1
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Krishnan VS, Kõks S. Transcriptional Landscape of Repetitive Elements in Psoriatic Skin from Large Cohort Studies: Relevance to Psoriasis Pathophysiology. Int J Mol Sci 2023; 24:16725. [PMID: 38069048 PMCID: PMC10706217 DOI: 10.3390/ijms242316725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
While studies demonstrating the expression of repetitive elements (REs) in psoriatic skin using RNA-seq have been published before, not many studies have focused on the genome-wide expression patterns using larger cohorts. This study investigated the transcriptional landscape of differentially expressed REs in lesional and non-lesional skin from two previously published large datasets. We observed significant differential expression of REs in lesional psoriatic skin as well as the skin of healthy controls. Significant downregulation of several ERVs, HERVs (including HERV-K) and LINEs was observed in lesional psoriatic skin from both datasets. The upregulation of a small subset of HERV-Ks and Alus in lesional psoriatic skin was also reported. An interesting finding from this expression data was the significant upregulation and overlapping of tRNA repetitive elements in lesional and non-lesional psoriatic skin. The data from this study indicate the potential role of REs in the immunopathogenesis of psoriasis. The expression data from the two independent large study cohorts are powerful enough to confidently verify the differential expression of REs in relation to psoriatic skin pathology. Further studies are warranted to understand the functional impact of these repetitive elements in psoriasis pathogenesis, thereby expanding their significance as a potential targeting pathway for the disease treatment of psoriasis and other inflammatory diseases.
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Affiliation(s)
- Vidya S. Krishnan
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Discovery Way, Murdoch, WA 1650, Australia;
- Perron Institute for Neurological and Translational Science, 8 Verdun St., Nedlands, WA 6009, Australia
| | - Sulev Kõks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Discovery Way, Murdoch, WA 1650, Australia;
- Perron Institute for Neurological and Translational Science, 8 Verdun St., Nedlands, WA 6009, Australia
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2
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Rasizadeh R, Aghbash PS, Nahand JS, Entezari-Maleki T, Baghi HB. SARS-CoV-2-associated organs failure and inflammation: a focus on the role of cellular and viral microRNAs. Virol J 2023; 20:179. [PMID: 37559103 PMCID: PMC10413769 DOI: 10.1186/s12985-023-02152-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023] Open
Abstract
SARS-CoV-2 has been responsible for the recent pandemic all over the world, which has caused many complications. One of the hallmarks of SARS-CoV-2 infection is an induced immune dysregulation, in some cases resulting in cytokine storm syndrome, acute respiratory distress syndrome and many organs such as lungs, brain, and heart that are affected during the SARS-CoV-2 infection. Several physiological parameters are altered as a result of infection and cytokine storm. Among them, microRNAs (miRNAs) might reflect this poor condition since they play a significant role in immune cellular performance including inflammatory responses. Both host and viral-encoded miRNAs are crucial for the successful infection of SARS-CoV-2. For instance, dysregulation of miRNAs that modulate multiple genes expressed in COVID-19 patients with comorbidities (e.g., type 2 diabetes, and cerebrovascular disorders) could affect the severity of the disease. Therefore, altered expression levels of circulating miRNAs might be helpful to diagnose this illness and forecast whether a COVID-19 patient could develop a severe state of the disease. Moreover, a number of miRNAs could inhibit the expression of proteins, such as ACE2, TMPRSS2, spike, and Nsp12, involved in the life cycle of SARS-CoV-2. Accordingly, miRNAs represent potential biomarkers and therapeutic targets for this devastating viral disease. In the current study, we investigated modifications in miRNA expression and their influence on COVID-19 disease recovery, which may be employed as a therapy strategy to minimize COVID-19-related disorders.
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Affiliation(s)
- Reyhaneh Rasizadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parisa Shiri Aghbash
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 5166/15731, Iran
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Taher Entezari-Maleki
- Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Bannazadeh Baghi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 5166/15731, Iran.
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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3
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Ramakrishna NB, Murison K, Miska EA, Leitch HG. Epigenetic Regulation during Primordial Germ Cell Development and Differentiation. Sex Dev 2021; 15:411-431. [PMID: 34847550 DOI: 10.1159/000520412] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/10/2021] [Indexed: 11/19/2022] Open
Abstract
Germline development varies significantly across metazoans. However, mammalian primordial germ cell (PGC) development has key conserved landmarks, including a critical period of epigenetic reprogramming that precedes sex-specific differentiation and gametogenesis. Epigenetic alterations in the germline are of unique importance due to their potential to impact the next generation. Therefore, regulation of, and by, the non-coding genome is of utmost importance during these epigenomic events. Here, we detail the key chromatin changes that occur during mammalian PGC development and how these interact with the expression of non-coding RNAs alongside broader epitranscriptomic changes. We identify gaps in our current knowledge, in particular regarding epigenetic regulation in the human germline, and we highlight important areas of future research.
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Affiliation(s)
- Navin B Ramakrishna
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Genome Institute of Singapore, A*STAR, Biopolis, Singapore, Singapore
| | - Keir Murison
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Harry G Leitch
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, United Kingdom
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4
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Salim U, Kumar A, Kulshreshtha R, Vivekanandan P. Biogenesis, characterization, and functions of mirtrons. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1680. [PMID: 34155810 DOI: 10.1002/wrna.1680] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 01/18/2023]
Abstract
MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression. They base pair with the complementary target mRNA at the 3'UTR and modulate cellular processes by repressing the mRNA translation or degrading the mRNA. There are well-documented mechanisms of biogenesis of miRNA; however, a sizeable number of miRNAs are also produced by non-canonical pathways. Mirtrons represent a predominant class of non-canonical miRNAs. Mirtrons originate from intronic regions and are produced in a splicing-dependent and Drosha-independent manner. Mirtrons constitute about 15% of all miRNAs produced in a human body and have caught attention of researchers worldwide due to their unconventional origin, sequence characteristics, evolutionary dynamics, ability to regulate variety of cellular processes and their immense potential in disease therapeutics. In this comprehensive review we collate the research done in the past decade including biogenesis, sequence characteristics, regulation, and emerging therapeutic roles of mirtrons. This article is categorized under: RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action.
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Affiliation(s)
- Uzma Salim
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Ashish Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
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5
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Liu X, Frost J, Bowcock A, Zhang W. Canonical and Interior Circular RNAs Function as Competing Endogenous RNAs in Psoriatic Skin. Int J Mol Sci 2021; 22:ijms22105182. [PMID: 34068434 PMCID: PMC8153647 DOI: 10.3390/ijms22105182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 12/14/2022] Open
Abstract
(1) Background: Understanding the function of circular RNAs (circRNAs), a class of noncoding RNA, in psoriatic skin can provide important insights into the complex regulation of genes contributing to the pathogenesis of psoriasis. (2) Methods: A novel method was applied to RNA-seq datasets from 93 skin biopsy samples to comprehensively identify circRNAs of all types, i.e., canonical circRNAs from the intron-exon junctions of mRNAs and interior circRNAs (i-circRNAs) from the interior regions of exons, introns, and intergenic regions. Selected circRNAs were experimentally validated by qRT-PCR and Sanger sequencing. CircRNAs with abundant and differential expression were identified and their putative function as competing endogenous RNAs (ceRNAs) was analyzed by an integrated analysis of circRNAs, microRNAs, and mRNAs. (3) Results: With a comprehensive search using no information of splicing signals, we systematically identified 179 highly abundant circRNAs in psoriatic skin. Many of these were reported for the first time and many were differentially expressed in involved versus normal or uninvolved skin. Validation based on three additional RNA-seq datasets confirmed most of the identified circRNAs in psoriatic skin. Experimental analyses confirmed the expression of the well-known circRNA CDR1as, a canonical circRNA, and a novel i-circRNA in psoriasis. We also identified many circRNAs that may act as ceRNAs to regulate the expression of mRNA genes in psoriasis-related signaling pathways in psoriasis. (4) Conclusions: The result of the study suggested that circRNAs are abundant in psoriatic skin, have distinct characteristics, and contribute to psoriatic pathogenesis.
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Affiliation(s)
- Xiaoxin Liu
- Institute for Systems Biology, Jianghan University, Wuhan 430056, China;
- Department of Computer Science and Engineering, Washington University, Saint Louis, MO 63130, USA
| | - Jacqueline Frost
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (J.F.); (A.B.)
| | - Anne Bowcock
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (J.F.); (A.B.)
- Departments of Dermatology and Genetics & Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weixiong Zhang
- Institute for Systems Biology, Jianghan University, Wuhan 430056, China;
- Department of Computer Science and Engineering, Washington University, Saint Louis, MO 63130, USA
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63130, USA
- Correspondence:
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6
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Bravo JI, Nozownik S, Danthi PS, Benayoun BA. Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation. Development 2020; 147:dev175786. [PMID: 32527937 PMCID: PMC10680986 DOI: 10.1242/dev.175786] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Our understanding of the molecular regulation of aging and age-related diseases is still in its infancy, requiring in-depth characterization of the molecular landscape shaping these complex phenotypes. Emerging classes of molecules with promise as aging modulators include transposable elements, circRNAs and the mitochondrial transcriptome. Analytical complexity means that these molecules are often overlooked, even though they exhibit strong associations with aging and, in some cases, may directly contribute to its progress. Here, we review the links between these novel factors and age-related phenotypes, and we suggest tools that can be easily incorporated into existing pipelines to better understand the aging process.
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Affiliation(s)
- Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Séverine Nozownik
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Magistère européen de Génétique, Université Paris Diderot-Paris 7, Paris 75014, France
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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7
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Serrano-Sevilla I, Artiga Á, Mitchell SG, De Matteis L, de la Fuente JM. Natural Polysaccharides for siRNA Delivery: Nanocarriers Based on Chitosan, Hyaluronic Acid, and Their Derivatives. Molecules 2019; 24:E2570. [PMID: 31311176 PMCID: PMC6680562 DOI: 10.3390/molecules24142570] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/03/2019] [Accepted: 07/10/2019] [Indexed: 12/14/2022] Open
Abstract
Natural polysaccharides are frequently used in the design of drug delivery systems due to their biocompatibility, biodegradability, and low toxicity. Moreover, they are diverse in structure, size, and charge, and their chemical functional groups can be easily modified to match the needs of the final application and mode of administration. This review focuses on polysaccharidic nanocarriers based on chitosan and hyaluronic acid for small interfering RNA (siRNA) delivery, which are highly positively and negatively charged, respectively. The key properties, strengths, and drawbacks of each polysaccharide are discussed. In addition, their use as efficient nanodelivery systems for gene silencing applications is put into context using the most recent examples from the literature. The latest advances in this field illustrate effectively how chitosan and hyaluronic acid can be modified or associated with other molecules in order to overcome their limitations to produce optimized siRNA delivery systems with promising in vitro and in vivo results.
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Affiliation(s)
- Inés Serrano-Sevilla
- Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
- CIBER-BBN, Instituto de Salud Carlos III, Madrid, Spain
| | - Álvaro Artiga
- Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
- CIBER-BBN, Instituto de Salud Carlos III, Madrid, Spain
| | - Scott G Mitchell
- Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
- CIBER-BBN, Instituto de Salud Carlos III, Madrid, Spain
| | - Laura De Matteis
- CIBER-BBN, Instituto de Salud Carlos III, Madrid, Spain.
- Instituto de Nanociencia de Aragón (INA), Universidad de Zaragoza, C/Mariano Esquillor s/n, 50018 Zaragoza, Spain.
| | - Jesús M de la Fuente
- Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain.
- CIBER-BBN, Instituto de Salud Carlos III, Madrid, Spain.
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8
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Tang L, He S, Zhu Y, Feng B, Su Z, Liu B, Xu F, Wang X, Liu H, Li C, Zhao J, Zheng X, Li C, Sun C, Lu C, Zheng G. Downregulated miR-187 contributes to the keratinocytes hyperproliferation in psoriasis. J Cell Physiol 2018; 234:3661-3674. [PMID: 30607907 DOI: 10.1002/jcp.27135] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 07/05/2018] [Indexed: 01/08/2023]
Abstract
Psoriasis is a common chronic skin disease characterized by epidermal hyperplasia and inflammation. However, the pathogenesis of psoriasis is multifactorial and is not fully understood. MicroRNAs (miRNAs) represent a promising class of small, noncoding RNA molecules that have a large impact on cellular functions by regulating gene expression. Here we reported that microRNA-187 (miR-187), which is one of the most dynamic microRNAs identified in the deep screening miRNAs profile, is downregulated in inflammatory cytokines-stimulated keratinocytes and psoriatic skins. By luciferase activity assay and gain-of-function studies, we showed that miR-187 inhibits keratinocytes hyperproliferation by targeting CD276. Moreover, overexpression of miR-187 decreases acanthosis and reduces the disease severity in psoriasis mouse models. Taken together, the results of our study implies miR-187 as a critical factor in psoriasis pathogenesis, which could be a potent target for psoriasis treatment.
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Affiliation(s)
- Lipeng Tang
- Deparment of Pharmacology of Traditional Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.,The Postdoctoral Research Station, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Songmin He
- Deparment of Pharmacology of Traditional Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Ying Zhu
- Deparment of Pharmacology of Traditional Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Bing Feng
- Deparment of Pharmacology of Traditional Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zuqing Su
- Deparment of Pharmacology of Traditional Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Bo Liu
- Department of Chemical Research and Structural Optimization based on Chinese Material Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Fangfang Xu
- Department of Chemical Research and Structural Optimization based on Chinese Material Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Xieqi Wang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Hongying Liu
- Department of Pathology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Chutian Li
- Department of Pathology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Jie Zhao
- Department of Pathology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Xirun Zheng
- Department of Pathology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Caiyun Li
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Chaoyue Sun
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Chuanjian Lu
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Guangjuan Zheng
- Deparment of Pharmacology of Traditional Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.,Department of Pathology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
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9
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Xia J, Li L, Li T, Fang Z, Zhang K, Zhou J, Peng H, Zhang W. Detecting and characterizing microRNAs of diverse genomic origins via miRvial. Nucleic Acids Res 2017; 45:e176. [PMID: 29036674 PMCID: PMC5716067 DOI: 10.1093/nar/gkx834] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 09/12/2017] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs form an essential class of post-transcriptional gene regulator of eukaryotic species, and play critical parts in development and disease and stress responses. MicroRNAs may originate from various genomic loci, have structural characteristics, and appear in canonical or modified forms, making them subtle to detect and analyze. We present miRvial, a robust computational method and companion software package that supports parameter adjustment and visual inspection of candidate microRNAs. Extensive results comparing miRvial and six existing microRNA finding methods on six model organisms, Mus musculus, Drosophila melanogaste, Arabidopsis thaliana, Oryza sativa, Physcomitrella patens and Chlamydomonas reinhardtii, demonstrated the utility and rigor of miRvial in detecting novel microRNAs and characterizing features of microRNAs. Experimental validation of several novel microRNAs in C. reinhardtii that were predicted by miRvial but missed by the other methods illustrated the superior performance of miRvial over the existing methods. miRvial is open source and available at https://github.com/SystemsBiologyOfJianghanUniversity/miRvial.
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Affiliation(s)
- Jing Xia
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China.,Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lun Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Tiantian Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Zhiwei Fang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Kevin Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China.,Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Junfei Zhou
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Hai Peng
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Weixiong Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China.,Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO 63130, USA
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10
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Zinad HS, Natasya I, Werner A. Natural Antisense Transcripts at the Interface between Host Genome and Mobile Genetic Elements. Front Microbiol 2017; 8:2292. [PMID: 29209299 PMCID: PMC5701935 DOI: 10.3389/fmicb.2017.02292] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/06/2017] [Indexed: 12/26/2022] Open
Abstract
Non-coding RNAs are involved in epigenetic processes, playing a role in the regulation of gene expression at the transcriptional and post-transcriptional levels. A particular group of ncRNA are natural antisense transcripts (NATs); these are transcribed in the opposite direction to protein coding transcripts and are widespread in eukaryotes. Their abundance, evidence of phylogenetic conservation and an increasing number of well-characterized examples of antisense-mediated gene regulation are indicative of essential biological roles of NATs. There is evidence to suggest that they interfere with their corresponding sense transcript to elicit concordant and discordant regulation. The main mechanisms involved include transcriptional interference as well as dsRNA formation. Sense–antisense hybrid formation can trigger RNA interference, RNA editing or protein kinase R. However, the exact molecular mechanisms elicited by NATs in the context of these regulatory roles are currently poorly understood. Several examples confirm that ectopic expression of antisense transcripts trigger epigenetic silencing of the related sense transcript. Genomic approaches suggest that the antisense transcriptome carries a broader biological significance which goes beyond the physiological regulation of the directly related sense transcripts. Because NATs show evidence of conservation we speculate that they played a role in evolution, with early eukaryotes gaining selective advantage through the regulatory effects. With the surge of genome and transcriptome sequencing projects, there is promise of a more comprehensive understanding of the biological role of NATs and the regulatory mechanisms involved.
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Affiliation(s)
- Hany S Zinad
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Inas Natasya
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andreas Werner
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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11
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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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12
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Biogenesis and Function of Ago-Associated RNAs. Trends Genet 2017; 33:208-219. [PMID: 28174021 DOI: 10.1016/j.tig.2017.01.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/10/2017] [Indexed: 12/20/2022]
Abstract
Numerous sophisticated high-throughput sequencing technologies have been developed over the past decade, and these have enabled the discovery of a diverse catalog of small non-coding (nc)RNA molecules that function as regulatory entities by associating with Argonaute (Ago) proteins. MicroRNAs (miRNAs) are currently the best-described class of post-transcriptional regulators that follow a specific biogenesis pathway characterized by Drosha/DGCR8 and Dicer processing. However, more exotic miRNA-like species that bypass particular steps of the canonical miRNA biogenesis pathway continue to emerge, with one of the most recent additions being the agotrons, which escape both Drosha/DGCR8- and Dicer-processing. We review here the current knowledge and most recent discoveries relating to alternative functions and biogenesis strategies for Ago-associated RNAs in mammals.
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13
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Feng C, Bai M, Yu NZ, Wang XJ, Liu Z. MicroRNA-181b negatively regulates the proliferation of human epidermal keratinocytes in psoriasis through targeting TLR4. J Cell Mol Med 2016; 21:278-285. [PMID: 27641447 PMCID: PMC5264133 DOI: 10.1111/jcmm.12963] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 08/01/2016] [Indexed: 01/22/2023] Open
Abstract
Our study aims to explore the role of microRNA‐181b (miR‐181b) and TLR in the regulation of cell proliferation of human epidermal keratinocytes (HEKs) in psoriasis. Twenty‐eight patients diagnosed with psoriasis vulgaris were selected as a case group with their lesional and non‐lesional skin tissues collected. A control group consisted of 20 patients who underwent plastic surgery with their healthy skin tissues collected. Real‐time quantitative fluorescence polymerase chain reaction (RT‐qPCR), in situ hybridization and immunohistochemistry were used to detect the expressions of miR‐181b and TLR4 in HEKs of healthy skin, psoriatic lesional skin and non‐lesional skin respectively. The 3′ untranslated region (3′UTR) of TLR4 combined with miR‐181b was verified by a dual‐luciferase reporter assay. Western blotting and bromodeoxyuridine were applied for corresponding detection of TLR4 expression and cell mitosis. The expression of miR‐181b in HEKs of psoriatic lesional skin was less than healthy skin and psoriatic non‐lesional skin. In psoriatic lesional and non‐lesional skin, TLR4‐positive cell rates and the number of positive cells per square millimetre were higher than healthy skin. The dual‐luciferase reporter assay verified that miR‐181b targets TLR4. HEKs transfected with miR‐181b mimics had decreased expression of TLR4, along with the decrease of mitotic indexes and Brdu labelling indexes. However, HEKs transfected with miR‐181b inhibitors showed increased TLR4 expression, mitotic indexes and Brdu labelling indexes. HEKs transfected with both miR‐181b inhibitors and siTLR4 had decreased mitotic indexes and Brdu labelling indexes. These results indicate that miR‐181b can negatively regulate the proliferation of HEKs in psoriasis by targeting TLR4.
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Affiliation(s)
- Cheng Feng
- Aesthetic Plastic Department of Peking Union Medical Collage Hospital, Beijing, China
| | - Ming Bai
- Aesthetic Plastic Department of Peking Union Medical Collage Hospital, Beijing, China
| | - Nan-Ze Yu
- Aesthetic Plastic Department of Peking Union Medical Collage Hospital, Beijing, China
| | - Xiao-Jun Wang
- Aesthetic Plastic Department of Peking Union Medical Collage Hospital, Beijing, China
| | - Zeng Liu
- Aesthetic Plastic Department of Peking Union Medical Collage Hospital, Beijing, China
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14
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Liu Y, Liu Q. MicroRNAs as regulatory elements in psoriasis. Open Med (Wars) 2016; 11:336-340. [PMID: 28352818 PMCID: PMC5329850 DOI: 10.1515/med-2016-0063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/12/2016] [Indexed: 12/31/2022] Open
Abstract
Psoriasis is a chronic, autoimmune, and complex genetic disorder that affects 23% of the European population. The symptoms of Psoriatic skin are inflammation, raised and scaly lesions. microRNA, which is short, nonprotein-coding, regulatory RNAs, plays critical roles in psoriasis. microRNA participates in nearly all biological processes, such as cell differentiation, development and metabolism. Recent researches reveal that multitudinous novel microRNAs have been identified in skin. Some of these substantial novel microRNAs play as a class of posttranscriptional gene regulator in skin disease, such as psoriasis. In order to insight into microRNAs biological functions and verify microRNAs biomarker, we review diverse references about characterization, profiling and subtype of microRNAs. Here we will share our opinions about how and which microRNAs are as regulatory in psoriasis.
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Affiliation(s)
- Yuan Liu
- Department of Dermatovenereology, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China
| | - Quanzhong Liu
- Department of Dermatovenereology, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China
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15
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Keam SP, Hutvagner G. tRNA-Derived Fragments (tRFs): Emerging New Roles for an Ancient RNA in the Regulation of Gene Expression. Life (Basel) 2015; 5:1638-51. [PMID: 26703738 PMCID: PMC4695841 DOI: 10.3390/life5041638] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 11/17/2015] [Accepted: 11/17/2015] [Indexed: 12/15/2022] Open
Abstract
This review will summarise the recent discoveries and current state of research on short noncoding RNAs derived from tRNAs—known as tRNA-derived fragments (tRFs). It will describe the features of the known subtypes of these RNAs; including sequence characteristics, protein interactors, expression characteristics, biogenesis, and similarity to canonical miRNA pathways. Also their role in regulating gene expression; including mediating translational suppression, will be discussed. We also highlight their potential use as biomarkers, functions in gene regulation and links to disease. Finally, this review will speculate as to the origin and rationale for the conservation of this novel class of noncoding RNAs amongst both prokaryotes and eukaryotes.
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Affiliation(s)
- Simon P Keam
- Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo 2007, Australia.
| | - Gyorgy Hutvagner
- Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo 2007, Australia.
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16
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Huang RY, Li L, Wang MJ, Chen XM, Huang QC, Lu CJ. An Exploration of the Role of MicroRNAs in Psoriasis: A Systematic Review of the Literature. Medicine (Baltimore) 2015; 94:e2030. [PMID: 26559308 PMCID: PMC4912302 DOI: 10.1097/md.0000000000002030] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Psoriasis is recently characterized by a specific microRNAs (miRNAs) expression profile, which guides the researchers' efforts to explore the therapeutic targets and objective biomarkers that reflect the diagnosis and disease activity in clinical use for psoriasis.The paper presents a state-of-the-art review of expression and function of miRNAs in psoriasis along with its clinical implications.We analyzed all literature searched by keywords "microRNA" and "psoriasis" in PubMed (Medline) from inception up to July 2015, and the references in the literature searched were also considered.Relevant literature was chosen according to the objective of this review. Relevant literature was searched by 3 independent investigators, and experts in the field of miRNAs and psoriasis were involved in analyzing process.We included any study in which role of miRNAs in psoriasis was examined in relation to disease pathogenesis, diagnosis, and treatment.The specific miRNAs profile has been identified from human psoriatic skin, blood, and hair samples. It is found that genetic polymorphisms related to some of specific miRNAs, miR-146a for example, are associated with psoriasis susceptibility. Key roles of several unique miRNAs, such as miR-203 and miR-125b, in inflammatory responses and immune dysfunction, as well as hyperproliferative disorders of psoriatic lesions have been revealed. Moreover, circulating miRNAs detected from blood samples have a potential of clinic application to be the biomarkers of diagnosis, prognosis, and treatment responses. Additionally, a new layer of regulatory mechanisms mediated by miRNAs is to some extent revealed in pathogenesis of psoriasis.The dramatically altered mRNA expression profiles are displayed in psoriasis, and some of these may become disease markers and therapeutic targets. Herein, this work underscores the potential importance of miRNAs to diagnosis, prognosis, and treatment of psoriasis. However, further study in this field is worth doing in the future, as the exact roles of miRNAs in psoriasis have not been fully elucidated.Systematic review registration number is not registered.
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Affiliation(s)
- Run-Yue Huang
- From the Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine) (RYH, XMC, QCH, CJL); and Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China (RYH, LL, MJW, XMC, CJL)
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17
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Desvignes T, Batzel P, Berezikov E, Eilbeck K, Eppig JT, McAndrews MS, Singer A, Postlethwait JH. miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants. Trends Genet 2015; 31:613-626. [PMID: 26453491 DOI: 10.1016/j.tig.2015.09.002] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/10/2015] [Accepted: 09/04/2015] [Indexed: 12/21/2022]
Abstract
High-throughput sequencing of miRNAs has revealed the diversity and variability of mature and functional short noncoding RNAs, including their genomic origins, biogenesis pathways, sequence variability, and newly identified products such as miRNA-offset RNAs (moRs). Here we review known cases of alternative mature miRNA-like RNA fragments and propose a revised definition of miRNAs to encompass this diversity. We then review nomenclature guidelines for miRNAs and propose to extend nomenclature conventions to align with those for protein-coding genes established by international consortia. Finally, we suggest a system to encompass the full complexity of sequence variations (i.e., isomiRs) in the analysis of small RNA sequencing experiments.
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Affiliation(s)
- T Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - P Batzel
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - E Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - K Eilbeck
- Utah Science, Technology, and Research Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA; Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84112, USA
| | - J T Eppig
- Mouse Genome Informatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - M S McAndrews
- Mouse Genome Informatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - A Singer
- ZFIN, 5291 University of Oregon, Eugene, OR 97403-5291, USA
| | - J H Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
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18
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Jha A, Panzade G, Pandey R, Shankar R. A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm. Nucleic Acids Res 2015; 43:8713-24. [PMID: 26354861 PMCID: PMC4605316 DOI: 10.1093/nar/gkv871] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/17/2015] [Indexed: 12/24/2022] Open
Abstract
Post ENCODE, regulatory sRNAs (rsRNAs) like miRNAs have established their status as one of the core regulatory elements of cell systems. However, large number of rsRNAs are compromised due to traditional approaches to identify miRNAs, limiting the otherwise vast world of rsRNAs mainly to hair-pin loop bred typical miRNAs. The present study has analyzed for the first time a huge volume of sequencing data from 4997 individuals and 25 cancer types to report 11 234 potentially regulatory small RNAs which appear to have deep reaching impact. The rsRNA-target interactions have been studied and validated extensively using experimental data from AGO-crosslinking, DGCR8 knockdown, CLASH, proteome and expression data. A subset of such interactions was also validated independently in the present study using multiple cell lines, by qPCR. Several of the potential rsRNAs have emerged as a critical cancer biomarker controlling some important spots of cell system. The entire study has been presented into an interactive info-analysis portal handling more than 260 GB of processed data. The possible degree of cell system regulation by sRNAs appears to be much higher than previously assumed.
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Affiliation(s)
- Ashwani Jha
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, HP, India Academy of Scientific & Innovative Research, Chennai, India
| | - Ganesh Panzade
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, HP, India Academy of Scientific & Innovative Research, Chennai, India
| | - Rajesh Pandey
- CSIR Ayurgenomics Unit -TRISUTRA, CSIR-Institute of Genomics & Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Ravi Shankar
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, HP, India Academy of Scientific & Innovative Research, Chennai, India
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19
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Abdelfattah AM, Park C, Choi MY. Update on non-canonical microRNAs. Biomol Concepts 2015; 5:275-87. [PMID: 25372759 DOI: 10.1515/bmc-2014-0012] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 07/07/2014] [Indexed: 12/14/2022] Open
Abstract
Non-canonical microRNAs are a recently-discovered subset of microRNAs. They structurally and functionally resemble canonical miRNAs, but were found to follow distinct maturation pathways, typically bypassing one or more steps of the classic canonical biogenesis pathway. Non-canonical miRNAs were found to have diverse origins, including introns, snoRNAs, endogenous shRNAs and tRNAs. Our knowledge about their functions remains relatively primitive; however, many interesting discoveries have taken place in the past few years. They have been found to take part in several cellular processes, such as immune response and stem cell proliferation. Adversely, their deregulation has pathologic effects on several different tissues, which strongly suggests an integral role for non-canonical miRNAs in disease pathogenesis. In this review, we discuss the recently-discovered functional characteristics of non-canonical miRNAs and illustrate their principal maturation pathways as well as debating their potential role in multiple cellular processes.
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20
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Løvendorf MB, Skov L. miRNAs in inflammatory skin diseases and their clinical implications. Expert Rev Clin Immunol 2015; 11:467-77. [PMID: 25719822 DOI: 10.1586/1744666x.2015.1020301] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
miRNAs are a class of non-coding RNA molecules that modulate gene expression post-transcriptionally. They have a major impact on several physiological and pathological cellular processes including modulation of the innate and the adaptive immune system. The role of miRNAs in skin biology is still incomplete; however, it is known that miRNAs are implicated in various cellular processes of both normal and diseased skin. Some miRNAs appear to be consistently deregulated in several different inflammatory skin diseases, including psoriasis and atopic dermatitis, indicating a common role in fundamental biological processes. The clinical implications of miRNAs are intriguing, both from a diagnostic and a therapeutic perspective. Accordingly, there is emerging evidence for the clinical potential of miRNAs as both biomarkers and possible therapeutic targets in skin diseases. Future studies will hopefully establish the biological significance of miRNAs in skin biology, paving the way for new miRNA-based diagnostic and therapeutic applications in dermatology.
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Affiliation(s)
- Marianne B Løvendorf
- Department of Dermato-Allergology, Gentofte Hospital, University of Copenhagen, Kildegårdsvej 28, 2900 Hellerup, Denmark
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21
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Quek XC, Thomson DW, Maag JLV, Bartonicek N, Signal B, Clark MB, Gloss BS, Dinger ME. lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res 2014; 43:D168-73. [PMID: 25332394 PMCID: PMC4384040 DOI: 10.1093/nar/gku988] [Citation(s) in RCA: 388] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Despite the prevalence of long noncoding RNA (lncRNA) genes in eukaryotic genomes, only a small proportion have been examined for biological function. lncRNAdb, available at http://lncrnadb.org, provides users with a comprehensive, manually curated reference database of 287 eukaryotic lncRNAs that have been described independently in the scientific literature. In addition to capturing a great proportion of the recent literature describing functions for individual lncRNAs, lncRNAdb now offers an improved user interface enabling greater accessibility to sequence information, expression data and the literature. The new features in lncRNAdb include the integration of Illumina Body Atlas expression profiles, nucleotide sequence information, a BLAST search tool and easy export of content via direct download or a REST API. lncRNAdb is now endorsed by RNAcentral and is in compliance with the International Nucleotide Sequence Database Collaboration.
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Affiliation(s)
- Xiu Cheng Quek
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Daniel W Thomson
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia
| | - Jesper L V Maag
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Nenad Bartonicek
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia
| | - Bethany Signal
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia
| | - Michael B Clark
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Brian S Gloss
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
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22
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Gantier MP. Processing of Double-Stranded RNA in Mammalian Cells: A Direct Antiviral Role? J Interferon Cytokine Res 2014; 34:469-77. [DOI: 10.1089/jir.2014.0003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Michael P. Gantier
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Australia
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23
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Swindell WR, Xing X, Voorhees JJ, Elder JT, Johnston A, Gudjonsson JE. Integrative RNA-seq and microarray data analysis reveals GC content and gene length biases in the psoriasis transcriptome. Physiol Genomics 2014; 46:533-46. [PMID: 24844236 DOI: 10.1152/physiolgenomics.00022.2014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Gene expression profiling of psoriasis has driven research advances and may soon provide the basis for clinical applications. For expression profiling studies, RNA-seq is now a competitive technology, but RNA-seq results may differ from those obtained by microarray. We therefore compared findings obtained by RNA-seq with those from eight microarray studies of psoriasis. RNA-seq and microarray datasets identified similar numbers of differentially expressed genes (DEGs), with certain genes uniquely identified by each technology. Correspondence between platforms and the balance of increased to decreased DEGs was influenced by mRNA abundance, GC content, and gene length. Weakly expressed genes, genes with low GC content, and long genes were all biased toward decreased expression in psoriasis lesions. The strength of these trends differed among array datasets, most likely due to variations in RNA quality. Gene length bias was by far the strongest trend and was evident in all datasets regardless of the expression profiling technology. The effect was due to differences between lesional and uninvolved skin with respect to the genome-wide correlation between gene length and gene expression, which was consistently more negative in psoriasis lesions. These findings demonstrate the complementary nature of RNA-seq and microarray technology and show that integrative analysis of both data types can provide a richer view of the transcriptome than strict reliance on a single method alone. Our results also highlight factors affecting correspondence between technologies, and we have established that gene length is a major determinant of differential expression in psoriasis lesions.
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Affiliation(s)
- William R Swindell
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Xianying Xing
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - John J Voorhees
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - James T Elder
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Andrew Johnston
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan
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24
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Xia J, Zhang W. A meta-analysis revealed insights into the sources, conservation and impact of microRNA 5'-isoforms in four model species. Nucleic Acids Res 2014; 42:1427-41. [PMID: 24178030 PMCID: PMC3919606 DOI: 10.1093/nar/gkt967] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 09/12/2013] [Accepted: 10/01/2013] [Indexed: 12/20/2022] Open
Abstract
MicroRNA (miRNA) 5'-isoforms, or 5'-isomiRs, are small-RNA species that originate from the same genomic loci as the major miRNAs with their 5' ends shifted from the 5' ends of the miRNAs by a few nucleotides. Although 5'-isomiRs have been reported, their origins, properties and potential functions remain to be examined. We systematically studied 5'-isomiRs in human, mouse, fruitfly and worm by analysing a large collection of small non-coding RNA and mRNA profiling data. The results revealed a broad existence of 5'-isomiRs in the four species, many of which were conserved and could arise from genomic loci of canonical and non-canonical miRNAs. The well-conserved 5'-isomiRs have several features, including a preference of the 3p over the 5p arms of hairpins of conserved mammalian miRNAs, altered 5'-isomiRs across species and across tissues, and association with structural variations of miRNA hairpins. Importantly, 5'-isomiRs and their major miRNAs may have different mRNA targets and thus potentially play distinct roles of gene regulation, as shown by an integrative analysis combining miRNA and mRNA profiling data from psoriatic and normal human skin and from murine miRNA knockout assays. Indeed, 18 5'-isomiRs had aberrant expression in psoriatic human skin, suggesting their potential function in psoriasis pathogenesis. The results of the current study deepened our understanding of the diversity and conservation of miRNAs, their plasticity in gene regulation and potential broad function in complex diseases.
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Affiliation(s)
- Jing Xia
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China, Department of Computer Science and Engineering, Washington University in Saint Louis, One Brookings Drive, St. Louis, MO 63130, USA and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Weixiong Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China, Department of Computer Science and Engineering, Washington University in Saint Louis, One Brookings Drive, St. Louis, MO 63130, USA and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
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25
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Abstract
Psoriasis is a chronic and common human skin disorder currently with no cure. Psoriatic skin displays inflammatory, raised, and scaly lesions with widely aberrant gene expression. Recent studies have revealed critical roles that microRNAs play as a class of posttranscriptional gene regulator in skin development and skin diseases. A substantial number of novel microRNAs have been identified in skin, and much has been learned about the dysregulated expression and functional roles of microRNAs in psoriasis, as well as the robustness and plasticity of microRNA-mediated gene expression regulation. Here we review recent progresses in discovery, profiling, and characterization of microRNAs in human psoriatic skin, discuss insights to their biological functions, and share our view on remaining challenges to be addressed.
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Affiliation(s)
- Jing Xia
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, China
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26
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Swindell WR, Johnston A, Xing X, Voorhees JJ, Elder JT, Gudjonsson JE. Modulation of epidermal transcription circuits in psoriasis: new links between inflammation and hyperproliferation. PLoS One 2013; 8:e79253. [PMID: 24260178 PMCID: PMC3829857 DOI: 10.1371/journal.pone.0079253] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/19/2013] [Indexed: 12/16/2022] Open
Abstract
Background Whole-genome expression profiling has been used to characterize molecular-level differences between psoriasis lesions and normal skin. Pathway analysis, however, is complicated by the fact that expression profiles have been derived from bulk skin biopsies with RNA derived from multiple cell types. Results We analyzed gene expression across a large sample of psoriatic (PP) and uninvolved/normal (PN) skin biopsies (n = 215 patients). We identified 1975 differentially expressed genes, including 8 associated with psoriasis susceptibility loci. To facilitate pathway analysis, PP versus PN differences in gene expression were analyzed with respect to 235 gene modules, each containing genes with a similar expression pattern in keratinocytes and epidermis. We identified 30 differentially expressed modules (DEMs) biased towards PP-increased or PP-decreased expression. These DEMs were associated with regulatory axes involving cytokines (e.g., IFN-γ, IL-17A, TNF-α), transcription factors (e.g., STAT1, NF-κB, E2F, RUNX1) and chromatin modifiers (SETDB1). We identified an interferon-induced DEM with genes encoding anti-viral proteins (designated “STAT1-57”), which was activated in psoriatic epidermis but repressed following biologic therapy. Genes within this DEM shared a motif near the transcription start site resembling the interferon-stimulated response element (ISRE). Conclusions We analyzed a large patient cohort and developed a new approach for delineating epidermis-specific pathways and regulatory mechanisms that underlie altered gene expression in psoriasis. Our findings highlight previously unrecognized “transcription circuits” that can provide targets for development of non-systemic therapies.
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Affiliation(s)
- William R. Swindell
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
- * E-mail:
| | - Andrew Johnston
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Xianying Xing
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - John J. Voorhees
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - James T. Elder
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Johann E. Gudjonsson
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
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27
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Zhernakova A, Withoff S, Wijmenga C. Clinical implications of shared genetics and pathogenesis in autoimmune diseases. Nat Rev Endocrinol 2013; 9:646-59. [PMID: 23959365 DOI: 10.1038/nrendo.2013.161] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Many endocrine diseases, including type 1 diabetes mellitus, Graves disease, Addison disease and Hashimoto disease, originate as an autoimmune reaction that affects disease-specific target organs. These autoimmune diseases are characterized by the development of specific autoantibodies and by the presence of autoreactive T cells. They are caused by a complex genetic predisposition that is attributable to multiple genetic variants, each with a moderate-to-low effect size. Most of the genetic variants associated with a particular autoimmune endocrine disease are shared between other systemic and organ-specific autoimmune and inflammatory diseases, such as rheumatoid arthritis, coeliac disease, systemic lupus erythematosus and psoriasis. Here, we review the shared and specific genetic background of autoimmune diseases, summarize their treatment options and discuss how identifying the genetic and environmental factors that predispose patients to an autoimmune disease can help in the diagnosis and monitoring of patients, as well as the design of new treatments.
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Affiliation(s)
- Alexandra Zhernakova
- University of Groningen, University Medical Centre Groningen, Department of Genetics, PO Box 30001, 9700 RB Groningen, Netherlands
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28
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Brandis KA, Gale S, Jinn S, Langmade SJ, Dudley-Rucker N, Jiang H, Sidhu R, Ren A, Goldberg A, Schaffer JE, Ory DS. Box C/D small nucleolar RNA (snoRNA) U60 regulates intracellular cholesterol trafficking. J Biol Chem 2013; 288:35703-13. [PMID: 24174535 DOI: 10.1074/jbc.m113.488577] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mobilization of plasma membrane (PM) cholesterol to the endoplasmic reticulum is essential for cellular cholesterol homeostasis. The mechanisms regulating this retrograde, intermembrane cholesterol transfer are not well understood. Because mutant cells with defects in PM to endoplasmic reticulum cholesterol trafficking can be isolated on the basis of resistance to amphotericin B, we conducted an amphotericin B loss-of-function screen in Chinese hamster ovary (CHO) cells using insertional mutagenesis to identify genes that regulate this trafficking mechanism. Mutant line A1 displayed reduced cholesteryl ester formation from PM-derived cholesterol and increased de novo cholesterol synthesis, indicating a deficiency in retrograde cholesterol transport. Genotypic analysis revealed that the A1 cell line contained one disrupted allele of the U60 small nucleolar RNA (snoRNA) host gene, resulting in haploinsufficiency of the box C/D snoRNA U60. Complementation and mutational studies revealed the U60 snoRNA to be the essential feature from this locus that affects cholesterol trafficking. Lack of alteration in predicted U60-mediated site-directed methylation of 28 S rRNA in the A1 mutant suggests that the U60 snoRNA modulates cholesterol trafficking by a mechanism that is independent of this canonical function. Our study adds to a growing body of evidence for participation of small noncoding RNAs in cholesterol homeostasis and is the first to implicate a snoRNA in this cellular function.
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Affiliation(s)
- Katrina A Brandis
- From the Diabetic Cardiovascular Disease Center, Washington University School of Medicine, St. Louis, Missouri 63110
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Perez P, Jang SI, Alevizos I. Emerging landscape of non-coding RNAs in oral health and disease. Oral Dis 2013; 20:226-35. [PMID: 23781896 DOI: 10.1111/odi.12142] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 12/20/2022]
Abstract
The world of non-coding RNAs has only recently started being discovered. For the past 40 years, coding genes, mRNA, and proteins have been the center of cellular and molecular biology, and pathologic alterations were attributed to either the aberration of gene sequence or altered promoter activity. It was only after the completion of the human genome sequence that the scientific community started seriously wondering why only a very small portion of the genome corresponded to protein-coding genes. New technologies such as the whole-genome and whole-transcriptome sequencing demonstrated that at least 90% of the genome is actively transcribed. The identification and cataloguing of multiple kinds of non-coding RNA (ncRNA) have exponentially increased, and it is now widely accepted that ncRNAs play major biological roles in cellular physiology, development, metabolism, and are also implicated in a variety of diseases. The aim of this review is to describe the two major classes (long and short forms) of non-coding RNAs and describe their subclasses in terms of function and their relevance and potential in oral diseases.
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Affiliation(s)
- P Perez
- Sjögren's Clinic, Molecular Physiology & Therapeutics, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
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Bicchi I, Morena F, Montesano S, Polidoro M, Martino S. MicroRNAs and Molecular Mechanisms of Neurodegeneration. Genes (Basel) 2013; 4:244-63. [PMID: 24705162 PMCID: PMC3899972 DOI: 10.3390/genes4020244] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/09/2013] [Accepted: 05/10/2013] [Indexed: 12/21/2022] Open
Abstract
During the last few years microRNAs (miRNAs) have emerged as key mediators of post-transcriptional and epigenetic regulation of gene expression. MiRNAs targets, identified through gene expression profiling and studies in animal models, depict a scenario where miRNAs are fine-tuning metabolic pathways and genetic networks in both plants and animals. MiRNAs have shown to be differentially expressed in brain areas and alterations of miRNAs homeostasis have been recently correlated to pathological conditions of the nervous system, such as cancer and neurodegeneration. Here, we review and discuss the most recent insights into the involvement of miRNAs in the neurodegenerative mechanisms and their correlation with significant neurodegenerative disorders.
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Affiliation(s)
- Ilaria Bicchi
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Via del Giochetto, 06126 Perugia, Italy.
| | - Francesco Morena
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Via del Giochetto, 06126 Perugia, Italy.
| | - Simona Montesano
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Via del Giochetto, 06126 Perugia, Italy.
| | - Mario Polidoro
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Via del Giochetto, 06126 Perugia, Italy.
| | - Sabata Martino
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Via del Giochetto, 06126 Perugia, Italy.
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Contribution of Long Noncoding RNAs to Autism Spectrum Disorder Risk. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2013; 113:35-59. [DOI: 10.1016/b978-0-12-418700-9.00002-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Garcia-Silva MR, Cabrera-Cabrera F, Güida MC, Cayota A. Novel aspects of tRNA-derived small RNAs with potential impact in infectious diseases. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/abb.2013.45a002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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