocytes and a length of 200-500 nt that did not overlap the gene mRNA by more than 300 nt, ultimately leaving us with 11 such transcripts. Using quantitative real-time PCR (qRT-PCR), we found a significant correlation between the expression of the mRNA and its corresponding paRNA for two studied genes: TYR and HSPC152. Ectopic overexpression of the paRNA of HSPC152 (designated paHSPC) enhanced the expression of the HSPC152 mRNA, and an siRNA targeting the paHSPC152 decreased the expression of the HSPC152 mRNA. Overexpression of paHSPC also affected the epigenetic structure of its putative promoter region along with effects on several biologic features of melanoma cells. The ectopic expression of the paRNA to TYR did not have any effect. Overall, our work indicates that paRNAs may serve as an additional layer in the regulation of gene expression in melanoma, thus meriting further investigation.
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40
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Woolnough JL, Atwood BL, Liu Z, Zhao R, Giles KE. The Regulation of rRNA Gene Transcription during Directed Differentiation of Human Embryonic Stem Cells. PLoS One 2016; 11:e0157276. [PMID: 27299313 PMCID: PMC4907514 DOI: 10.1371/journal.pone.0157276] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 05/26/2016] [Indexed: 11/18/2022] Open
Abstract
It has become increasingly clear that proper cellular control of pluripotency and differentiation is related to the regulation of rRNA synthesis. To further our understanding of the role that the regulation of rRNA synthesis has in pluripotency we monitored rRNA synthesis during the directed differentiation of human embryonic stem cells (hESCs). We discovered that the rRNA synthesis rate is reduced ~50% within 6 hours of ACTIVIN A treatment. This precedes reductions in expression of specific stem cell markers and increases in expression of specific germ layer markers. The reduction in rRNA synthesis is concomitant with dissociation of the Pol I transcription factor, UBTF, from the rRNA gene promoter and precedes any increase to heterochromatin throughout the rRNA gene. To directly investigate the role of rRNA synthesis in pluripotency, hESCs were treated with the Pol I inhibitor, CX-5461. The direct reduction of rRNA synthesis by CX-5461 induces the expression of markers for all three germ layers, reduces the expression of pluripotency markers, and is overall similar to the ACTIVIN A induced changes. This work indicates that the dissociation of UBTF from the rRNA gene, and corresponding reduction in transcription, represent early regulatory events during the directed differentiation of pluripotent stem cells.
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Affiliation(s)
- Jessica L Woolnough
- UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Blake L Atwood
- UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Zhong Liu
- UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Rui Zhao
- UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Keith E Giles
- UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
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41
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Stojic L, Niemczyk M, Orjalo A, Ito Y, Ruijter AEM, Uribe-Lewis S, Joseph N, Weston S, Menon S, Odom DT, Rinn J, Gergely F, Murrell A. Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions. Nat Commun 2016; 7:10406. [PMID: 26832224 PMCID: PMC4740813 DOI: 10.1038/ncomms10406] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/08/2015] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) regulate gene expression via their RNA product or through transcriptional interference, yet a strategy to differentiate these two processes is lacking. To address this, we used multiple small interfering RNAs (siRNAs) to silence GNG12-AS1, a nuclear lncRNA transcribed in an antisense orientation to the tumour-suppressor DIRAS3. Here we show that while most siRNAs silence GNG12-AS1 post-transcriptionally, siRNA complementary to exon 1 of GNG12-AS1 suppresses its transcription by recruiting Argonaute 2 and inhibiting RNA polymerase II binding. Transcriptional, but not post-transcriptional, silencing of GNG12-AS1 causes concomitant upregulation of DIRAS3, indicating a function in transcriptional interference. This change in DIRAS3 expression is sufficient to impair cell cycle progression. In addition, the reduction in GNG12-AS1 transcripts alters MET signalling and cell migration, but these are independent of DIRAS3. Thus, differential siRNA targeting of a lncRNA allows dissection of the functions related to the process and products of its transcription.
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Affiliation(s)
- Lovorka Stojic
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Malwina Niemczyk
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Arturo Orjalo
- Biosearch Technologies Inc., 2199S. McDowell Boulevard, Petaluma, California 94954, USA
| | - Yoko Ito
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Anna Elisabeth Maria Ruijter
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Santiago Uribe-Lewis
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Nimesh Joseph
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Stephen Weston
- Centre for Regenerative Medicine, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Suraj Menon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Duncan T. Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - John Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Fanni Gergely
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Adele Murrell
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Centre for Regenerative Medicine, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
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42
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Kalantari R, Chiang CM, Corey DR. Regulation of mammalian transcription and splicing by Nuclear RNAi. Nucleic Acids Res 2016; 44:524-37. [PMID: 26612865 PMCID: PMC4737150 DOI: 10.1093/nar/gkv1305] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 12/21/2022] Open
Abstract
RNA interference (RNAi) is well known as a mechanism for controlling mammalian mRNA translation in the cytoplasm, but what would be the consequences if it also functions in cell nuclei? Although RNAi has also been found in nuclei of plants, yeast, and other organisms, there has been relatively little progress towards understanding the potential involvement of mammalian RNAi factors in nuclear processes including transcription and splicing. This review summarizes evidence for mammalian RNAi factors in cell nuclei and mechanisms that might contribute to the control of gene expression. When RNAi factors bind small RNAs, they form ribonucleoprotein complexes that can be selective for target sequences within different classes of nuclear RNA substrates. The versatility of nuclear RNAi may supply a previously underappreciated layer of regulation to transcription, splicing, and other nuclear processes.
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Affiliation(s)
- Roya Kalantari
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Cheng-Ming Chiang
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-8807, USA
| | - David R Corey
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
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43
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Bhargavan B, Woollard SM, Kanmogne GD. Toll-like receptor-3 mediates HIV-1 transactivation via NFκB and JNK pathways and histone acetylation, but prolonged activation suppresses Tat and HIV-1 replication. Cell Signal 2015; 28:7-22. [PMID: 26569339 DOI: 10.1016/j.cellsig.2015.11.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/03/2015] [Accepted: 11/09/2015] [Indexed: 01/13/2023]
Abstract
TLR3 has been implicated in the pathogenesis of several viral infections, including SIV- and HIV-1-induced inflammation and AIDS. However the molecular mechanisms of these TLR3-mediated effects are not known, and it is not known whether HIV interacts with cellular TLR3 to affect disease process. Here we investigate the effects of TLR3 ligands on HIV-1 transactivation using both primary human macrophages and cells containing integrated copies of the HIV-1 promoter. We demonstrate that TLR3 activation induced upregulation of transcription factors such as c-Jun, CCAAT/enhancer-binding protein alpha (CEBPA), signal transducer and activator of transcription (STAT)-1, STAT-2, RELB, and nuclear factor kappa-B1 (NFκB1), most of which are known to regulate the HIV promoter activity. We also demonstrate that TLR3 activation increased HIV-1 transactivation via the c-Jun N-terminal kinase (JNK) and NFκB pathways. This was associated with epigenetic modifications, including decreased histone deacetylase activity, increased histone acetyl transferase (HAT) activity, and increased acetylation of histones H3 and H4 at lysine residues in the nucleosome-0 and nucleosome-1 of the HIV-1 promoter. However, prolonged TLR3 activation decreased HIV-1 transactivation, decreased HAT activity and Tat transcription, and suppressed viral replication. Overall, data suggests that TLR3 can act as viral sensor to mediate viral transactivation, cellular signaling, innate immune response, and inflammation in HIV-infected humans. Our study provides novel insights into the molecular basis for these TLR3-mediated effects.
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Affiliation(s)
- Biju Bhargavan
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA.
| | - Shawna M Woollard
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA.
| | - Georgette D Kanmogne
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA.
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44
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Husso T, Turunen MP, Parker N, Ylä-Herttuala S. Epigenetherapy, a new concept. Biomol Concepts 2015; 2:127-34. [PMID: 25962024 DOI: 10.1515/bmc.2011.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 02/26/2011] [Indexed: 11/15/2022] Open
Abstract
Small RNAs have been shown to regulate gene transcription by interacting with the promoter region and modifying the histone code. The exact mechanism of function is still unclear but the feasibility to activate or repress endogenous gene expression with small RNA molecules has already been demonstrated in vitro and in vivo. In traditional gene therapy non-mutated or otherwise useful genes are inserted into patient's cells to treat a disease. In epigenetherapy the action of small RNAs is utilized by delivering only the small RNAs to patient's cells where they then regulate gene expression by epigenetic mechanisms. This method could be widely useful not only for basic research but also for clinical applications of small RNAs.
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45
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Ahlenstiel CL, Suzuki K, Marks K, Symonds GP, Kelleher AD. Controlling HIV-1: Non-Coding RNA Gene Therapy Approaches to a Functional Cure. Front Immunol 2015; 6:474. [PMID: 26441979 PMCID: PMC4584958 DOI: 10.3389/fimmu.2015.00474] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/31/2015] [Indexed: 12/27/2022] Open
Abstract
The current treatment strategy for HIV-1 involves prolonged and intensive combined antiretroviral therapy (cART), which successfully suppresses plasma viremia. It has transformed HIV-1 infection into a chronic disease. However, despite the success of cART, a latent form of HIV-1 infection persists as integrated provirus in resting memory CD4(+) T cells. Virus can reactivate from this reservoir upon cessation of treatment, and hence HIV requires lifelong therapy. The reservoir represents a major barrier to eradication. Understanding molecular mechanisms regulating HIV-1 transcription and latency are crucial to develop alternate treatment strategies, which impact upon the reservoir and provide a path toward a "functional cure" in which there is no detectable viremia in the absence of cART. Numerous reports have suggested ncRNAs are involved in regulating viral transcription and latency. This review will discuss the latest developments in ncRNAs, specifically short interfering (si)RNA and short hairpin (sh)RNA, targeting molecular mechanisms of HIV-1 transcription, which may represent potential future therapeutics. It will also briefly address animal models for testing potential therapeutics and current gene therapy clinical trials.
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Affiliation(s)
| | - Kazuo Suzuki
- The Kirby Institute, UNSW Australia, Sydney, NSW, Australia
- Immunovirology Laboratory, St. Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | - Katherine Marks
- Immunovirology Laboratory, St. Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | | | - Anthony D. Kelleher
- The Kirby Institute, UNSW Australia, Sydney, NSW, Australia
- Immunovirology Laboratory, St. Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
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46
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Lillycrop KA, Burdge GC. Environmental challenge, epigenetic plasticity and the induction of altered phenotypes in mammals. Epigenomics 2015; 6:623-36. [PMID: 25531256 DOI: 10.2217/epi.14.51] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The level of transcriptional activity of a gene is regulated by epigenetic processes. There is compelling evidence that environmental challenges throughout the life course can induce phenotypic change. In this review, we summarize the current evidence, focusing specifically on the effects of nutrition and of environmental pollutants, that epigenetic processes underpin the induction by environmental change of altered phenotypic traits, emphasizing the implications for health outcomes. We also discuss whether epigenetic processes may be involved in the passage of induced traits between generations. Overall, current findings indicate that epigenetic processes may play an important role in determining disease risk, but there is a lack of studies that demonstrate causal links between epigenetic change and tissue function.
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Affiliation(s)
- Karen A Lillycrop
- Faculty of Natural & Environmental Sciences, Southampton General Hospital, University of Southampton, SO16 6YD, UK
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47
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Khan I, Zakaria MK, Kumar M, Mani P, Chattopadhyay P, Sarkar DP, Sinha S. A novel placental like alkaline phosphatase promoter driven transcriptional silencing combined with single chain variable fragment antibody based virosomal delivery for neoplastic cell targeting [corrected]. J Transl Med 2015; 13:254. [PMID: 26242403 PMCID: PMC4524171 DOI: 10.1186/s12967-015-0602-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/10/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Placental like alkaline phosphatase (PLAP), an oncofetal antigen, is highly expressed in germ cell, cervical, ovarian and several other tumour types but minimally in normal tissues [corrected]. The expression of a PLAP promoter based transcriptional unit following antigen mediated cell specific delivery is a possible approach for tumour targeting. METHODS PLAP promoter alone or in combination with NFκB DNA response elements was used for expressing shRNA targeting the long control region (LCR) of human papillomavirus (HPV)-16 oncogenes E6 and E7 via transcriptional gene silencing in PLAP expressing cervical cancer cell lines, SiHa and CaSki. This was packaged in a Sendai virus envelope incorporating a single chain variable fragment antibody (scFv) for antibody mediated targeting. Specificity and efficacy of the shRNA was assessed by studying the heterochromatization, down regulation of the HPV-16 E6/E7 genes and subsequent effects on their targets and cell growth properties. RESULTS Reduction of HPV-16 E6 and E7 expression by TGS led to the activation of the previously suppressed target genes of p53 (PUMA and NOXA) and Rb (cyclins A2 and E). Cell death was seen only in PLAP expressing HPV-16 infected SiHa and CaSki cells but not in the HPV-18 integrated HeLa and non-PLAP CHO cells. There was reduction in the enhancer associated transcripts of the long control region (LCR) of HPV-16 E6/E7 genes. Also, an increase in the enrichment of dimethylated histone three lysine nine (H3K9Me2) and trimethylated histone three lysine twenty-seven (H3K27Me3) was observed by ChIP assay, which decreased upon trichostatin A treatment, indicating a possible mechanism for the heterochromatization of the target LCR region. CONCLUSION A combination of novel PLAP promoter and antibody based specificities has the potential for being developed as a possible therapeutic strategy for PLAP positive neoplasia.
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Affiliation(s)
- Imran Khan
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India.
| | - Mohammad Khalid Zakaria
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India. .,National Brain Research Centre, Manesar, Gurgaon, Haryana, 122051, India.
| | - Mukesh Kumar
- National Brain Research Centre, Manesar, Gurgaon, Haryana, 122051, India.
| | - Prashant Mani
- Department of Biochemistry, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India.
| | | | - Debi P Sarkar
- Department of Biochemistry, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India.
| | - Subrata Sinha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India. .,National Brain Research Centre, Manesar, Gurgaon, Haryana, 122051, India.
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48
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Matsui M, Li L, Janowski BA, Corey DR. Reduced Expression of Argonaute 1, Argonaute 2, and TRBP Changes Levels and Intracellular Distribution of RNAi Factors. Sci Rep 2015; 5:12855. [PMID: 26242502 PMCID: PMC4525381 DOI: 10.1038/srep12855] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/06/2015] [Indexed: 11/25/2022] Open
Abstract
Until recently, Argonaute 2 (AGO2) and other RNA factors were believed to be restricted to the cytoplasm of mammalian somatic cells. It is now becoming appreciated that RNAi factors can also be found in cell nuclei, but much remains to be learned about their transport, molecular recognition, and function. We find that siRNA-mediated reduction of AGO1 or AGO2 increases the proportion of AGO1 or AGO2 in cell nuclei. Inhibition of AGO1 expression led to increased AGO2 levels, while knockdown of AGO2 led to increased levels of AGO1. Blocking AGO1, AGO2, or TRBP expression changed expression levels and nuclear distribution of RNAi factors Dicer, TNRC6A (GW182), and TRBP. These data reveal the expression of RNAi proteins is mutually dependent and that perturbation can affect subcellular distribution of those factors inside cells.
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Affiliation(s)
- Masayuki Matsui
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
| | - Liande Li
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
| | - Bethany A Janowski
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
| | - David R Corey
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
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49
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Roberts TC, Hart JR, Kaikkonen MU, Weinberg MS, Vogt PK, Morris KV. Quantification of nascent transcription by bromouridine immunocapture nuclear run-on RT-qPCR. Nat Protoc 2015; 10:1198-211. [PMID: 26182239 PMCID: PMC4790731 DOI: 10.1038/nprot.2015.076] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nuclear run-on (NRO) is a method that measures transcriptional activity via the quantification of biochemically labeled nascent RNA molecules derived from nuclear isolates. Widespread use of this technique has been limited because of its technical difficulty relative to steady-state total mRNA analyses. Here we describe a detailed protocol for the quantification of transcriptional activity in human cell cultures. Nuclei are first isolated and NRO transcription is performed in the presence of bromouridine. Labeled nascent transcripts are purified by immunoprecipitation, and transcript levels are determined by reverse-transcription quantitative PCR (RT-qPCR). Data are then analyzed using standard techniques described elsewhere. This method is rapid (the protocol can be completed in 2 d) and cost-effective, exhibits negligible detection of background noise from unlabeled transcripts, requires no radioactive materials and can be performed from as few as 500,000 nuclei. It also takes advantage of the high sensitivity, specificity and dynamic range of RT-qPCR.
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Affiliation(s)
- Thomas C. Roberts
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX, United Kingdom
- Sanford-Burnham Medical Research Institute, Development, Aging and Regeneration Program, 10901 N. Torrey pines Road, La Jolla, CA, 92037, USA
| | - Jonathan R. Hart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Minna U. Kaikkonen
- University of Eastern Finland, A.I. Virtanen institute, Department of Biotechnology and Molecular Medicine, P.O.B. 1627, 70211 Kuopio, Finland
| | - Marc S. Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
- Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, WITS 2050, South Africa
| | - Peter K. Vogt
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Kevin V. Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
- School of Biotechnology and Biomedical Sciences, University of New South Wales, NSW 2052, Australia
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50
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Kassab MA, Mudassir M, Singh A, N M, Bhagat M, Palanichamy JK, Ramalingam P, Chosdol K, Sinha S, Chattopadhyay P. Gene Silencing and Activation of Human Papillomavirus 18 Is Modulated by Sense Promoter Associated RNA in Bidirectionally Transcribed Long Control Region. PLoS One 2015; 10:e0128416. [PMID: 26047143 PMCID: PMC4457724 DOI: 10.1371/journal.pone.0128416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/27/2015] [Indexed: 12/02/2022] Open
Abstract
Background Recently various studies have demonstrated the role of promoter associated non-coding RNAs (pRNA) in dsRNA induced transcriptional gene silencing and activation. However the exact mechanistic details of these processes with respect to the orientation of pRNAs are poorly defined. Methodology/Principal Findings We have identified novel sense and antisense long control region (LCR) associated RNAs (pRNAs) in HPV18 positive cervical cancer cell lines HeLa, C-4 I and C-4 II. Using dsRNAs against these pRNAs, we were able to achieve upregulation or downregulation of the sense and antisense pRNAs and the downstream E6 and E7 oncogenes. We present evidence that knockdown of the sense pRNA is associated with reduction in E6 and E7 oncogenes and an upregulation of antisense pRNA. Conversely upregulation of sense pRNA is accompanied by an induction of the oncogenes and a concomitant reduction in antisense pRNA. Moreover, the exact role of sense and antisense pRNAs in dsRNA mediated gene modulation was confirmed by their selective degradation using antisense phosphorothioate oligodeoxynucleotides (ODN). Degradation of sense pRNA with antisense ODN led to loss of dsRNA induced silencing and activation, suggesting that dsRNA mediated gene modulation requires sense pRNA. Both processes were accompanied with congruent changes in the methylation pattern of activating and repressive histones. Conclusion/Significance Thus this data identifies and demonstrates the role of previously unknown important regulatory transcripts in HPV18 gene expression which can prove valuable targets in cervical cancer therapeutics. This mode of gene regulation by bidirectional transcription could be operational in other promoters as well and serve as a mechanism of regulating gene expression.
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Affiliation(s)
- Muzaffer Ahmad Kassab
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Madeeha Mudassir
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Anand Singh
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, United States of America
| | - Muthuraman N
- Department of Biochemistry, Institute of Liver and Biliary Sciences, New Delhi, Vasant Kunj, India
| | - Mohita Bhagat
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | | | - Pradeep Ramalingam
- Weill Cornell Medical College, York Avenue, New York, NY, United States of America
| | - Kunzang Chosdol
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Subrata Sinha
- National Brain Research Center, Manesar, Gurgaon, Haryana, India
| | - Parthaprasad Chattopadhyay
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
- * E-mail:
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