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Legaz I, Jimenez-Coll V, González-López R, Fernández-González M, Alegría-Marcos MJ, Galián JA, Botella C, Moya-Quiles R, Muro-Pérez M, Minguela A, Llorente S, Muro M. MicroRNAs as Potential Graft Rejection or Tolerance Biomarkers and Their Dilemma in Clinical Routines Behaving like Devilish, Angelic, or Frightening Elements. Biomedicines 2024; 12:116. [PMID: 38255221 PMCID: PMC10813128 DOI: 10.3390/biomedicines12010116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Allograft rejection is a widespread complication in allograft recipients with chronic kidney disease. Undertreatment of subclinical and clinical rejection and later post-transplant problems are caused by an imperfect understanding of the mechanisms at play and a lack of adequate diagnostic tools. Many different biomarkers have been analyzed and proposed to detect and monitor these crucial events in transplant outcomes. In this sense, microRNAs may help diagnose rejection or tolerance and indicate appropriate treatment, especially in patients with chronic allograft rejection. As key epigenetic regulators of physiological homeostasis, microRNAs have therapeutic potential and may indicate allograft tolerance or rejection. However, more evidence and clinical validation are indispensable before microRNAs are ready for clinical prime time.
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Affiliation(s)
- Isabel Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute of Murcia (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum,” Faculty of Medicine, University of Murcia (UMU), 30100 Murcia, Spain
| | - Víctor Jimenez-Coll
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
| | - Rosana González-López
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
| | | | | | - José Antonio Galián
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
| | - Carmen Botella
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
| | - Rosa Moya-Quiles
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
| | - Manuel Muro-Pérez
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
| | - Alfredo Minguela
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
| | - Santiago Llorente
- Service of Nephrology, Unit Hospital Clinic Universitario Virgen de la Arrixaca, IMIB-Arrixaca, 30120 Murcia, Spain
| | - Manuel Muro
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
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2
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Zulian V, Fiscon G, Paci P, Garbuglia AR. Hepatitis B Virus and microRNAs: A Bioinformatics Approach. Int J Mol Sci 2023; 24:17224. [PMID: 38139051 PMCID: PMC10743825 DOI: 10.3390/ijms242417224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
In recent decades, microRNAs (miRNAs) have emerged as key regulators of gene expression, and the identification of viral miRNAs (v-miRNAs) within some viruses, including hepatitis B virus (HBV), has attracted significant attention. HBV infections often progress to chronic states (CHB) and may induce fibrosis/cirrhosis and hepatocellular carcinoma (HCC). The presence of HBV can dysregulate host miRNA expression, influencing several biological pathways, such as apoptosis, innate and immune response, viral replication, and pathogenesis. Consequently, miRNAs are considered a promising biomarker for diagnostic, prognostic, and treatment response. The dynamics of miRNAs during HBV infection are multifaceted, influenced by host variability and miRNA interactions. Given the ability of miRNAs to target multiple messenger RNA (mRNA), understanding the viral-host (human) interplay is complex but essential to develop novel clinical applications. Therefore, bioinformatics can help to analyze, identify, and interpret a vast amount of miRNA data. This review explores the bioinformatics tools available for viral and host miRNA research. Moreover, we introduce a brief overview focusing on the role of miRNAs during HBV infection. In this way, this review aims to help the selection of the most appropriate bioinformatics tools based on requirements and research goals.
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Affiliation(s)
- Verdiana Zulian
- Virology Laboratory, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy;
| | - Giulia Fiscon
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (P.P.)
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, 00185 Rome, Italy
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (P.P.)
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, 00185 Rome, Italy
| | - Anna Rosa Garbuglia
- Virology Laboratory, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy;
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MicroRNA Expression Changes in Kidney Transplant: Diagnostic Efficacy of miR-150-5p as Potential Rejection Biomarker, Pilot Study. J Clin Med 2021; 10:jcm10132748. [PMID: 34206682 PMCID: PMC8268834 DOI: 10.3390/jcm10132748] [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: 05/19/2021] [Revised: 06/13/2021] [Accepted: 06/17/2021] [Indexed: 12/14/2022] Open
Abstract
Background: The kidney allograft biopsy is considered the gold standard for rejection diagnosis but is invasive and could be indeterminate. Several publications point to the role of miRNA expression in suggesting its involvement in the acceptance or rejection of organ transplantation. This study aimed to analyze microRNAs involved in the differentiation and activation of B and T lymphocytes from kidney transplant (KT) patients’ peripheral blood leukocytes to be used as biomarkers of acute renal rejection (AR). Methods: A total of 15 KT patients with and without acute rejection (AR/NAR) were analyzed and quantified by miRNA PCR array. A total of 84 miRNAs related to lymphocyte differentiation and activation B and T were studied. The functions and biological pathways were analyzed to predict the potential targets of differential expressed miRNAs. Results: Six miRNA were increased in the AR group (miR-191-5p, miR-223-3p, miR-346, miR-423-5p, miR-574-3p, and miR-181d) and miR-150-5p was increased in the NAR group. In silico studies showed a total of 2603 target genes for the increased miRNAs in AR, while for the decrease miRNA, a total of 1107 target-potential genes were found. Conclusions: Our results show that KT with AR shows a decrease in miR-150-5p expression compared to NAR, suggesting that the decrease in miR-150-5p could be related to an increased MBD6 whose deregulation could have clinical consequences.
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Aishwarya S, Gunasekaran K, Margret AA. Computational gene expression profiling in the exploration of biomarkers, non-coding functional RNAs and drug perturbagens for COVID-19. J Biomol Struct Dyn 2020; 40:3681-3696. [PMID: 33228475 PMCID: PMC7754930 DOI: 10.1080/07391102.2020.1850360] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The coronavirus disease, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is a global health crisis that is being endured with an increased alarm of transmission each day. Though the pandemic has activated innumerable research attention to decipher an antidote, fundamental understanding of the molecular mechanisms is necessary to halt the disease progression. The study focused on comparison of the COVID-19 infected lung tissue gene expression datasets -GSE155241 and GSE150316 with the GEO2R-limma package. The significant up- and downregulated genes were annotated. Further evaluation of the enriched pathways, transcription factors, kinases, noncoding RNAs and drug perturbations revealed the significant molecular mechanisms of the host response. The results revealed a surge in mitochondrial respiration, cytokines, neurodegenerative mechanisms and deprived oxygen, iron, copper, and glucose transport. Hijack of ubiquitination by SARS-CoV-2, hox gene differentiation, histone modification, and miRNA biogenesis were the notable molecular mechanisms inferred. Long non-coding RNAs such as C058791.1, TTTY15 and TPTEP1 were predicted to be efficient in regulating the disease mechanisms. Drugs-F-1566-0341, Digoxin, Proscillaridin and Linifanib that reverse the gene expression signatures were predicted from drug perturbations analysis. The binding efficiency and interaction of proscillaridin and digoxin as obtained from the molecular docking studies confirmed their therapeutic potential. Two overlapping upregulated genes MDH1, SGCE and one downregulated gene PFKFB3 were appraised as potential biomarkers candidates. The upregulation of PGM5, ISLR and ANK2 as measured from their expressions in normal lungs affirmed their possible prognostic biomarker competence. The study explored significant insights for better diagnosis, and therapeutic options for COVID-19. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- S Aishwarya
- Department of Bioinformatics, Stella Maris College, Chennai, Tamil Nadu, India.,Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, Tamil Nadu, India
| | - K Gunasekaran
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, Tamil Nadu, India
| | - A Anita Margret
- Department of Biotechnology, Bishop Heber College, Tiruchirappalli, Tamil Nadu, India
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TET2 functions as a resistance factor against DNA methylation acquisition during Epstein-Barr virus infection. Oncotarget 2018; 7:81512-81526. [PMID: 27829228 PMCID: PMC5348409 DOI: 10.18632/oncotarget.13130] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/17/2016] [Indexed: 12/13/2022] Open
Abstract
Extensive DNA methylation is observed in gastric cancer with Epstein-Barr virus (EBV) infection, and EBV infection is the cause to induce this extensive hypermethylaton phenotype in gastric epithelial cells. However, some 5′ regions of genes do not undergo de novo methylation, despite the induction of methylation in surrounding regions, suggesting the existence of a resistance factor against DNA methylation acquisition. We conducted an RNA-seq analysis of gastric epithelial cells with and without EBV infection and found that TET family genes, especially TET2, were repressed by EBV infection at both mRNA and protein levels. TET2 was found to be downregulated by EBV transcripts, e.g. BARF0 and LMP2A, and also by seven human miRNAs targeting TET2, e.g., miR-93 and miR-29a, which were upregulated by EBV infection, and transfection of which into gastric cells repressed TET2. Hydroxymethylation target genes by TET2 were detected by hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq) with and without TET2 overexpression, and overlapped significantly with methylation target genes in EBV-infected cells. When TET2 was knocked down by shRNA, EBV infection induced de novo methylation more severely, including even higher methylation in methylation-acquired promoters or de novo methylation acquisition in methylation-protected promoters, leading to gene repression. TET2 knockdown alone without EBV infection did not induce de novo DNA methylation. These data suggested that TET2 functions as a resistance factor against DNA methylation in gastric epithelial cells and repression of TET2 contributes to DNA methylation acquisition during EBV infection.
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6
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Singh NK. miRNAs target databases: developmental methods and target identification techniques with functional annotations. Cell Mol Life Sci 2017; 74:2239-2261. [PMID: 28204845 PMCID: PMC11107700 DOI: 10.1007/s00018-017-2469-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 01/09/2017] [Accepted: 01/18/2017] [Indexed: 12/13/2022]
Abstract
PURPOSE microRNA (miRNA) regulates diverse biological mechanisms and metabolisms in plants and animals. Thus, the discoveries of miRNA has revolutionized the life sciences and medical research.The miRNA represses and cleaves the targeted mRNA by binding perfect or near perfect or imperfect complementary base pairs by RNA-induced silencing complex (RISC) formation during biogenesis process. One miRNA interacts with one or more mRNA genes and vice versa, hence takes part in causing various diseases. In this paper, the different microRNA target databases and their functional annotations developed by various researchers have been reviewed. The concurrent research review aims at comprehending the significance of miRNA and presenting the existing status of annotated miRNA target resources built by researchers henceforth discovering the knowledge for diagnosis and prognosis. METHODS AND RESULTS This review discusses the applications and developmental methodologies for constructing target database as well as the utility of user interface design. An integrated architecture is drawn and a graphically comparative study of present status of miRNA targets in diverse diseases and various biological processes is performed. These databases comprise of information such as miRNA target-associated disease, transcription factor binding sites (TFBSs) in miRNA genomic locations, polymorphism in miRNA target, A-to-I edited target, Gene Ontology (GO), genome annotations, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, target expression analysis, TF-miRNA and miRNA-mRNA interaction networks, drugs-targets interactions, etc. CONCLUSION miRNA target databases contain diverse experimentally and computationally predicted target through various algorithms. The comparison of various miRNA target database has been performed on various parameters. The computationally predicted target databases suffer from false positive information as there is no common theory for prediction of miRNA targets. The review conclusion emphasizes the need of more intelligent computational improvement for the miRNA target identification, their functional annotations and datasbase development.
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Affiliation(s)
- Nagendra Kumar Singh
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, 462003, India.
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Wang K, Dantec C, Lemaire P, Onuma TA, Nishida H. Genome-wide survey of miRNAs and their evolutionary history in the ascidian, Halocynthia roretzi. BMC Genomics 2017; 18:314. [PMID: 28427349 PMCID: PMC5399378 DOI: 10.1186/s12864-017-3707-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/12/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND miRNAs play essential roles in the modulation of cellular functions via degradation and/or translation attenuation of target mRNAs. They have been surveyed in a single ascidian genus, Ciona. Recently, an annotated draft genome sequence for a distantly related ascidian, Halocynthia roretzi, has become available, but miRNAs in H. roretzi have not been previously studied. RESULTS We report the prediction of 319 candidate H. roretzi miRNAs, obtained through three complementary methods. Experimental validation suggests that more than half of these candidate miRNAs are expressed during embryogenesis. The majority of predicted H. roretzi miRNAs appear specific to ascidians or tunicates, and only 32 candidates, belonging to 25 families, are widely conserved across metazoans. CONCLUSION Our study presents a comprehensive identification of candidate H. roretzi miRNAs. This resource will facilitate the study of the mechanisms for miRNA-controlled gene regulatory networks during ascidian development. Further, our analysis suggests that the majority of Halocynthia miRNAs are specific to ascidian or tunicates, with only a small number of widely conserved miRNAs. This result is consistent with the general notion that animal miRNAs are less conserved between taxa than plant ones.
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Affiliation(s)
- Kai Wang
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan. .,Present address: Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Science, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, People's Republic of China.
| | - Christelle Dantec
- Centre de Recherches de Biologie cellulaire de Montpellier (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090, Montpellier, France
| | - Patrick Lemaire
- Centre de Recherches de Biologie cellulaire de Montpellier (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090, Montpellier, France
| | - Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
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8
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Computational Approaches and Related Tools to Identify MicroRNAs in a Species: A Bird’s Eye View. Interdiscip Sci 2017; 10:616-635. [DOI: 10.1007/s12539-017-0223-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 12/20/2016] [Accepted: 03/09/2017] [Indexed: 12/26/2022]
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9
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Eggenhofer F, Hofacker IL, Höner Zu Siederdissen C. RNAlien - Unsupervised RNA family model construction. Nucleic Acids Res 2016; 44:8433-41. [PMID: 27330139 PMCID: PMC5041467 DOI: 10.1093/nar/gkw558] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 06/06/2016] [Accepted: 06/08/2016] [Indexed: 02/06/2023] Open
Abstract
Determining the function of a non-coding RNA requires costly and time-consuming wet-lab experiments. For this reason, computational methods which ascertain the homology of a sequence and thereby deduce functionality and family membership are often exploited. In this fashion, newly sequenced genomes can be annotated in a completely computational way. Covariance models are commonly used to assign novel RNA sequences to a known RNA family. However, to construct such models several examples of the family have to be already known. Moreover, model building is the work of experts who manually edit the necessary RNA alignment and consensus structure. Our method, RNAlien, starting from a single input sequence collects potential family member sequences by multiple iterations of homology search. RNA family models are fully automatically constructed for the found sequences. We have tested our method on a subset of the Rfam RNA family database. RNAlien models are a starting point to construct models of comparable sensitivity and specificity to manually curated ones from the Rfam database. RNAlien Tool and web server are available at http://rna.tbi.univie.ac.at/rnalien/.
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Affiliation(s)
- Florian Eggenhofer
- Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria Bioinformatics Group, Department of Computer Science University of Freiburg, Georges-Köhler-Allee, 79110 Freiburg, Germany
| | - Ivo L Hofacker
- Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria
| | - Christian Höner Zu Siederdissen
- Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria Bioinformatics Group, Department of Computer Science, University of Leipzig, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
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10
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Systematic Genome-wide Screening and Prediction of microRNAs in EBOV During the 2014 Ebolavirus Outbreak. Sci Rep 2015; 5:9912. [PMID: 26011078 PMCID: PMC4603304 DOI: 10.1038/srep09912] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/23/2015] [Indexed: 12/15/2022] Open
Abstract
Recently, several thousand people have been killed by the Ebolavirus disease (EVD) in West Africa, yet no current antiviral medications and treatments are available. Systematic investigation of ebolavirus whole genomes during the 2014 outbreak may shed light on the underlying mechanisms of EVD development. Here, using the genome-wide screening in ebolavirus genome sequences, we predicted four putative viral microRNA precursors (pre-miRNAs) and seven putative mature microRNAs (miRNAs). Combing bioinformatics analysis and prediction of the potential ebolavirus miRNA target genes, we suggest that two ebolavirus coding possible miRNAs may be silence and down-regulate the target genes NFKBIE and RIPK1, which are the central mediator of the pathways related with host cell defense mechanism. Additionally, the ebolavirus exploits the miRNAs to inhibit the NF-kB and TNF factors to evade the host defense mechanisms that limit replication by killing infected cells, or to conversely trigger apoptosis as a mechanism to increase virus spreading. This is the first study to use the genome-wide scanning to predict microRNAs in the 2014 outbreak EVD and then to apply systematic bioinformatics to analyze their target genes. We revealed a potential mechanism of miRNAs in ebolavirus infection and possible therapeutic targets for Ebola viral infection treatment.
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11
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Kharbanda N, Jalali SK, Ojha R, Bhatnagar RK. Temporal expression profiling of novel Spodoptera litura nucleopolyhedrovirus-encoded microRNAs upon infection of Sf21 cells. J Gen Virol 2014; 96:688-700. [PMID: 25481752 DOI: 10.1099/jgv.0.000008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Baculoviruses are arthropod-specific pathogens, and find extensive applications in pest control strategies and recombinant protein expression. Spodoptera litura nucleopolyhedrovirus (SpltNPV) infects the tropical armyworm Spodoptera litura, which is an important polyphagous crop pest widely distributed in regions of Asia and Oceania. Using next-generation sequencing, we report stage-specific profiling of SpltNPV-encoded microRNAs (miRNAs) at different time intervals post-infection (p.i.) of Sf21 cells. Sequence length distribution analysis of the small RNA libraries revealed a significant increase in 20 nt reads and a reduction of other size fractions during late phases of infection. In silico miRNA prediction tools identified 48 novel SpltNPV-encoded miRNAs, of which 10 were validated experimentally in Sf21 cells using Northern blot analysis and TaqMan quantitative real-time (qRT)-PCR. The viral miRNAs were also found to be expressed in fat-body and mid-gut tissues of infected fifth-instar S. litura larva. qRT-PCR analysis confirmed that expression of most viral miRNAs was triggered 12 h p.i. and continued thereafter. Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway annotation of computationally predicted targets of the reported miRNAs suggested a major impact of these miRNAs on cell signalling, protein translation and metabolic processes.
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Affiliation(s)
- Nishtha Kharbanda
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | | | - Raj Kamal Bhatnagar
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
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12
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Yang H, Zhang R, Jing Y, Zhu L, Zhang W, Liu C, Wang J, Yang J, Zhang J, Zen K, Zhang C, Li D. Identification and characterization of microRNAs in the crab-eating macaque (Macaca fascicularis) using transcriptome analysis. Gene 2013; 536:308-15. [PMID: 24355555 DOI: 10.1016/j.gene.2013.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/26/2013] [Accepted: 12/06/2013] [Indexed: 01/15/2023]
Abstract
MicroRNAs (miRNAs), with an average length between 16 nt and 26 nt, are small non-coding RNAs that can repress gene expression on the post-transcriptional level. Macaca fascicularis (M. fascicularis), one of the most important nonhuman primate animal models, is widely used in basic and applied preclinical research, especially in studies that involve neuroscience and disease. However, due to the lack of a complete genome sequence, the miRNAs in M. fascicularis have not been completely characterized. In this study, 86 putative M. fascicularis miRNAs were identified using a strategy of our design. The expression of some of these miRNAs in the tissue was confirmed by qRT-PCR. The function and pathway of their targeted genes were analyzed to reveal the potential relevance of miRNA regulation on diseases and physiological processes. The current study provides insight into potential miRNAs and forms a useful knowledge base for the future understanding of the function of miRNAs in M. fascicularis.
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Affiliation(s)
- Hao Yang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Rui Zhang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Ying Jing
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Lin Zhu
- Institute of Discovery Biology, Jiangsu Simcere Pharmaceutical R&D Co., Ltd, 699-18 Xuan Wu Avenue, Nanjing 210042, China
| | - Wen Zhang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Chang Liu
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Jin Wang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Jie Yang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Junfeng Zhang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Ke Zen
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China.
| | - Chenyu Zhang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China.
| | - Donghai Li
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China.
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13
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Barozai MYK, Din M, Baloch IA. Structural and functional based identification of the bean (Phaseolus) microRNAs and their targets from expressed sequence tags. ACTA ACUST UNITED AC 2013; 14:11-8. [PMID: 23605779 DOI: 10.1007/s10969-013-9152-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 04/01/2013] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are small, 18-26 nucleotides long, non-coding RNAs that play role in post-transcriptional gene regulation. Many of these are evolutionarily conserved. This suggests a powerful approach to predict new miRNAs in other species. In this research, structural and functional approaches were combined to make computational prediction of potential miRNAs and their targets in Bean (Phaseolus). Total 55 novel miRNAs were detected from 38 miRNAs families in Bean (Phaseolus). These families are; miR156, 160, 164, 168, 170, 171, 172, 319, 393, 396, 397, 398, 408, 414, 438, 444, 535, 1310, 1424, 1426, 1848, 1860, 1863, 2055, 2091, 2093, 2094, 2102, 2103, 2105, 2864, 2866, 2925, 2926, 4221, 4245, 4246 and 4250. In the 55 putative miRNAs; 28 miRNAs belong to Phaseolus acutifolius, 23 to Phaseolus vulgaris, 4 to Phaseolus coccineus. All the mature miRNAs reside in the stem portion of the hairpin structures. Total 146 potential protein targets were predicted for these miRNAs.
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14
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Gao R, Liu P, Wong SM. Identification of a plant viral RNA genome in the nucleus. PLoS One 2012; 7:e48736. [PMID: 23155403 PMCID: PMC3498252 DOI: 10.1371/journal.pone.0048736] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 09/28/2012] [Indexed: 01/04/2023] Open
Abstract
Viruses contain either DNA or RNA as genomes. DNA viruses replicate within nucleus, while most RNA viruses, especially (+)-sense single-stranded RNA, replicate and are present within cytoplasm. We proposed a new thought that is contrary to the common notion that (+)-sense single-stranded RNA viruses are present only in the cytoplasm. In this study, we question whether the genome of a plant RNA virus (non-retroviral) is present in the nucleus of infected cells? Hibiscus chlorotic ringspot virus (HCRSV) RNA was detected in the nucleus of infected cells, as shown by fluorescent in situ hybridization. Western blot using anti-histone 3 and anti-phosphoenolpyruvate carboxylase showed that nuclei were highly purified from mock and HCRSV-infected kenaf (Hibiscus cannabilis L.) leaves, respectively. The p23 and HCRSV coat protein (CP) coding regions were both amplified from total RNA extracted from isolated nuclei. Viral RNA in the nucleus may be used to generate viral microRNAs (vir-miRNAs), as five putative vir-miRNAs were predicted from HCRSV using the vir-miRNAs prediction database. The vir-miRNA (hcrsv-miR-H1-5p) was detected using TaqMan® stem-loop real-time PCR, and by northern blot using DIG-end labeled probe in HCRSV-infected kenaf leaves. Finally, a novel nuclear localization signal (NLS) was discovered in p23 of HCRSV. The NLS interacts with importin α and facilitates viral RNA genome to enter nucleus. We demonstrate the presence of a (+)-sense single-stranded viral RNA within nucleus.
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Affiliation(s)
- Ruimin Gao
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Peng Liu
- Temasek Life Sciences Laboratory, Singapore
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore, Singapore
- Temasek Life Sciences Laboratory, Singapore
- * E-mail:
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Ahn K, Gim JA, Ha HS, Han K, Kim HS. The novel MER transposon-derived miRNAs in human genome. Gene 2012; 512:422-8. [PMID: 22926102 DOI: 10.1016/j.gene.2012.08.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 08/16/2012] [Accepted: 08/17/2012] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are small RNA molecules (~20-30 nucleotides) that generally act in gene silencing and translational repression through the RNA interference pathway. They generally originate from intergenic genomic regions, but some are found in genomic regions that have been characterized such as introns, exons, and transposable elements (TE). To identify the miRNAs that are derived from palindromic MERs, we analyzed MER paralogs in human genome. The structures of the palindromic MERs were similar to the hairpin structure of miRNA in humans. Three miRNAs derived from MER96 located on chromosome 3, and MER91C paralogs located on chromosome 8 and chromosome 17 were identified in HeLa, HCT116, and HEK293 cell lines. The interactions between these MER-derived miRNAs and AGO1, AGO2, and AGO3 proteins were validated by immunoprecipitation assays. The data suggest that miRNAs derived from transposable elements could widely affect various target genes in the human genome.
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Affiliation(s)
- Kung Ahn
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
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16
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Identification and Characterization of MicroRNAs in Macaca fascicularis by EST Analysis. Comp Funct Genomics 2012; 2012:957607. [PMID: 22829752 PMCID: PMC3398586 DOI: 10.1155/2012/957607] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 04/16/2012] [Accepted: 04/30/2012] [Indexed: 01/18/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs which repress gene expression at the posttranscriptional level. In this study, an expressed sequence tag (EST)-based combined method was applied for the detection of miRNAs in Macaca fascicularis which is used as a model animal extensively in medical experiments, particularly those involved with neuroscience and disease. Initially, previously known miRNA sequences from metazoans were used to blast with the EST databases of Macaca fascicularis, and then a range of filtering criteria was conducted to remove some pseudo ones. At last a total of 8 novel conserved miRNAs were identified; their functions were further predicted and analyzed. Together, our study provides insight into miRNAs and their functions in Macaca fascicularis, indicating that the EST analysis is an efficient and affordable alternative approach for identifying novel miRNA candidates.
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Bizuayehu TT, Lanes CFC, Furmanek T, Karlsen BO, Fernandes JMO, Johansen SD, Babiak I. Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development. BMC Genomics 2012; 13:11. [PMID: 22233483 PMCID: PMC3398304 DOI: 10.1186/1471-2164-13-11] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 01/10/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) play a major role in animal ontogenesis. Size variants of miRNAs, isomiRs, are observed along with the main miRNA types, but their origin and possible biological role are uncovered yet. Developmental profiles of miRNAs have been reported in few fish species only and, to our knowledge, differential expressions of isomiRs have not yet been shown during fish development. Atlantic halibut, Hippoglossus hippoglossus L., undergoes dramatic metamorphosis during early development from symmetrical pelagic larval stage to unsymmetrical flatfish. No data exist on role of miRNAs in halibut metamorphosis. RESULTS miRNA profiling using SOLiD deep sequencing technology revealed a total of 199 conserved, one novel antisense, and one miRNA* mature form. Digital expression profiles of selected miRNAs were validated using reverse transcription quantitative PCR. We found developmental transition-specific miRNA expression. Expression of some miRNA* exceeded the guide strand miRNA. We revealed that nucleotide truncations and/or additions at the 3' end of mature miRNAs resulted in size variants showing differential expression patterns during the development in a number of miRNA families. We confirmed the presence of isomiRs by cloning and Sanger sequencing. Also, we found inverse relationship between expression levels of sense/antisense miRNAs during halibut development. CONCLUSION Developmental transitions during early development of Atlantic halibut are associated with expression of certain miRNA types. IsomiRs are abundant and often show differential expression during the development.
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Affiliation(s)
- Teshome T Bizuayehu
- University of Nordland, Faculty of Biosciences and Aquaculture, Postbox 1490, 8049 Bodø, Norway
| | - Carlos FC Lanes
- University of Nordland, Faculty of Biosciences and Aquaculture, Postbox 1490, 8049 Bodø, Norway
| | - Tomasz Furmanek
- University of Bergen, Department of Biomedicine, Postbox 7804, N-5020 Bergen, Norway
| | - Bård O Karlsen
- University of Nordland, Faculty of Biosciences and Aquaculture, Postbox 1490, 8049 Bodø, Norway
| | - Jorge MO Fernandes
- University of Nordland, Faculty of Biosciences and Aquaculture, Postbox 1490, 8049 Bodø, Norway
| | - Steinar D Johansen
- University of Nordland, Faculty of Biosciences and Aquaculture, Postbox 1490, 8049 Bodø, Norway
- University of Tromsø, Department of Medical Biology, Faculty of Health Sciences, 9037 Tromsø, Norway
| | - Igor Babiak
- University of Nordland, Faculty of Biosciences and Aquaculture, Postbox 1490, 8049 Bodø, Norway
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18
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Small RNA transcriptome investigation based on next-generation sequencing technology. J Genet Genomics 2011; 38:505-13. [DOI: 10.1016/j.jgg.2011.08.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 08/25/2011] [Accepted: 08/25/2011] [Indexed: 12/28/2022]
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Li SC, Liao YL, Chan WC, Ho MR, Tsai KW, Hu LY, Lai CH, Hsu CN, Lin WC. Interrogation of rabbit miRNAs and their isomiRs. Genomics 2011; 98:453-9. [PMID: 21930198 DOI: 10.1016/j.ygeno.2011.08.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 08/05/2011] [Accepted: 08/31/2011] [Indexed: 11/28/2022]
Abstract
Rabbit (Oryctolagus cuniculus) is the only lagomorph animal of which the genome has been sequenced. Establishing a rabbit miRNA resource will benefit subsequent functional genomic studies in mammals. We have generated small RNA sequence reads with SOLiD and Solexa platforms to identify rabbit miRNAs, where we identified 464 pre-miRNAs and 886 mature miRNAs. The brain and heart miRNA libraries were used for further in-depth analysis of isomiR distributions. There are several intriguing findings. First, several rabbit pre-miRNAs form highly conserved clusters. Second, there is a preference in selecting one strand as mature miRNA, resulting in an arm selection preference. Third, we analyzed the isomiR expression and validated the expression of isomiR types in different rabbit tissues. Moreover, we further performed additional small RNA libraries and defined miRNAs differentially expressed between brain and heart. We conclude also that isomiR distribution profiles could vary between brain and heart tissues.
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Affiliation(s)
- Sung-Chou Li
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.
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20
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Krzyzanowski PM, Price FD, Muro EM, Rudnicki MA, Andrade-Navarro MA. Integration of expressed sequence tag data flanking predicted RNA secondary structures facilitates novel non-coding RNA discovery. PLoS One 2011; 6:e20561. [PMID: 21698286 PMCID: PMC3115948 DOI: 10.1371/journal.pone.0020561] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 05/04/2011] [Indexed: 01/05/2023] Open
Abstract
Many computational methods have been used to predict novel non-coding RNAs (ncRNAs), but none, to our knowledge, have explicitly investigated the impact of integrating existing cDNA-based Expressed Sequence Tag (EST) data that flank structural RNA predictions. To determine whether flanking EST data can assist in microRNA (miRNA) prediction, we identified genomic sites encoding putative miRNAs by combining functional RNA predictions with flanking ESTs data in a model consistent with miRNAs undergoing cleavage during maturation. In both human and mouse genomes, we observed that the inclusion of flanking ESTs adjacent to and not overlapping predicted miRNAs significantly improved the performance of various methods of miRNA prediction, including direct high-throughput sequencing of small RNA libraries. We analyzed the expression of hundreds of miRNAs predicted to be expressed during myogenic differentiation using a customized microarray and identified several known and predicted myogenic miRNA hairpins. Our results indicate that integrating ESTs flanking structural RNA predictions improves the quality of cleaved miRNA predictions and suggest that this strategy can be used to predict other non-coding RNAs undergoing cleavage during maturation.
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Affiliation(s)
- Paul M Krzyzanowski
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, Canada.
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21
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Barozai MYK, Baloch IA, Din M. Identification of MicroRNAs and their targets in Helianthus. Mol Biol Rep 2011; 39:2523-32. [PMID: 21670966 DOI: 10.1007/s11033-011-1004-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 06/01/2011] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs about 20-24 nucleotides long, playing regulatory role. The conserved nature among the various organisms makes them a good source of new miRNAs discovery by comparative genomics approach using bioinformatic tools. A systematic search approach was used for inter-species homologs of miRNA precursors (pre-miRNAs), from known Helianthus expressed sequence tags (ESTs). The study resulted in 61 novel miRNAs belonging to 34 families from Helianthus ESTs. The 28 miRNA families; mir 159,160, 164, 170, 390, 393, 413, 415, 419, 426, 446, 530, 822, 842, 846, 1310, 1888, 2086, 2657, 2667, 2678, 2659, 2911, 2938, 3440, 3521, 3623, and 3630 are reporting for the first time in Helianthus. In the 61 new miRNAs, 20 are from H. tuberosus, 17 miRNAs belong to H. annus, 8 are from H. ciliaris, 5 to H. exilis, 4 is from H. argophyllous, H. petiolaris each and 3 are from H. paradoxus. All the pre-miRNAs form stable minimum free energy (mfe) stem-loop structure as their orthologues form and the mature miRNAs reside in the stem portion of the stem-loop structures. Their targets consist of growth and development related, transcription factors, signalling pathway kinases, stress resistant proteins and transport related proteins.
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22
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Genome-wide identification of novel microRNAs and their target genes in the human parasite Schistosoma mansoni. Genomics 2011; 98:96-111. [PMID: 21640815 DOI: 10.1016/j.ygeno.2011.05.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Revised: 05/06/2011] [Accepted: 05/17/2011] [Indexed: 11/22/2022]
Abstract
Mature microRNAs (miRNAs) are small, non-coding regulatory RNAs which can elicit post-transcriptional repression of mRNA levels of target genes. Here, we report the identification of 67 mature and 42 precursor miRNAs in the Schistosoma mansoni parasite. The evolutionarily conserved S. mansoni miRNAs consisted of 26 precursor miRNAs and 35 mature miRNAs, while we identified 16 precursor miRNAs and 32 mature miRNAs that displayed no conservation. These S. mansoni miRNAs are located on seven autosomal chromosomes and a sex (W) chromosome. miRNA expansion through gene duplication was suggested for at least two miRNA families miR-71 and mir-2. miRNA target finding analysis identified 389 predicted mRNA targets for the identified miRNAs and suggests that the sma-mir-71 may be involved in female sexual maturation. Given the important roles of miRNAs in animals, the identification and characterization of miRNAs in S. mansoni will facilitate novel approaches towards prevention and treatment of Schistosomiasis.
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Barozai MYK, Din M, Baloch IA. Identification of microRNAs in ecological model plant <i>Mimulus</i>. ACTA ACUST UNITED AC 2011. [DOI: 10.4236/jbpc.2011.23037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Li SC, Chan WC, Ho MR, Tsai KW, Hu LY, Lai CH, Hsu CN, Hwang PP, Lin WC. Discovery and characterization of medaka miRNA genes by next generation sequencing platform. BMC Genomics 2010; 11 Suppl 4:S8. [PMID: 21143817 PMCID: PMC3005926 DOI: 10.1186/1471-2164-11-s4-s8] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Background MicroRNAs (miRNAs) are endogenous non-protein-coding RNA genes which exist in a wide variety of organisms, including animals, plants, virus and even unicellular organisms. Medaka (Oryzias latipes) is a useful model organism among vertebrate animals. However, no medaka miRNAs have been investigated systematically. It is beneficial to conduct a genome-wide miRNA discovery study using the next generation sequencing (NGS) technology, which has emerged as a powerful sequencing tool for high-throughput analysis. Results In this study, we adopted ABI SOLiD platform to generate small RNA sequence reads from medaka tissues, followed by mapping these sequence reads back to medaka genome. The mapped genomic loci were considered as candidate miRNAs and further processed by a support vector machine (SVM) classifier. As result, we identified 599 novel medaka pre-miRNAs, many of which were found to encode more than one isomiRs. Besides, additional minor miRNAs (also called miRNA star) can be also detected with the improvement of sequencing depth. These quantifiable isomiRs and minor miRNAs enable us to further characterize medaka miRNA genes in many aspects. First of all, many medaka candidate pre-miRNAs position close to each other, forming many miRNA clusters, some of which are also conserved across other vertebrate animals. Secondly, during miRNA maturation, there is an arm selection preference of mature miRNAs within precursors. We observed the differences on arm selection preference between our candidate pre-miRNAs and their orthologous ones. We classified these differences into three categories based on the distribution of NGS reads. Finally, we also investigated the relationship between conservation status and expression level of miRNA genes. We concluded that the evolutionally conserved miRNAs were usually the most abundant ones. Conclusions Medaka is a widely used model animal and usually involved in many biomedical studies, including the ones on development biology. Identifying and characterizing medaka miRNA genes would benefit the studies using medaka as a model organism.
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Affiliation(s)
- Sung-Chou Li
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
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25
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Jia Q, Lin K, Liang J, Yu L, Li F. Discovering conserved insect microRNAs from expressed sequence tags. JOURNAL OF INSECT PHYSIOLOGY 2010; 56:1763-1769. [PMID: 20655920 DOI: 10.1016/j.jinsphys.2010.07.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Revised: 07/13/2010] [Accepted: 07/15/2010] [Indexed: 05/29/2023]
Abstract
MicroRNAs (miRNA) participate in regulating diverse biological pathways by translational repression in animals. They have attracted increasing attention recently. However, little work has been done on the miRNA genes in agriculturally important pests. Because the transcripts of most miRNA genes are the products of type-II RNA polymerase, pri-miRNA has a poly(A) tail and appears in expressed sequence tags (EST). We developed a computational pipeline to identify miRNA genes from insect ESTs. First, 980,697 ESTs from 63 insects were collected and used to search the nr database. The ESTs which did not share significant similarities with any known protein-coding genes were treated as non-coding ESTs. Next, known mature miRNAs were used to align with non-coding ESTs. The ESTs which contain the sequence of mature miRNA were treated as candidate ESTs. Finally, putative precursors were extracted flanking the mature miRNA region in candidate ESTs and evaluated by the Triplet-SVM algorithm. As a result, 86 miRNAs from 30 insect species were found based on a strict criterion while 330 miRNAs from 51 species were found based on a loose criterion. Evolution analysis indicated that mir-467, mir-297 and mir-466 were the highest conserved miRNA families in insects. To confirm the reliability of putative insect miRNAs, the expression profile of nine predicted miRNAs in Locusta migratoria was investigated. Eight miRNAs were successfully detected by RT-PCR. Most miRNAs were expressed ubiquitously at all examined tissues and developmental stages whereas Lmi-mir-509 was specifically expressed in the thorax of the 2nd, 4th and 5th instars and adult locust. In all, our work reported an efficient computational strategy for predicting miRNA genes from insect ESTs and presented tens of miRNAs in diverse insect species which are expected to participate in many important physiological processes.
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Affiliation(s)
- Qidong Jia
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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26
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Wahid F, Shehzad A, Khan T, Kim YY. MicroRNAs: synthesis, mechanism, function, and recent clinical trials. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:1231-43. [PMID: 20619301 DOI: 10.1016/j.bbamcr.2010.06.013] [Citation(s) in RCA: 566] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 06/30/2010] [Accepted: 06/30/2010] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are a class of small, endogenous RNAs of 21-25 nucleotides (nts) in length. They play an important regulatory role in animals and plants by targeting specific mRNAs for degradation or translation repression. Recent scientific advances have revealed the synthesis pathways and the regulatory mechanisms of miRNAs in animals and plants. miRNA-based regulation is implicated in disease etiology and has been studied for treatment. Furthermore, several preclinical and clinical trials have been initiated for miRNA-based therapeutics. In this review, the existing knowledge about miRNAs synthesis, mechanisms for regulation of the genome, and their widespread functions in animals and plants is summarized. The current status of preclinical and clinical trials regarding miRNA therapeutics is also reviewed. The recent findings in miRNA studies, summarized in this review, may add new dimensions to small RNA biology and miRNA therapeutics.
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Affiliation(s)
- Fazli Wahid
- School of life Sciences and Biotechnology, College of Natural sciences, Kyungpook National University, Buk-ku, Taegu, Korea
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27
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Biscontin A, Casara S, Cagnin S, Tombolan L, Rosolen A, Lanfranchi G, De Pittà C. New miRNA labeling method for bead-based quantification. BMC Mol Biol 2010; 11:44. [PMID: 20553585 PMCID: PMC2900262 DOI: 10.1186/1471-2199-11-44] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 06/16/2010] [Indexed: 12/26/2022] Open
Abstract
Background microRNAs (miRNAs) are small single-stranded non-coding RNAs that act as crucial regulators of gene expression. Different methods have been developed for miRNA expression profiling in order to better understand gene regulation in normal and pathological conditions. miRNAs expression values obtained from large scale methodologies such as microarrays still need a validation step with alternative technologies. Results Here we have applied with an innovative approach, the Luminex® xMAP™ technology validate expression data of differentially expressed miRNAs obtained from high throughput arrays. We have developed a novel labeling system of small RNA molecules (below 200 nt), optimizing the sensitive cloning method for miRNAs, termed miRNA amplification profiling (mRAP). The Luminex expression patterns of three miRNAs (miR-23a, miR-27a and miR-199a) in seven different cell lines have been validated by TaqMan miRNA assay. In all cases, bead-based meas were confirmed by the data obtained by TaqMan and microarray technologies. Conclusions We demonstrate that the measure of individual miRNA by the bead-based method is feasible, high speed, sensitive and low cost. The Luminex® xMAP™ technology also provides flexibility, since the central reaction can be scaled up with additional miRNA capturing beads, allowing validation of many differentially expressed miRNAs obtained from microarrays in a single experiment. We propose this technology as an alternative method to qRT-PCR for validating miRNAs expression data obtained with high-throughput technologies.
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Affiliation(s)
- Alberto Biscontin
- Department of Biology and CRIBI Biotechnology Centre, Università degli Studi di Padova, Via U. Bassi, 58/B, 35121 Padova, Italy
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28
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Identification of homologous microRNAs in 56 animal genomes. Genomics 2010; 96:1-9. [PMID: 20347954 DOI: 10.1016/j.ygeno.2010.03.009] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 02/07/2010] [Accepted: 03/17/2010] [Indexed: 12/29/2022]
Abstract
MicroRNAs (miRNAs) are endogenous non-protein-coding RNAs of approximately 22 nucleotides. Thousands of miRNA genes have been identified (computationally and/or experimentally) in a variety of organisms, which suggests that miRNA genes have been widely shared and distributed among species. Here, we used unique miRNA sequence patterns to scan the genome sequences of 56 bilaterian animal species for locating candidate miRNAs first. The regions centered surrounding these candidate miRNAs were then extracted for folding and calculating the features of their secondary structure. Using a support vector machine (SVM) as a classifier combined with these features, we identified an additional 13,091 orthologous or paralogous candidate pre-miRNAs, as well as their corresponding candidate mature miRNAs. Stem-loop RT-PCR and deep sequencing methods were used to experimentally validate the prediction results in human, medaka and rabbit. Our prediction pipeline allows the rapid and effective discovery of homologous miRNAs in a large number of genomes.
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Guerra Cardoso H, Doroteia Campos M, Rita Costa A, Catarina Campos M, Nothnagel T, Arnholdt-Schmitt B. Carrot alternative oxidase gene AOX2a demonstrates allelic and genotypic polymorphisms in intron 3. PHYSIOLOGIA PLANTARUM 2009; 137:592-608. [PMID: 19941625 DOI: 10.1111/j.1399-3054.2009.01299.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) are becoming important genetic markers for major crop species. In this study, we focus on variations at genomic level of the Daucus carota L. AOX2a gene. The use of gene-specific primers designed in exon regions on the boundaries of introns permitted to recognize intron length polymorphism (ILP) in intron 3 AOX2a by simple polymerase chain reaction (PCR) assays. The length of intron 3 can vary in individual carrot plants. Thus, allelic variation can be used as a tool to discriminate between single plant genotypes. Using this approach, individual plants from cv. Rotin and from diverse breeding lines and cultivars were identified that showed genetic variability by AOX2a ILPs. Repetitive patterns of intron length variation have been observed which allows grouping of genotypes. Polymorphic and identical PCR fragments revealed underlying high levels of sequence polymorphism. Variability was due to InDel events and intron single nucleotide polymorphisms (ISNPs), with a repetitive deletion in intron 3 affecting a putative pre-miRNA site. The results suggest that high AOX2a gene diversity in D. carota can be explored for the development of functional markers related to agronomic traits.
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Affiliation(s)
- Hélia Guerra Cardoso
- EU Marie Curie Chair, ICAAM, University of Evora, Apartado 94, 7002-554 Evora, Portugal
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Abstract
MicroRNAs play an essential role in diverse cellular processes, such as proliferation, differentiation, apoptosis, and stress response. Recent studies demonstrate that miRNAs are important for timing developmental decisions and fine-tuning cellular determination in vertebrate heart development. In an elegant set of experiments reported in this issue of Genes & Development, Liu et al. (3242-3254) demonstrate that miR-133a functions as an inhibitor of cardiomyocyte proliferation and a modifier of serum response factor (SRF)-dependent transcriptional signaling in the murine heart. Both targeted deletion and transgenic overexpression of miR-133a can result in the same cardiac phenotype, ventricular septal defect (VSD) and heart failure. The new data add another piece to the puzzle of regulatory networks that are implicated in cardiac disease. It will be interesting to see, if miR-133a is also involved in human heart diseases, especially VSD and dilated cardiomyopathy.
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Affiliation(s)
- Benjamin Meder
- Department of Medicine III, University of Heidelberg, Heidelberg 69120, Germany
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Hou YY, Ying XM, Li WJ. [Computational approaches to microRNA discovery]. YI CHUAN = HEREDITAS 2009; 30:687-96. [PMID: 18550489 DOI: 10.3724/sp.j.1005.2008.00687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
microRNAs (miRNAs) are endogenous non-coding RNAs of ~21 nucleotides in length discovered in recent years. They are involved in diverse pathways and play an important role in gene regulation in plants and animals. There are two main groups of approaches to miRNA discovery, which are cDNA cloning and computational identification. Since some miRNAs are expressed at a low level and the expression of many miRNAs has spatio-temporal specificity, it is difficult to find them through cDNA cloning. However, computational approaches can predict the miRNAs specifically expressed or with low abundance, which is complement to cDNA cloning. Computational approaches have hence gained wide attention. In this review, the computational approaches to miRNA discovery were summarized. According to their intrinsic characteristics, computational approaches were categorized into five classes: (1) homology search; (2) prediction based on comparative genomics; (3) scoring candidates using the sequence and structure characteristics; (4) prediction combined with targets; and (5) prediction with machine learning. The principles of each class of the approaches and their advantages and limitations in miRNA discovery were discussed. Finally, the future direction in miRNA discovery was pointed out.
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Affiliation(s)
- Yan-Yan Hou
- Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China.
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Abstract
Small RNAs of 20-30 nucleotides can target both chromatin and transcripts, and thereby keep both the genome and the transcriptome under extensive surveillance. Recent progress in high-throughput sequencing has uncovered an astounding landscape of small RNAs in eukaryotic cells. Various small RNAs of distinctive characteristics have been found and can be classified into three classes based on their biogenesis mechanism and the type of Argonaute protein that they are associated with: microRNAs (miRNAs), endogenous small interfering RNAs (endo-siRNAs or esiRNAs) and Piwi-interacting RNAs (piRNAs). This Review summarizes our current knowledge of how these intriguing molecules are generated in animal cells.
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Affiliation(s)
- V Narry Kim
- School of Biological Sciences and Center for National Creative Research, Seoul National University, Seoul, 151-742, Korea.
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Identification of microRNA in the protist Trichomonas vaginalis. Genomics 2009; 93:487-93. [PMID: 19442639 DOI: 10.1016/j.ygeno.2009.01.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 12/31/2008] [Accepted: 01/17/2009] [Indexed: 01/11/2023]
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs that have important regulatory roles in multicellular organisms. However, miRNA has never been identified experimentally in protist. Direct cloning of 438 expressed miRNA tags by microRNA serial analysis of gene expression from the parasitic protist Trichomonas vaginalis identified nine candidate miRNAs. Bioinformatics analysis of the corresponding genomic region revealed that these miRNA candidates contain a classical stem-loop-stem structure of pre-microRNAs. Analysis of the 20 nt long mature tva-miR-001 showed that it is an intergenic miRNA located at the scaffold DS113596. Tva-miR-001 was differentially expressed in the trophozoite, pseudocyst and amoeboid stages. Based on the experimental results of the present study, we provided solid evidence that protist possesses a miRNA regulating network comparable with multicellular organisms for the first time.
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Yu X, Zhou Q, Li SC, Luo Q, Cai Y, Lin WC, Chen H, Yang Y, Hu S, Yu J. The silkworm (Bombyx mori) microRNAs and their expressions in multiple developmental stages. PLoS One 2008; 3:e2997. [PMID: 18714353 PMCID: PMC2500172 DOI: 10.1371/journal.pone.0002997] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2008] [Accepted: 07/28/2008] [Indexed: 12/21/2022] Open
Abstract
Background MicroRNAs (miRNAs) play crucial roles in various physiological processes through post-transcriptional regulation of gene expressions and are involved in development, metabolism, and many other important molecular mechanisms and cellular processes. The Bombyx mori genome sequence provides opportunities for a thorough survey for miRNAs as well as comparative analyses with other sequenced insect species. Methodology/Principal Findings We identified 114 non-redundant conserved miRNAs and 148 novel putative miRNAs from the B. mori genome with an elaborate computational protocol. We also sequenced 6,720 clones from 14 developmental stage-specific small RNA libraries in which we identified 35 unique miRNAs containing 21 conserved miRNAs (including 17 predicted miRNAs) and 14 novel miRNAs (including 11 predicted novel miRNAs). Among the 114 conserved miRNAs, we found six pairs of clusters evolutionarily conserved cross insect lineages. Our observations on length heterogeneity at 5′ and/or 3′ ends of nine miRNAs between cloned and predicted sequences, and three mature forms deriving from the same arm of putative pre-miRNAs suggest a mechanism by which miRNAs gain new functions. Analyzing development-related miRNAs expression at 14 developmental stages based on clone-sampling and stem-loop RT PCR, we discovered an unusual abundance of 33 sequences representing 12 different miRNAs and sharply fluctuated expression of miRNAs at larva-molting stage. The potential functions of several stage-biased miRNAs were also analyzed in combination with predicted target genes and silkworm's phenotypic traits; our results indicated that miRNAs may play key regulatory roles in specific developmental stages in the silkworm, such as ecdysis. Conclusions/Significance Taking a combined approach, we identified 118 conserved miRNAs and 151 novel miRNA candidates from the B. mori genome sequence. Our expression analyses by sampling miRNAs and real-time PCR over multiple developmental stages allowed us to pinpoint molting stages as hotspots of miRNA expression both in sorts and quantities. Based on the analysis of target genes, we hypothesized that miRNAs regulate development through a particular emphasis on complex stages rather than general regulatory mechanisms.
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Affiliation(s)
- Xiaomin Yu
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Qing Zhou
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Sung-Chou Li
- Institute of BioMedical Informatics, National Yang-Ming University, Taipei, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Qibin Luo
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
| | - Yimei Cai
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Wen-chang Lin
- Institute of BioMedical Informatics, National Yang-Ming University, Taipei, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Huan Chen
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
| | - Yue Yang
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jun Yu
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Khan Barozai MY, Irfan M, Yousaf R, Ali I, Qaisar U, Maqbool A, Zahoor M, Rashid B, Hussnain T, Riazuddin S. Identification of micro-RNAs in cotton. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2008; 46:739-751. [PMID: 18603441 DOI: 10.1016/j.plaphy.2008.05.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Indexed: 05/26/2023]
Abstract
The plant genome has conserved small non-coding microRNAs (miRNAs) genes about 20-24 nucleotides long. They play a vital role in the gene regulation at various stages of plant life. Their conserved nature among the various organisms not only suggests their early evolution in eukaryotes but also makes them a good source of new miRNA discovery by homology search using bioinformatics tools. A systematic search approach was used for interspecies orthologues of miRNA precursors, from known sequences of Gossypium in GenBank. The study resulted in 22 miRNAs belonging to 13 families. We found 7 miRNA families (miR160, 164, 827, 829, 836, 845 and 865) for the first time in cotton. All 22 miRNA precursors form stable minimum free energy (mfe) stem loop structure as their orthologues form in Arabidopsis and the mature miRNAs reside in the stem portion of the stem loop structure. Fifteen miRNAs belong to the world's most commercial fiber producing upland cotton (Gossypium hirsutum), five are from Gossypium raimondii and one each is from Gossypium herbaceum and Gossypium arboreum. Their targets consist of transcription factors, cell division regulating proteins and virus response gene. The discovery of 22 miRNAs will be helpful in future for detection of precise function of each miRNA at a particular stage in life cycle of cotton.
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Terai G, Komori T, Asai K, Kin T. miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity. RNA (NEW YORK, N.Y.) 2007; 13:2081-2090. [PMID: 17959929 PMCID: PMC2080609 DOI: 10.1261/rna.655107] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Accepted: 09/11/2007] [Indexed: 05/25/2023]
Abstract
The identification of novel miRNAs has significant biological and clinical importance. However, none of the known miRNA features alone is sufficient for accurately detecting novel miRNAs. The aim of this paper is to integrate these features in a straightforward manner for detecting miRNAs with better accuracy. Since most miRNA regions are highly conserved among vertebrates for the ability to form stable hairpin structures, we implemented a hidden Markov model that outputs multidimensional feature vectors composed of both evolutionary features and secondary structural ones. The proposed method, called miRRim, outperformed existing ones in terms of detection/prediction performance: The total number of predictions was smaller than with existing methods when the number of miRNAs detected was adjusted to be the same. Moreover, there were several candidates predicted only by our method that are clustered with the known miRNAs, suggesting that our method is able to detect novel miRNAs. Genomic coordinates of predicted miRNA can be obtained from http://mirrim.ncrna.org/.
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Affiliation(s)
- Goro Terai
- Intec Web and Genome Informatics Corporation, Koto-ku, Tokyo, Japan, 136-0075.
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Tang GQ, Maxwell ES. Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation. Genome Res 2007; 18:104-12. [PMID: 18032731 DOI: 10.1101/gr.6539108] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The amphibian Xenopus provides a model organism for investigating microRNA expression during vertebrate embryogenesis and development. Searching available Xenopus genome databases using known human pre-miRNAs as query sequences, more than 300 genes encoding 142 Xenopus tropicalis miRNAs were identified. Analysis of Xenopus tropicalis miRNA genes revealed a predominate positioning within introns of protein-coding and nonprotein-coding RNA Pol II-transcribed genes. MiRNA genes were also located in pre-mRNA exons and positioned intergenically between known protein-coding genes. Many miRNA species were found in multiple locations and in more than one genomic context. MiRNA genes were also clustered throughout the genome, indicating the potential for the cotranscription and coordinate expression of miRNAs located in a given cluster. Northern blot analysis confirmed the expression of many identified miRNAs in both X. tropicalis and X. laevis. Comparison of X. tropicalis and X. laevis blots revealed comparable expression profiles, although several miRNAs exhibited species-specific expression in different tissues. More detailed analysis revealed that for some miRNAs, the tissue-specific expression profile of the pri-miRNA precursor was distinctly different from that of the mature miRNA profile. Differential miRNA precursor processing in both the nucleus and cytoplasm was implicated in the observed tissue-specific differences. These observations indicated that post-transcriptional processing plays an important role in regulating miRNA expression in the amphibian Xenopus.
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Affiliation(s)
- Guo-Qing Tang
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622, USA
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Barthelson RA, Lambert GM, Vanier C, Lynch RM, Galbraith DW. Comparison of the contributions of the nuclear and cytoplasmic compartments to global gene expression in human cells. BMC Genomics 2007; 8:340. [PMID: 17894886 PMCID: PMC2048942 DOI: 10.1186/1471-2164-8-340] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Accepted: 09/25/2007] [Indexed: 11/10/2022] Open
Abstract
Background In the most general sense, studies involving global analysis of gene expression aim to provide a comprehensive catalog of the components involved in the production of recognizable cellular phenotypes. These studies are often limited by the available technologies. One technology, based on microarrays, categorizes gene expression in terms of the abundance of RNA transcripts, and typically employs RNA prepared from whole cells, where cytoplasmic RNA predominates. Results Using microarrays comprising oligonucleotide probes that represent either protein-coding transcripts or microRNAs (miRNA), we have studied global transcript accumulation patterns for the HepG2 (human hepatoma) cell line. Through subdividing the total pool of RNA transcripts into samples from nuclei, the cytoplasm, and whole cells, we determined the degree of correlation of these patterns across these different subcellular locations. The transcript and miRNA abundance patterns for the three RNA fractions were largely similar, but with some exceptions: nuclear RNA samples were enriched with respect to the cytoplasm in transcripts encoding proteins associated with specific nuclear functions, such as the cell cycle, mitosis, and transcription. The cytoplasmic RNA fraction also was enriched, when compared to the nucleus, in transcripts for proteins related to specific nuclear functions, including the cell cycle, DNA replication, and DNA repair. Some transcripts related to the ubiquitin cycle, and transcripts for various membrane proteins were sorted into either the nuclear or cytoplasmic fractions. Conclusion Enrichment or compartmentalization of cell cycle and ubiquitin cycle transcripts within the nucleus may be related to the regulation of their expression, by preventing their translation to proteins. In this way, these cellular functions may be tightly controlled by regulating the release of mRNA from the nucleus and thereby the expression of key rate limiting steps in these pathways. Many miRNA precursors were also enriched in the nuclear samples, with significantly fewer being enriched in the cytoplasm. Studies of mRNA localization will help to clarify the roles RNA processing and transport play in the regulation of cellular function.
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Affiliation(s)
- Roger A Barthelson
- Bio5 Institute for Collaborative Bioresearch and Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Georgina M Lambert
- Bio5 Institute for Collaborative Bioresearch and Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Cheryl Vanier
- Department of Biological Sciences, University of Nevada, Las Vegas, Nevada 89154, USA
| | - Ronald M Lynch
- Department of Physiology, University of Arizona, Tucson, Arizona 85721, USA
| | - David W Galbraith
- Bio5 Institute for Collaborative Bioresearch and Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
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Abstract
MicroRNAs have been found in various organisms and play essential roles in gene expression regulation of many critical cellular processes. Large-scale computational prediction of miRNAs has been conducted for many organisms using known genomic sequences; however, there has been no such effort for the thousands of known viral genomes. Some viruses utilize existing host cellular pathways for their own benefit. Furthermore, viruses are capable of encoding miRNAs and using them to repress host genes. Thus, identifying potential miRNAs in all viral genomes would be valuable to virologists who study virus–host interactions. Based on our previously reported hairpin secondary structure and feature selection filters, we have examined the 2266 available viral genome sequences for putative miRNA hairpins and identified 33 691 hairpin candidates in 1491 genomes. Evaluation of the system performance indicated that our discovery pipeline exhibited 84.4% sensitivity. We established an interface for users to query the predicted viral miRNA hairpins based on taxonomic classification, and a host target gene prediction service based on the RNAhybrid program and the 3′-UTR gene sequences of human, mouse, rat, zebrafish, rice and Arabidopsis. The viral miRNA prediction database (Vir-Mir) can be accessed via http://alk.ibms.sinica.edu.tw.
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Affiliation(s)
- Sung-Chou Li
- Institute of BioMedical Informatics, National Yang-Ming University, Taipei 112 and Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, Republic of China
| | - Cheng-Kai Shiau
- Institute of BioMedical Informatics, National Yang-Ming University, Taipei 112 and Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, Republic of China
| | - Wen-chang Lin
- Institute of BioMedical Informatics, National Yang-Ming University, Taipei 112 and Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, Republic of China
- *To whom correspondence should be addressed.+886226523967886227827654
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Chaudhuri K, Chatterjee R. MicroRNA detection and target prediction: integration of computational and experimental approaches. DNA Cell Biol 2007; 26:321-37. [PMID: 17504028 DOI: 10.1089/dna.2006.0549] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In recent years, microRNAs (miRNAs), a class of 19-25 nucleotides noncoding RNAs, have been shown to play a major role in gene regulation across a broad range of metazoans and are important for a diverse biological functions. These miRNAs are involved in the regulation of protein expression primarily by binding to one or more target sites on an mRNA transcript and causing cleavage or repression of translation. Computer-based approaches for miRNA gene identification and miRNA target prediction are being considered as indispensable in miRNA research. Similarly, effective experimental techniques validating in silico predictions are crucial to the testing and finetuning of computational algorithms. Iterative interactions between in silico and experimental methods are now playing a central role in the biology of miRNAs. In this review, we summarize the various computational methods for identification of miRNAs and their targets as well as the technologies that have been developed to validate the predictions.
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Affiliation(s)
- Keya Chaudhuri
- Molecular & Human Genetics Division, Indian Institute of Chemical Biology, Kolkata, India.
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Doran J, Strauss WM. Bio-informatic trends for the determination of miRNA-target interactions in mammals. DNA Cell Biol 2007; 26:353-60. [PMID: 17504030 DOI: 10.1089/dna.2006.0546] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate mRNAs through a sequence-specific mechanism. By virtue of their structure and mechanism of action, computational methods have been devised to investigate the encoding of miRNA genes and the targets of miRNA action. A variety of assumptions have predicated the implementation of these various computational solutions. Evolutionary sequence conservation, secondary structure, and folding energetics are some of the assumptions that have been used. The success of these different computational solutions has been evaluated for both elucidation of new miRNAs and deducing targets of miRNA action. While the focus is on search techniques for new miRNAs, we have compared the programs miRseeker, miRScan, PalGrade, ProMiR, and miRAlign as examples of implementation of these techniques. For these programs, a benchmark comparison between theoretical estimation and actual identification is possible. We have also compared the target prediction programs TargetScanS, PicTar, DIANA-microT, miRanda, and RNAhybrid. However, it is difficult to rigorously assess the benchmark performance of these programs due to the difficulty in confirming their theoretical predictions.
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Affiliation(s)
- Jonathon Doran
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Colorado 80309, USA
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Abstract
Identification of microRNAs (miRNAs) is essential to studying their physiological functions. Due to the difficulties in discovering truly expressed miRNAs from genomic random hairpin secondary structure sequences, it is beneficial to predict them from expressed sequences--expressed sequence tags (ESTs) and intronic sequences. We used a modified scanning pipeline using criteria based on the features of known pre-miRNAs and phylogenetic conservation for predicting intronic miRNAs. Upon examination, we found that 25% of known human miRNAs belong to intronic regions of known protein-coding genes. About 50% of these intronic miRNAs reside in introns whose length is longer than 5,000 bps. It is likely that these intronic miRNAs can have their own independently regulated transcription units, which can be regulated by RNA polymerase II (Pol II) or RNA polymerase III (Pol III). It was recently demonstrated that RNA Pol III could transcribe human miRNAs through associated repetitive elements. Since various repetitive elements are often found to be present in the intronic regions, the distribution of intronic miRNAs and their possible transcription regulation are presented. Although the intronic miRNAs and their host genes could be regulated independently, it is possible that the intronic miRNA can still down-regulate its own host protein-coding gene by targeting the untranslated region (UTR) of the host gene. Another biological implication is that intronic miRNAs could play an important role as negative feedback regulators. We propose hypothetical models of such feedback regulation on host protein-coding genes by selecting the transcription factors as miRNA targets or by protein-protein interactions between intronic miRNA host gene product and miRNA target gene products.
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Affiliation(s)
- Sung-Chou Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, Republic of China
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Piriyapongsa J, Mariño-Ramírez L, Jordan IK. Origin and evolution of human microRNAs from transposable elements. Genetics 2007; 176:1323-37. [PMID: 17435244 PMCID: PMC1894593 DOI: 10.1534/genetics.107.072553] [Citation(s) in RCA: 254] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We sought to evaluate the extent of the contribution of transposable elements (TEs) to human microRNA (miRNA) genes along with the evolutionary dynamics of TE-derived human miRNAs. We found 55 experimentally characterized human miRNA genes that are derived from TEs, and these TE-derived miRNAs have the potential to regulate thousands of human genes. Sequence comparisons revealed that TE-derived human miRNAs are less conserved, on average, than non-TE-derived miRNAs. However, there are 18 TE-derived miRNAs that are relatively conserved, and 14 of these are related to the ancient L2 and MIR families. Comparison of miRNA vs. mRNA expression patterns for TE-derived miRNAs and their putative target genes showed numerous cases of anti-correlated expression that are consistent with regulation via mRNA degradation. In addition to the known human miRNAs that we show to be derived from TE sequences, we predict an additional 85 novel TE-derived miRNA genes. TE sequences are typically disregarded in genomic surveys for miRNA genes and target sites; this is a mistake. Our results indicate that TEs provide a natural mechanism for the origination miRNAs that can contribute to regulatory divergence between species as well as a rich source for the discovery of as yet unknown miRNA genes.
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Affiliation(s)
- Jittima Piriyapongsa
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 and National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894
| | - Leonardo Mariño-Ramírez
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 and National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894
| | - I. King Jordan
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 and National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894
- Corresponding author: School of Biology, Georgia Institute of Technology, 310 Ferst Dr., Atlanta, GA 30332-0230. E-mail:
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Abstract
BACKGROUND MicroRNAs (miRNAs) have been shown to play important roles in regulating gene expression. Since miRNAs are often evolutionarily conserved and their precursors can be folded into stem-loop hairpins, many miRNAs have been predicted. Yet experimental confirmation is difficult since miRNA expression is often specific to particular tissues and developmental stages. RESULTS Analysis of 29 human and 230 mouse longSAGE libraries revealed the expression of 22 known and 10 predicted mammalian miRNAs. Most were detected in embryonic tissues. Four SAGE tags detected in human embryonic stem cells specifically match a cluster of four human miRNAs (mir-302a, b, c&d) known to be expressed in embryonic stem cells. LongSAGE data also suggest the existence of a mouse homolog of human and rat mir-493. CONCLUSION The observation that some orphan longSAGE tags uniquely match miRNA precursors provides information about the expression of some known and predicted miRNAs.
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Affiliation(s)
- Xijin Ge
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, 1001 University Place, Evanston, IL 60201 USA
| | - Qingfa Wu
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, 1001 University Place, Evanston, IL 60201 USA
| | - San Ming Wang
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, 1001 University Place, Evanston, IL 60201 USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 1001 University Place, Evanston, IL 60201 USA
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