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Tyagi S, Sharma S, Ganie SA, Tahir M, Mir RR, Pandey R. Plant microRNAs: biogenesis, gene silencing, web-based analysis tools and their use as molecular markers. 3 Biotech 2019; 9:413. [PMID: 31696018 DOI: 10.1007/s13205-019-1942-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are tiny (20-24 nt bp) regulatory non-protein-coding RNA molecules that have been extensively characterized and found important for many physiological and developmental processes. The miss-expression of miRNAs leads to various defects in plants. MicroRNAs repress gene expression by directing mRNA degradation or translational arrest. Several proteins such as PP43A, HYL1, DCL, HST are indispensable role players in promoting miRNA biogenesis in plants. During miRNA biogenesis, lariat RNAs are produced as by-products of pre-mRNA splicing which have a negative role in regulation of miRNA homeostasis. By acting as a decoy and by sequestering to the dicing complex, lariat RNA can prevent the processing of miRNAs. A number of bioinformatic tools with different methodologies are available to identify and validate miRNAs and their targets. Many miRNAs have been reported in different crops for different traits; however, no reports are available on their use in plant breeding. Recently, researchers have developed trait specific miRNA-based molecular markers (miRNA-SSRs/SNP) for many quantitative traits in different plant species. In the future, these molecular markers can be used for plant breeding programs. In this review, a comprehensive up-to-date information is provided on the bioinformatic tools used for analysis of plant miRNAs and their targets, the number of miRNAs, their biogenesis, gene silencing mechanism and miRNA-based molecular markers.
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Thivierge C, Tseng HW, Mayya VK, Lussier C, Gravel SP, Duchaine TF. Alternative polyadenylation confers Pten mRNAs stability and resistance to microRNAs. Nucleic Acids Res 2019; 46:10340-10352. [PMID: 30053103 PMCID: PMC6212768 DOI: 10.1093/nar/gky666] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 07/16/2018] [Indexed: 12/20/2022] Open
Abstract
Fine regulation of the phosphatase and tensin homologue (PTEN) phosphatase dosage is critical for homeostasis and tumour suppression. The 3'-untranslated region (3'-UTR) of Pten mRNA was extensively linked to post-transcriptional regulation by microRNAs (miRNAs). In spite of this critical regulatory role, alternative 3'-UTRs of Pten have not been systematically characterized. Here, we reveal an important diversity of Pten mRNA isoforms generated by alternative polyadenylation sites. Several 3'-UTRs are co-expressed and their relative expression is dynamically regulated. In spite of encoding multiple validated miRNA-binding sites, longer isoforms are largely refractory to miRNA-mediated silencing, are more stable and contribute to the bulk of PTEN protein and signalling functions. Taken together, our results warrant a mechanistic re-interpretation of the post-transcriptional mechanisms involving Pten mRNAs and raise concerns on how miRNA-binding sites are being validated.
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Affiliation(s)
- Caroline Thivierge
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3A 1A3 Canada
| | - Hsin-Wei Tseng
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3A 1A3 Canada
| | - Vinay K Mayya
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3A 1A3 Canada
| | - Carine Lussier
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3A 1A3 Canada
| | | | - Thomas F Duchaine
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3A 1A3 Canada
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Lang X, Zhao W, Huang D, Liu W, Shen H, Xu L, Xu S, Huang Y, Cheng W. The role of NUDT21 in microRNA-binging sites of EZH2 gene increases the of risk preeclampsia. J Cell Mol Med 2019; 23:3202-3213. [PMID: 30883033 PMCID: PMC6484293 DOI: 10.1111/jcmm.14179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/11/2018] [Accepted: 01/04/2019] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES Preeclampsia (PE) is a major cause of mortality and morbidity among pregnant mothers and their fetuses worldwide. Recent studies have shown that several microRNAs (miRNAs) play crucial role in pathogenesis of PE patients; however, the mechanisms responsible for differences in miRNA function in PE largely remain to be determined. MATERIALS AND METHODS We studied that NUDT21 expression was markedly increased, whereas EZH2 was decreased in placental samples from patients with PE. We identified NUDT21 as an interaction partner of enhancer of zeste homologue 2 (EZH2). NUDT21 co-localized with EZH2 in the human trophoblast cell line, HTR-8/SVneo and NUDT21 was shown to bind to EZH2 in RNA immunoprecipitation assays. NUDT21 has previously been reported to be involved in alternative polyadenylation; thus, the interaction between NUDT21 and EZH2 may play an important role in the crosstalk between alternative polyadenylation (APA) and miRNA-mediated gene silencing in PE. RESULTS In the human trophoblast cell line HTR-8/SVneo, loss-of-function assays indicated that knockdown of NUDT21 suppressed cell proliferation, migration and tube formation. Furthermore, functional studies showed that NUDT21 elongated the 3'-UTR of mRNAs thereby exposing more miRNA binding sites (including miR138 and miR363), which enhanced the efficiency of miRNA-mediated gene silencing and promoted EZH2 binding. CONCLUSIONS This is the first report about the relationship of NUDT21 and EZH2. The data indicate that the aberrant expression of NUDT21 contributes to PE by targeting 3'-UTR of EZH2 mRNA. These findings may provide novel targets for future investigations into therapeutic strategies for PE.
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Affiliation(s)
- Xiao Lang
- Department of Obstetrics and Gynecology, School of MedicineInternational Peace Maternity and Child Health Hospital, Shanghai Jiao Tong UniversityShanghaiChina
| | - Wenxia Zhao
- Department of Obstetrics and GynecologyJiangwan Hospital of Shanghai Hongkou DistrictShanghaiChina
| | - Ding Huang
- Department of Obstetrics and Gynecology, School of MedicineInternational Peace Maternity and Child Health Hospital, Shanghai Jiao Tong UniversityShanghaiChina
| | - Wei Liu
- Department of Obstetrics and Gynecology, School of MedicineInternational Peace Maternity and Child Health Hospital, Shanghai Jiao Tong UniversityShanghaiChina
| | - Hong Shen
- Department of Obstetrics and Gynecology, School of MedicineInternational Peace Maternity and Child Health Hospital, Shanghai Jiao Tong UniversityShanghaiChina
| | - Liang Xu
- Department of Obstetrics and Gynecology, School of MedicineInternational Peace Maternity and Child Health Hospital, Shanghai Jiao Tong UniversityShanghaiChina
| | - Shan Xu
- Department of Obstetrics and GynecologyJiangwan Hospital of Shanghai Hongkou DistrictShanghaiChina
| | - Yongfang Huang
- Department of Obstetrics and GynecologyJiangwan Hospital of Shanghai Hongkou DistrictShanghaiChina
| | - Weiwei Cheng
- Department of Obstetrics and Gynecology, School of MedicineInternational Peace Maternity and Child Health Hospital, Shanghai Jiao Tong UniversityShanghaiChina
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Shirokikh NE, Preiss T. Translation initiation by cap-dependent ribosome recruitment: Recent insights and open questions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1473. [PMID: 29624880 DOI: 10.1002/wrna.1473] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 12/14/2022]
Abstract
Gene expression universally relies on protein synthesis, where ribosomes recognize and decode the messenger RNA template by cycling through translation initiation, elongation, and termination phases. All aspects of translation have been studied for decades using the tools of biochemistry and molecular biology available at the time. Here, we focus on the mechanism of translation initiation in eukaryotes, which is remarkably more complex than prokaryotic initiation and is the target of multiple types of regulatory intervention. The "consensus" model, featuring cap-dependent ribosome entry and scanning of mRNA leader sequences, represents the predominantly utilized initiation pathway across eukaryotes, although several variations of the model and alternative initiation mechanisms are also known. Recent advances in structural biology techniques have enabled remarkable molecular-level insights into the functional states of eukaryotic ribosomes, including a range of ribosomal complexes with different combinations of translation initiation factors that are thought to represent bona fide intermediates of the initiation process. Similarly, high-throughput sequencing-based ribosome profiling or "footprinting" approaches have allowed much progress in understanding the elongation phase of translation, and variants of them are beginning to reveal the remaining mysteries of initiation, as well as aspects of translation termination and ribosomal recycling. A current view on the eukaryotic initiation mechanism is presented here with an emphasis on how recent structural and footprinting results underpin axioms of the consensus model. Along the way, we further outline some contested mechanistic issues and major open questions still to be addressed. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
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Translation efficiency is a determinant of the magnitude of miRNA-mediated repression. Sci Rep 2017; 7:14884. [PMID: 29097662 PMCID: PMC5668238 DOI: 10.1038/s41598-017-13851-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/02/2017] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs are well known regulators of mRNA stability and translation. However, the magnitude of both translational repression and mRNA decay induced by miRNA binding varies greatly between miRNA targets. This can be the result of cis and trans factors that affect miRNA binding or action. We set out to address this issue by studying how various mRNA characteristics affect miRNA-mediated repression. Using a dual luciferase reporter system, we systematically analyzed the ability of selected mRNA elements to modulate miRNA-mediated repression. We found that changing the 3'UTR of a miRNA-targeted reporter modulates translational repression by affecting the translation efficiency. This 3'UTR dependent modulation can be further altered by changing the codon-optimality or 5'UTR of the luciferase reporter. We observed maximal repression with intermediate codon optimality and weak repression with very high or low codon optimality. Analysis of ribosome profiling and RNA-seq data for endogenous miRNA targets revealed translation efficiency as a key determinant of the magnitude of miRNA-mediated translational repression. Messages with high translation efficiency were more robustly repressed. Together our results reveal modulation of miRNA-mediated repression by characteristics and features of the 5'UTR, CDS and 3'UTR.
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Zhang X, Mofers A, Hydbring P, Olofsson MH, Guo J, Linder S, D'Arcy P. MYC is downregulated by a mitochondrial checkpoint mechanism. Oncotarget 2017; 8:90225-90237. [PMID: 29163823 PMCID: PMC5685744 DOI: 10.18632/oncotarget.21653] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 08/25/2017] [Indexed: 12/19/2022] Open
Abstract
The MYC proto-oncogene serves as a rheostat coupling mitogenic signaling with the activation of genes regulating growth, metabolism and mitochondrial biogenesis. Here we describe a novel link between mitochondria and MYC levels. Perturbation of mitochondrial function using a number of conventional and novel inhibitors resulted in the decreased expression of MYC mRNA. This decrease in MYC mRNA occurred concomitantly with an increase in the levels of tumor-suppressive miRNAs such as members of the let-7 family and miR-34a-5p. Knockdown of let-7 family or miR-34a-5p could partially restore MYC levels following mitochondria damage. We also identified let-7-dependent downregulation of the MYC mRNA chaperone, CRD-BP (coding region determinant-binding protein) as an additional control following mitochondria damage. Our data demonstrates the existence of a homeostasis mechanism whereby mitochondrial function controls MYC expression.
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Affiliation(s)
- Xiaonan Zhang
- Cancer Center Karolinska, Department of Oncology and Pathology, Karolinska Institute, SE-171 76 Stockholm, Sweden
| | - Arjan Mofers
- Department of Medical and Health Sciences, Linköping University, SE-581 83 Linköping, Sweden
| | - Per Hydbring
- Cancer Center Karolinska, Department of Oncology and Pathology, Karolinska Institute, SE-171 76 Stockholm, Sweden
| | - Maria Hägg Olofsson
- Cancer Center Karolinska, Department of Oncology and Pathology, Karolinska Institute, SE-171 76 Stockholm, Sweden
| | - Jing Guo
- Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institute, SE-171 77 Stockholm, Sweden.,Cardiovascular and Metabolic Disorders Program, Duke-NUS (National University of Singapore) Medical School, 16957 Singapore, Singapore
| | - Stig Linder
- Cancer Center Karolinska, Department of Oncology and Pathology, Karolinska Institute, SE-171 76 Stockholm, Sweden.,Department of Medical and Health Sciences, Linköping University, SE-581 83 Linköping, Sweden
| | - Padraig D'Arcy
- Department of Medical and Health Sciences, Linköping University, SE-581 83 Linköping, Sweden
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NUDT21 regulates 3'-UTR length and microRNA-mediated gene silencing in hepatocellular carcinoma. Cancer Lett 2017; 410:158-168. [PMID: 28964783 DOI: 10.1016/j.canlet.2017.09.026] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/05/2017] [Accepted: 09/21/2017] [Indexed: 12/12/2022]
Abstract
Recent studies have shown that several microRNAs (miRNAs) are involved in hepatocellular carcinoma (HCC) tumorigenesis and metastasis; however, the mechanisms responsible for the differences in the functions of these miRNAs in liver cancer remain a mystery. In our previous study, we identified NUDT21 as an interaction partner of argonaute 2 (AGO2). NUDT21 has been reported to be involved in alternative polyadenylation (APA); thus, the interaction between NUDT21 and AGO2 may be a key component of the crosstalk between APA and miRNA-mediated gene silencing in HCC. Our data showed that NUDT21 expression was decreased in HCC. Moreover, our results showed that NUDT21 co-localized with AGO2 in P/GW bodies in normal liver cells; however, this co-localization was diminished in cancer cells. Functional studies showed that NUDT21 elongated the 3'-UTR of mRNA and enhanced the efficiency of miRNA-mediated gene silencing by increasing the efficiency of AGO2-mRNA binding, which played an important role in cell proliferation. In summary, loss of NUDT21 shortened the 3'-UTR of various oncogenes in HCC cells. The shorter 3'-UTR contained less miRNA binding sites, which enabled the oncogenes to evade miRNA regulation and become overexpressed in HCC, leading to unregulated cancer cell proliferation.
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Soetanto R, Hynes CJ, Patel HR, Humphreys DT, Evers M, Duan G, Parker BJ, Archer SK, Clancy JL, Graham RM, Beilharz TH, Smith NJ, Preiss T. Role of miRNAs and alternative mRNA 3'-end cleavage and polyadenylation of their mRNA targets in cardiomyocyte hypertrophy. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:744-56. [PMID: 27032571 DOI: 10.1016/j.bbagrm.2016.03.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 02/25/2016] [Accepted: 03/20/2016] [Indexed: 12/19/2022]
Abstract
miRNAs play critical roles in heart disease. In addition to differential miRNA expression, miRNA-mediated control is also affected by variable miRNA processing or alternative 3'-end cleavage and polyadenylation (APA) of their mRNA targets. To what extent these phenomena play a role in the heart remains unclear. We sought to explore miRNA processing and mRNA APA in cardiomyocytes, and whether these change during cardiac hypertrophy. Thoracic aortic constriction (TAC) was performed to induce hypertrophy in C57BL/6J mice. RNA extracted from cardiomyocytes of sham-treated, pre-hypertrophic (2 days post-TAC), and hypertrophic (7 days post-TAC) mice was subjected to small RNA- and poly(A)-test sequencing (PAT-Seq). Differential expression analysis matched expectations; nevertheless we identified ~400 mRNAs and hundreds of noncoding RNA loci as altered with hypertrophy for the first time. Although multiple processing variants were observed for many miRNAs, there was little change in their relative proportions during hypertrophy. PAT-Seq mapped ~48,000 mRNA 3'-ends, identifying novel 3' untranslated regions (3'UTRs) for over 7000 genes. Importantly, hypertrophy was associated with marked changes in APA with a net shift from distal to more proximal mRNA 3'-ends, which is predicted to decrease overall miRNA repression strength. We independently validated several examples of 3'UTR proportion change and showed that alternative 3'UTRs associate with differences in mRNA translation. Our work suggests that APA contributes to altered gene expression with the development of cardiomyocyte hypertrophy and provides a rich resource for a systems-level understanding of miRNA-mediated regulation in physiological and pathological states of the heart.
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Affiliation(s)
- R Soetanto
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - C J Hynes
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - H R Patel
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - D T Humphreys
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - M Evers
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - G Duan
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - B J Parker
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - S K Archer
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia; Monash Bioinformatics Platform, Monash University, Melbourne, Victoria 3800, Australia
| | - J L Clancy
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - R M Graham
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - T H Beilharz
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - N J Smith
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - T Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia; Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia.
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9
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Wong QWL, Vaz C, Lee QY, Zhao TY, Luo R, Archer SK, Preiss T, Tanavde V, Vardy LA. Embryonic Stem Cells Exhibit mRNA Isoform Specific Translational Regulation. PLoS One 2016; 11:e0143235. [PMID: 26799392 PMCID: PMC4723142 DOI: 10.1371/journal.pone.0143235] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 11/02/2015] [Indexed: 01/08/2023] Open
Abstract
The presence of multiple variants for many mRNAs is a major contributor to protein diversity. The processing of these variants is tightly controlled in a cell-type specific manner and has a significant impact on gene expression control. Here we investigate the differential translation rates of individual mRNA variants in embryonic stem cells (ESCs) and in ESC derived Neural Precursor Cells (NPCs) using polysome profiling coupled to RNA sequencing. We show that there are a significant number of detectable mRNA variants in ESCs and NPCs and that many of them show variant specific translation rates. This is correlated with differences in the UTRs of the variants with the 5'UTR playing a predominant role. We suggest that mRNA variants that contain alternate UTRs are under different post-transcriptional controls. This is likely due to the presence or absence of miRNA and protein binding sites that regulate translation rate. This highlights the importance of addressing translation rate when using mRNA levels as a read out of protein abundance. Additional analysis shows that many annotated non-coding mRNAs are present on the polysome fractions in ESCs and NPCs. We believe that the use of polysome fractionation coupled to RNA sequencing is a useful method for analysis of the translation state of many different RNAs in the cell.
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Affiliation(s)
- Queenie Wing-Lei Wong
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, 138648, Singapore, Singapore
| | - Candida Vaz
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, 138671, Singapore, Singapore
| | - Qian Yi Lee
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, 138671, Singapore, Singapore
| | - Tian Yun Zhao
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, 138648, Singapore, Singapore
| | - Raymond Luo
- Life Technologies, 10 Biopolis Road, 138670, Singapore, Singapore
| | - Stuart K. Archer
- Monash Bioinformatics Platform, Monash University, Clayton, Victoria, Australia
| | - Thomas Preiss
- EMBL–Australia Collaborating Group, Department of Genome Science, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton (Canberra), Australian Capital Territory, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales, Australia
| | - Vivek Tanavde
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, 138648, Singapore, Singapore
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, 138671, Singapore, Singapore
| | - Leah A. Vardy
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, 138648, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore, Singapore
- * E-mail:
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10
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Nishimura T, Padamsi Z, Fakim H, Milette S, Dunham W, Gingras AC, Fabian M. The eIF4E-Binding Protein 4E-T Is a Component of the mRNA Decay Machinery that Bridges the 5′ and 3′ Termini of Target mRNAs. Cell Rep 2015; 11:1425-36. [DOI: 10.1016/j.celrep.2015.04.065] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/17/2015] [Accepted: 04/30/2015] [Indexed: 12/26/2022] Open
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11
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Cloonan N. Re-thinking miRNA-mRNA interactions: intertwining issues confound target discovery. Bioessays 2015; 37:379-88. [PMID: 25683051 PMCID: PMC4671252 DOI: 10.1002/bies.201400191] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 12/20/2022]
Abstract
Despite a library full of literature on miRNA biology, core issues relating to miRNA target detection, biological effect, and mode of action remain controversial. This essay proposes that the predominant mechanism of direct miRNA action is translational inhibition, whereas the bulk of miRNA effects are mRNA based. It explores several issues confounding miRNA target detection, and discusses their impact on the dominance of “miRNA seed” dogma and the exploration of non-canonical binding sites. Finally, it makes comparisons between miRNA target prediction and transcription factor binding prediction, and questions the value of characterizing miRNA binding sites based on which miRNA nucleotides are paired with an mRNA.
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Affiliation(s)
- Nicole Cloonan
- QIMR Berghofer Medical Research Institute, Genomic Biology Lab, Herston, QLD, Australia
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12
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miRNA-based buffering of the cobblestone-lissencephaly-associated extracellular matrix receptor dystroglycan via its alternative 3'-UTR. Nat Commun 2014; 5:4906. [PMID: 25232965 PMCID: PMC4199286 DOI: 10.1038/ncomms5906] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 08/02/2014] [Indexed: 11/08/2022] Open
Abstract
Many proteins are expressed dynamically during different stages of cellular life and the accuracy of protein amounts is critical for cell endurance. Therefore, cells should have a perceptive system that notifies about fluctuations in the amounts of certain components and an executive system that efficiently restores their precise levels. At least one mechanism that evolution has employed for this task is regulation of 3'-UTR length for microRNA targeting. Here we show that in Drosophila the microRNA complex miR-310s acts as an executive mechanism to buffer levels of the muscular dystrophy-associated extracellular matrix receptor dystroglycan via its alternative 3'-UTR. miR-310s gene expression fluctuates depending on dystroglycan amounts and nitric oxide signalling, which perceives dystroglycan levels and regulates microRNA gene expression. Aberrant levels of dystroglycan or deficiencies in miR-310s and nitric oxide signalling result in cobblestone brain appearance, resembling human lissencephaly type II phenotype.
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13
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Keam SP, Young PE, McCorkindale AL, Dang THY, Clancy JL, Humphreys DT, Preiss T, Hutvagner G, Martin DIK, Cropley JE, Suter CM. The human Piwi protein Hiwi2 associates with tRNA-derived piRNAs in somatic cells. Nucleic Acids Res 2014; 42:8984-95. [PMID: 25038252 PMCID: PMC4132735 DOI: 10.1093/nar/gku620] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/26/2014] [Accepted: 06/26/2014] [Indexed: 01/31/2023] Open
Abstract
The Piwi-piRNA pathway is active in animal germ cells where its functions are required for germ cell maintenance and gamete differentiation. Piwi proteins and piRNAs have been detected outside germline tissue in multiple phyla, but activity of the pathway in mammalian somatic cells has been little explored. In particular, Piwi expression has been observed in cancer cells, but nothing is known about the piRNA partners or the function of the system in these cells. We have surveyed the expression of the three human Piwi genes, Hiwi, Hili and Hiwi2, in multiple normal tissues and cancer cell lines. We find that Hiwi2 is ubiquitously expressed; in cancer cells the protein is largely restricted to the cytoplasm and is associated with translating ribosomes. Immunoprecipitation of Hiwi2 from MDAMB231 cancer cells enriches for piRNAs that are predominantly derived from processed tRNAs and expressed genes, species which can also be found in adult human testis. Our studies indicate that a Piwi-piRNA pathway is present in human somatic cells, with an uncharacterised function linked to translation. Taking this evidence together with evidence from primitive organisms, we propose that this somatic function of the pathway predates the germline functions of the pathway in modern animals.
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Affiliation(s)
- Simon P Keam
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia Faculty of Engineering and Information Technology, Centre of Health Technologies, University of Technology Sydney, 235 Jones Street, Ultimo, NSW, 2007, Australia
| | - Paul E Young
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - Alexandra L McCorkindale
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - Thurston H Y Dang
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - Jennifer L Clancy
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - David T Humphreys
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - Thomas Preiss
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - Gyorgy Hutvagner
- Faculty of Engineering and Information Technology, Centre of Health Technologies, University of Technology Sydney, 235 Jones Street, Ultimo, NSW, 2007, Australia
| | - David I K Martin
- Center for Genetics, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA
| | - Jennifer E Cropley
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia Faculty of Medicine, University of New South Wales, Kensington, 2052, Australia
| | - Catherine M Suter
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia Faculty of Medicine, University of New South Wales, Kensington, 2052, Australia
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14
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Murat P, Zhong J, Lekieffre L, Cowieson NP, Clancy JL, Preiss T, Balasubramanian S, Khanna R, Tellam J. G-quadruplexes regulate Epstein-Barr virus-encoded nuclear antigen 1 mRNA translation. Nat Chem Biol 2014; 10:358-64. [PMID: 24633353 PMCID: PMC4188979 DOI: 10.1038/nchembio.1479] [Citation(s) in RCA: 194] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 02/14/2014] [Indexed: 01/29/2023]
Abstract
Viruses that establish latent infections have evolved unique mechanisms to avoid host immune recognition. Maintenance proteins of these viruses regulate their synthesis to levels sufficient for maintaining persistent infection but below threshold levels for host immune detection. The mechanisms governing this finely tuned regulation of viral latency are unknown. Here we show that mRNAs encoding gammaherpesviral maintenance proteins contain within their open reading frames clusters of unusual structural elements, G-quadruplexes, which are responsible for the cis-acting regulation of viral mRNA translation. By studying the Epstein-Barr virus-encoded nuclear antigen 1 (EBNA1) mRNA, we demonstrate that destabilization of G-quadruplexes using antisense oligonucleotides increases EBNA1 mRNA translation. In contrast, pretreatment with a G-quadruplex-stabilizing small molecule, pyridostatin, decreases EBNA1 synthesis, highlighting the importance of G-quadruplexes within virally encoded transcripts as unique regulatory signals for translational control and immune evasion. Furthermore, these findings suggest alternative therapeutic strategies focused on targeting RNA structure within viral ORFs.
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Affiliation(s)
- Pierre Murat
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Jie Zhong
- Tumour Immunology, Department of Immunology, Clive Berghofer Cancer Research Centre, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- QIMR Centre for Immunotherapy and Vaccine Development, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Lea Lekieffre
- Tumour Immunology, Department of Immunology, Clive Berghofer Cancer Research Centre, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- QIMR Centre for Immunotherapy and Vaccine Development, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Nathan P Cowieson
- Centre for Synchrotron Science, Monash University, Melbourne, Victoria, Australia
| | - Jennifer L Clancy
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Thomas Preiss
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cambridge Institute, Cancer Research UK, Li Ka Shing Center, Cambridge, UK
- School of Clinical Medicine, The University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge, UK
| | - Rajiv Khanna
- Tumour Immunology, Department of Immunology, Clive Berghofer Cancer Research Centre, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- QIMR Centre for Immunotherapy and Vaccine Development, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Judy Tellam
- Tumour Immunology, Department of Immunology, Clive Berghofer Cancer Research Centre, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- QIMR Centre for Immunotherapy and Vaccine Development, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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15
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Martin HC, Wani S, Steptoe AL, Krishnan K, Nones K, Nourbakhsh E, Vlassov A, Grimmond SM, Cloonan N. Imperfect centered miRNA binding sites are common and can mediate repression of target mRNAs. Genome Biol 2014; 15:R51. [PMID: 24629056 PMCID: PMC4053950 DOI: 10.1186/gb-2014-15-3-r51] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 02/19/2014] [Indexed: 12/31/2022] Open
Abstract
Background MicroRNAs (miRNAs) bind to mRNAs and target them for translational inhibition or transcriptional degradation. It is thought that most miRNA-mRNA interactions involve the seed region at the 5′ end of the miRNA. The importance of seed sites is supported by experimental evidence, although there is growing interest in interactions mediated by the central region of the miRNA, termed centered sites. To investigate the prevalence of these interactions, we apply a biotin pull-down method to determine the direct targets of ten human miRNAs, including four isomiRs that share centered sites, but not seeds, with their canonical partner miRNAs. Results We confirm that miRNAs and their isomiRs can interact with hundreds of mRNAs, and that imperfect centered sites are common mediators of miRNA-mRNA interactions. We experimentally demonstrate that these sites can repress mRNA activity, typically through translational repression, and are enriched in regions of the transcriptome bound by AGO. Finally, we show that the identification of imperfect centered sites is unlikely to be an artifact of our protocol caused by the biotinylation of the miRNA. However, the fact that there was a slight bias against seed sites in our protocol may have inflated the apparent prevalence of centered site-mediated interactions. Conclusions Our results suggest that centered site-mediated interactions are much more frequent than previously thought. This may explain the evolutionary conservation of the central region of miRNAs, and has significant implications for decoding miRNA-regulated genetic networks, and for predicting the functional effect of variants that do not alter protein sequence.
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16
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Khurana R, Verma VK, Rawoof A, Tiwari S, Nair RA, Mahidhara G, Idris MM, Clarke AR, Kumar LD. OncomiRdbB: a comprehensive database of microRNAs and their targets in breast cancer. BMC Bioinformatics 2014; 15:15. [PMID: 24428888 PMCID: PMC3926854 DOI: 10.1186/1471-2105-15-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 01/02/2014] [Indexed: 01/08/2023] Open
Abstract
Background Given the estimate that 30% of our genes are controlled by microRNAs, it is essential that we understand the precise relationship between microRNAs and their targets. OncomiRs are microRNAs (miRNAs) that have been frequently shown to be deregulated in cancer. However, although several oncomiRs have been identified and characterized, there is as yet no comprehensive compilation of this data which has rendered it underutilized by cancer biologists. There is therefore an unmet need in generating bioinformatic platforms to speed the identification of novel therapeutic targets. Description We describe here OncomiRdbB, a comprehensive database of oncomiRs mined from different existing databases for mouse and humans along with novel oncomiRs that we have validated in human breast cancer samples. The database also lists their respective predicted targets, identified using miRanda, along with their IDs, sequences, chromosome location and detailed description. This database facilitates querying by search strings including microRNA name, sequence, accession number, target genes and organisms. The microRNA networks and their hubs with respective targets at 3'UTR, 5'UTR and exons of different pathway genes were also deciphered using the 'R' algorithm. Conclusion OncomiRdbB is a comprehensive and integrated database of oncomiRs and their targets in breast cancer with multiple query options which will help enhance both understanding of the biology of breast cancer and the development of new and innovative microRNA based diagnostic tools and targets of therapeutic significance. OncomiRdbB is freely available for download through the URL link http://tdb.ccmb.res.in/OncomiRdbB/index.htm.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lekha Dinesh Kumar
- Cancer Biology, Centre for Cellular & Molecular Biology, Council of scientific and Industrial Research, Hyderabad, A,P, India.
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Abstract
The role of microRNAs (miRNAs) as fine-tuners of gene expression is now well established in most aspects of cellular biology. Critically, it is becoming apparent that characterization of miRNA regulation could further the understanding of elusive cellular processes. Here, I briefly review the current literature assessing the role of miRNAs in the modulation of neutrophil biology and discuss how the definition of such miRNA regulation could help in the better understanding of neutrophil function.
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18
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Ragusa M, Statello L, Maugeri M, Majorana A, Barbagallo D, Salito L, Sammito M, Santonocito M, Angelica R, Cavallaro A, Scalia M, Caltabiano R, Privitera G, Biondi A, Di Vita M, Cappellani A, Vasquez E, Lanzafame S, Tendi E, Celeste S, Di Pietro C, Basile F, Purrello M. Specific alterations of the microRNA transcriptome and global network structure in colorectal cancer after treatment with MAPK/ERK inhibitors. J Mol Med (Berl) 2012; 90:1421-1438. [PMID: 22660396 DOI: 10.1007/s00109-012-0918-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 04/12/2012] [Accepted: 05/10/2012] [Indexed: 12/11/2022]
Abstract
The mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) pathway has a master control role in various cancer-related biological processes as cell growth, proliferation, differentiation, migration, and apoptosis. It also regulates many transcription factors that control microRNAs (miRNAs) and their biosynthetic machinery. To investigate on the still poorly characterised global involvement of miRNAs within the pathway, we profiled the expression of 745 miRNAs in three colorectal cancer (CRC) cell lines after blocking the pathway with three different inhibitors. This allowed the identification of two classes of post-treatment differentially expressed (DE) miRNAs: (1) common DE miRNAs in all CRC lines after treatment with a specific inhibitor (class A); (2) DE miRNAs in a single CRC line after treatment with all three inhibitors (class B). By determining the molecular targets, biological roles, network position of chosen miRNAs from class A (miR-372, miR-663b, miR-1226*) and class B (miR-92a-1*, miR-135b*, miR-720), we experimentally demonstrated that they are involved in cell proliferation, migration, apoptosis, and globally affect the regulation circuits centred on MAPK/ERK signaling. Interestingly, the levels of miR-92a-1*, miR-135b*, miR-372, miR-720 are significantly higher in biopsies from CRC patients than in normal controls; they also are significantly higher in CRC patients with mutated KRAS than in those with wild-type genotypes (Wilcoxon test, p < 0.05): the latter could be a downstream effect of ERK pathway overactivation, triggered by KRAS mutations. Finally, our functional data strongly suggest the following miRNA/target pairs: miR-92a-1*/PTEN-SOCS5; miR-135b*/LATS2; miR-372/TXNIP; miR-663b/CCND2. Altogether, these results contribute to deepen current knowledge on still uncharacterized features of MAPK/ERK pathway, pinpointing new oncomiRs in CRC and allowing their translation into clinical practice and CRC therapy.
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Affiliation(s)
- Marco Ragusa
- Dipartimento Gian Filippo Ingrassia, Unità di BioMedicina Molecolare Genomica e dei Sistemi Complessi, Genetica, Biologia Computazionale, Università di Catania, Via Santa Sofia 87, 95123 Catania, Italy.
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19
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Hynes CJ, Clancy JL, Preiss T. miRNAs in cardiac disease: Sitting duck or moving target? IUBMB Life 2012; 64:872-8. [DOI: 10.1002/iub.1082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 08/04/2012] [Indexed: 12/31/2022]
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20
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Fabbri E, Brognara E, Borgatti M, Lampronti I, Finotti A, Bianchi N, Sforza S, Tedeschi T, Manicardi A, Marchelli R, Corradini R, Gambari R. miRNA therapeutics: delivery and biological activity of peptide nucleic acids targeting miRNAs. Epigenomics 2012; 3:733-45. [PMID: 22126292 DOI: 10.2217/epi.11.90] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Peptide nucleic acids (PNAs) are DNA/RNA mimics extensively used for pharmacological regulation of gene expression in a variety of cellular and molecular systems, and they have been described as excellent candidates for antisense and antigene therapies. At present, very few data are available on the use of PNAs as molecules targeting miRNAs. miRNAs are a family of small nc RNAs that regulate gene expression by sequence-selective targeting of mRNAs, leading to a translational repression or mRNA degradation to the control of highly regulated biological functions, such as differentiation, cell cycle and apoptosis. The aim of this article is to present the state-of-the-art concerning the possible use of PNAs to target miRNAs and modify their biological metabolism within the cells. The results present in the literature allow to propose PNA-based molecules as very promising reagents to modulate the biological activity of miRNAs. In consideration of the involvement of miRNAs in human pathologies, PNA-mediated targeting of miRNAs has been proposed as a potential novel therapeutic approach.
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Affiliation(s)
- Enrica Fabbri
- Department of Biochemistry & Molecular Biology, University of Ferrara, Ferrara, Italy
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Coussens MJ, Forbes K, Kreader C, Sago J, Cupp C, Swarthout J. Genome-wide screen for miRNA targets using the MISSION target ID library. J Vis Exp 2012:e3303. [PMID: 22508434 DOI: 10.3791/3303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The Target ID Library is designed to assist in discovery and identification of microRNA (miRNA) targets. The Target ID Library is a plasmid-based, genome-wide cDNA library cloned into the 3'UTR downstream from the dual-selection fusion protein, thymidine kinase-zeocin (TKzeo). The first round of selection is for stable transformants, followed with introduction of a miRNA of interest, and finally, selecting for cDNAs containing the miRNA's target. Selected cDNAs are identified by sequencing (see Figure 1-3 for Target ID Library Workflow and details). To ensure broad coverage of the human transcriptome, Target ID Library cDNAs were generated via oligo-dT priming using a pool of total RNA prepared from multiple human tissues and cell lines. Resulting cDNA range from 0.5 to 4 kb, with an average size of 1.2 kb, and were cloned into the p3Î"TKzeo dual-selection plasmid (see Figure 4 for plasmid map). The gene targets represented in the library can be found on the Sigma-Aldrich webpage. Results from Illumina sequencing (Table 3), show that the library includes 16,922 of the 21,518 unique genes in UCSC RefGene (79%), or 14,000 genes with 10 or more reads (66%).
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