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Zhang L, Yang B, Zhang C, Chen H, Xu J, Qu C, Lu K, Li J. Genome-Wide Identification and Posttranscriptional Regulation Analyses Elucidate Roles of Key Argonautes and Their miRNA Triggers in Regulating Complex Yield Traits in Rapeseed. Int J Mol Sci 2023; 24:ijms24032543. [PMID: 36768865 PMCID: PMC9916703 DOI: 10.3390/ijms24032543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Argonautes (AGOs) interact with microRNAs (miRNAs) to form the RNA-induced silencing complex (RISC), which can posttranscriptionally regulate the expression of targeted genes. To date, however, the AGOs and their miRNA triggers remain elusive in rapeseed (Brassica napus). Here, we systematically performed a phylogenetic analysis and examined the collinear relationships of the AGOs among four Brassicaceae species. Their physicochemical properties, gene structures, and expression patterns among 81 tissues from multiple materials and developmental stages were further analyzed. Additionally, their posttranscriptional regulation was analyzed using psRNATarget prediction, miRNA-/mRNA-Seq analyses, and a qRT-PCR verification. We finally identified 10 AtAGOs, 13 BolAGOs, 11 BraAGOs, and 24 BnaAGOs. An expression analysis of the BnaAGOs in the B. napus cultivar ZS11, as well as genotypes with extreme phenotypes in various yield-related traits, revealed the conservation and diversity of these genes. Furthermore, we speculated the posttranscriptional regulation of the B. napus miR168a-AGO1s and miR403-AGO2s modules. Combining miRNA-Seq and mRNA-Seq analyses, we found that the B. napus miR168a-AGO1s module may play an essential role in negatively regulating yield traits, whereas the miR403-AGO2s module positively impacts yield. This is the first attempt to comprehensively analyze the AGOs and their miRNA triggers in B. napus and provides a theoretical basis for breeding high-yielding varieties through the manipulation of the miRNA-AGOs modules.
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Affiliation(s)
- Liyuan Zhang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Bo Yang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Chao Zhang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Huan Chen
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Jinxiong Xu
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Cunmin Qu
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Kun Lu
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jiana Li
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Correspondence: ; Tel.: +86-23-68250642
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Jungers CF, Djuranovic S. Modulation of miRISC-Mediated Gene Silencing in Eukaryotes. Front Mol Biosci 2022; 9:832916. [PMID: 35237661 PMCID: PMC8882679 DOI: 10.3389/fmolb.2022.832916] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
Gene expression is regulated at multiple levels in eukaryotic cells. Regulation at the post-transcriptional level is modulated by various trans-acting factors that bind to specific sequences in the messenger RNA (mRNA). The binding of different trans factors influences various aspects of the mRNA such as degradation rate, translation efficiency, splicing, localization, etc. MicroRNAs (miRNAs) are short endogenous ncRNAs that combine with the Argonaute to form the microRNA-induced silencing complex (miRISC), which uses base-pair complementation to silence the target transcript. RNA-binding proteins (RBPs) contribute to post-transcriptional control by influencing the mRNA stability and translation upon binding to cis-elements within the mRNA transcript. RBPs have been shown to impact gene expression through influencing the miRISC biogenesis, composition, or miRISC-mRNA target interaction. While there is clear evidence that those interactions between RBPs, miRNAs, miRISC and target mRNAs influence the efficiency of miRISC-mediated gene silencing, the exact mechanism for most of them remains unclear. This review summarizes our current knowledge on gene expression regulation through interactions of miRNAs and RBPs.
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Das B, Sahoo S, Mallick B. HIWI2 induces G2/M cell cycle arrest and apoptosis in human fibrosarcoma via the ROS/DNA damage/p53 axis. Life Sci 2022; 293:120353. [PMID: 35074406 DOI: 10.1016/j.lfs.2022.120353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 12/14/2022]
Abstract
AIMS Piwi, like RNA-mediated gene silencing 4 (PIWIL4) or HIWI2, are seen deregulated in human cancers and possibly play critical roles in tumorigenesis. It is unknown what role HIWI2 plays in the regulation of fibrosarcoma, an early metastatic lethal type of soft tissue sarcoma (STS). The present study aimed to investigate the role of HIWI2 in the tumorigenesis of fibrosarcoma. MAIN METHODS The expression of HIWI2 in HT1080 fibrosarcoma cells was determined by qRT-PCR and western blotting. The MTT assay, colony formation assay, cell cycle, and PE-AnnexinV/7AAD apoptosis assay using flow cytometry, DNA laddering assay, comet assay, and γH2AX accumulation assay were performed to study the effect of HIWI2 overexpression in HT1080 cells. Further, the effect of silencing of HIWI2 was determined by cell viability assay, transwell migration, and invasion assay. KEY FINDINGS HIWI2 is under-expressed in STS cell lines and tissues, which is associated with poor disease-free survival, disease-specific survival, and progression-free survival of the patients. Overexpression of HIWI2 in HT1080 cells causes DNA damage by increasing intracellular ROS by inhibiting the expression of antioxidant genes (SOD1, SOD2, GPX1, GPX4, and CAT). Furthermore, an increase in H2AX phosphorylation was observed, which activates p53 that promotes p21 expression and caspase-3 activation, leading to G2/M phase cell cycle arrest and apoptosis. HIWI2 silencing, on the contrary, promotes cell growth, migration, and invasion by activating MMP2 and MMP9. SIGNIFICANCE These results are the first to show that HIWI2 acts as a tumor suppressor in fibrosarcoma by modulating the ROS/DNA damage/p53 pathway.
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Affiliation(s)
- Basudeb Das
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Swapnil Sahoo
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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4
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Parekh F, Daughenbaugh KF, Flenniken ML. Chemical Stimulants and Stressors Impact the Outcome of Virus Infection and Immune Gene Expression in Honey Bees ( Apis mellifera). Front Immunol 2021; 12:747848. [PMID: 34804032 PMCID: PMC8596368 DOI: 10.3389/fimmu.2021.747848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022] Open
Abstract
Western honey bees (Apis mellifera) are ecologically, agriculturally, and economically important plant pollinators. High average annual losses of honey bee colonies in the US have been partially attributed to agrochemical exposure and virus infections. To examine the potential negative synergistic impacts of agrochemical exposure and virus infection, as well as the potential promise of phytochemicals to ameliorate the impact of pathogenic infections on honey bees, we infected bees with a panel of viruses (i.e., Flock House virus, deformed wing virus, or Sindbis virus) and exposed to one of three chemical compounds. Specifically, honey bees were fed sucrose syrup containing: (1) thyme oil, a phytochemical and putative immune stimulant, (2) fumagillin, a beekeeper applied fungicide, or (3) clothianidin, a grower-applied insecticide. We determined that virus abundance was lower in honey bees fed 0.16 ppb thyme oil augmented sucrose syrup, compared to bees fed sucrose syrup alone. Parallel analysis of honey bee gene expression revealed that honey bees fed thyme oil augmented sucrose syrup had higher expression of key RNAi genes (argonaute-2 and dicer-like), antimicrobial peptide expressing genes (abaecin and hymenoptaecin), and vitellogenin, a putative honey bee health and age indicator, compared to bees fed only sucrose syrup. Virus abundance was higher in bees fed fumagillin (25 ppm or 75 ppm) or 1 ppb clothianidin containing sucrose syrup relative to levels in bees fed only sucrose syrup. Whereas, honey bees fed 10 ppb clothianidin had lower virus levels, likely because consuming a near lethal dose of insecticide made them poor hosts for virus infection. The negative impact of fumagillin and clothianidin on honey bee health was indicated by the lower expression of argonaute-2, dicer-like, abaecin, and hymenoptaecin, and vitellogenin. Together, these results indicate that chemical stimulants and stressors impact the outcome of virus infection and immune gene expression in honey bees.
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Affiliation(s)
- Fenali Parekh
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States.,Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, United States.,Pollinator Health Center, Montana State University, Bozeman, MT, United States
| | - Katie F Daughenbaugh
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, United States.,Pollinator Health Center, Montana State University, Bozeman, MT, United States
| | - Michelle L Flenniken
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States.,Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, United States.,Pollinator Health Center, Montana State University, Bozeman, MT, United States
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5
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Kimoto C, Nakagawa H, Hasegawa R, Nodono H, Matsumoto M. Co-localization of DrPiwi-1 and DrPiwi-2 in the oogonial cytoplasm is essential for oocyte differentiation in sexualized planarians. Cells Dev 2021; 167:203710. [PMID: 34171535 DOI: 10.1016/j.cdev.2021.203710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/02/2021] [Accepted: 06/11/2021] [Indexed: 11/18/2022]
Abstract
P-Element-induced wimpy testis (Piwi) subfamily proteins form complexes that bind to Piwi-interacting RNA. This interaction is crucial for stem cell regulation and formation, maintenance of germline stem cells, and gametogenesis in several metazoans. Planarians are effective models for studying stem cells. In the planarian Dugesia ryukyuensis, DrPiwi-1 is essential for the development of germ cells, but not somatic cells and sexual organs. DrPiwi-2 is indispensable for regeneration. In this study, we aimed to investigate the effects of Piwi on the differentiation of germ cells using monoclonal antibodies against DrPiwi-1 and DrPiwi-2. DrPiwi-1 and DrPiwi-2 co-localized more in immature germ cells than in mature germ cells in the ovary. DrPiwi-1 was found in the cytoplasm of early oogonia as undifferentiated germ cells, whereas DrPiwi-2 was found to localize not only in the nuclei but also in the cytoplasm of early oogonia. In descendant germ cells (oocytes), DrPiwi-2 was not present in the cytoplasm, but was strongly detected in the nucleolus. Moreover, we found that DrPiwi-1 forms a complex with DrPiwi-2. The cause of DrPiwi-1 depletion may be the severe reduction in the DrPiwi-2 level in the cytoplasm of oogonia. These results suggest that the formation of the DrPiwi-1 and DrPiwi-2 complex in the cytoplasm of oogonia is essential for oocyte differentiation. Our findings support the conclusion that DrPiwi-1 forms a complex with DrPiwi-2 in the cytoplasm of undifferentiated germ cells, and it signifies the start of gametogenesis. In contrast, in the testes, Drpiwi-1 was found in undifferentiated germ cells (spermatogonia), whereas DrPiwi-2 was found in descendant germ cells (spermatocytes). The process of germ cell differentiation from adult stem cells in planarians may be regulated in different ways in female and male germ lines by the Piwi family.
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Affiliation(s)
- Chiaki Kimoto
- Department of Biological Sciences and Informatics, Keio University, 3-14-1, Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Haruka Nakagawa
- Department of Biological Sciences and Informatics, Keio University, 3-14-1, Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Reiko Hasegawa
- Department of Biological Sciences and Informatics, Keio University, 3-14-1, Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Hanae Nodono
- Department of Biological Sciences and Informatics, Keio University, 3-14-1, Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Midori Matsumoto
- Department of Biological Sciences and Informatics, Keio University, 3-14-1, Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan.
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6
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Dong P, Xiong Y, Konno Y, Ihira K, Xu D, Kobayashi N, Yue J, Watari H. Critical Roles of PIWIL1 in Human Tumors: Expression, Functions, Mechanisms, and Potential Clinical Implications. Front Cell Dev Biol 2021; 9:656993. [PMID: 33718392 PMCID: PMC7952444 DOI: 10.3389/fcell.2021.656993] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/11/2021] [Indexed: 11/17/2022] Open
Abstract
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a class of small non-coding RNA molecules that are 24-31 nucleotides in length. PiRNAs are thought to bind to PIWI proteins (PIWL1-4, a subfamily of Argonaute proteins), forming piRNA/PIWI complexes that influence gene expression at the transcriptional or post-transcriptional levels. However, it has been recently reported that the interaction of PIWI proteins with piRNAs does not encompass the entire function of PIWI proteins in human tumor cells. PIWIL1 (also called HIWI) is specifically expressed in the testis but not in other normal tissues. In tumor tissues, PIWIL1 is frequently overexpressed in tumor tissues compared with normal tissues. Its high expression is closely correlated with adverse clinicopathological features and shorter patient survival. Upregulation of PIWIL1 drastically induces tumor cell proliferation, epithelial-mesenchymal transition (EMT), invasion, cancer stem-like properties, tumorigenesis, metastasis and chemoresistance, probably via piRNA-independent mechanisms. In this article, we summarize the current existing literature on PIWIL1 in human tumors, including its expression, biological functions and regulatory mechanisms, providing new insights into how the dysregulation of PIWIL1 contributes to tumor initiation, development and chemoresistance through diverse signaling pathways. We also discuss the most recent findings on the potential clinical applications of PIWIL1 in cancer diagnosis and treatment.
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Affiliation(s)
- Peixin Dong
- Department of Obstetrics and Gynecology, Hokkaido University School of Medicine, Hokkaido University, Sapporo, Japan
| | - Ying Xiong
- State Key Laboratory of Oncology in South China, Department of Gynecology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yosuke Konno
- Department of Obstetrics and Gynecology, Hokkaido University School of Medicine, Hokkaido University, Sapporo, Japan
| | - Kei Ihira
- Department of Obstetrics and Gynecology, Hokkaido University School of Medicine, Hokkaido University, Sapporo, Japan
| | - Daozhi Xu
- Department of Obstetrics and Gynecology, Hokkaido University School of Medicine, Hokkaido University, Sapporo, Japan
| | - Noriko Kobayashi
- Department of Obstetrics and Gynecology, Hokkaido University School of Medicine, Hokkaido University, Sapporo, Japan
| | - Junming Yue
- Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Hidemichi Watari
- Department of Obstetrics and Gynecology, Hokkaido University School of Medicine, Hokkaido University, Sapporo, Japan
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VCP Machinery Mediates Autophagic Degradation of Empty Argonaute. Cell Rep 2020; 28:1144-1153.e4. [PMID: 31365860 DOI: 10.1016/j.celrep.2019.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/12/2019] [Accepted: 06/27/2019] [Indexed: 12/29/2022] Open
Abstract
The Argonaute subfamily of proteins (AGO) loads microRNAs (miRNAs) to form the effector complex that mediates target gene silencing. Empty AGO, but not miRNA-loaded AGO, is selectively degraded across species. We have reported that the degradation of empty AGO is part of a quality control pathway that eliminates dysfunctional AGO. However, how empty AGO is degraded remains unclear. Here we show that the empty state of Drosophila Ago1 is degraded by autophagy. Comprehensive LC-MS/MS analyses, together with manipulation of the Ago1 ubiquitination level, revealed that VCP, which mediates selective autophagy, recognizes empty Ago1 via the Ufd1-Npl4 heterodimer. Depletion of VCP-Ufd1-Npl4 machinery impairs degradation of empty Ago1 and miRNA-mediated target gene silencing. Our findings reveal a direct link between empty AGO degradation and selective autophagy that ensures efficient miRNA function.
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Tian L, Zeng Y, Xie W, Wu Q, Wang S, Zhou X, Zhang Y. Genome-wide identification and analysis of genes associated with RNA interference in Bemisia tabaci. PEST MANAGEMENT SCIENCE 2019; 75:3005-3014. [PMID: 30891929 DOI: 10.1002/ps.5415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/10/2019] [Accepted: 03/16/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND As a method of RNA-mediated gene silencing, RNA interference (RNAi) is a useful reverse genetic tool with which to study gene function, and holds great promise for pest management. Bemisia tabaci is a cosmopolitan pest that causes extensive damage to crops. The mechanism underlying RNAi efficiency in B. tabaci is not well known. We identified and analyzed candidate genes in the RNAi pathway to understand the RNAi mechanism and provide a basis for the application of RNAi in pest management. RESULTS We identified 33 genes putatively involved in the RNAi pathway from the B. tabaci Q genome. Phylogenetic and structural analyses confirmed the characteristics of these genes. Furthermore, quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) and transcriptomic analysis profiled gene expression patterns during different developmental stages. Gene expression levels estimated by qRT-PCR and RNA-seq analyses were significantly correlated. Moreover, gene functions were verified by RNAi. When accompanied by knockdown of AGO2, Dicer2 and Sid1, the efficiency of CYP6DB3 RNAi decreased correspondingly. CONCLUSION In this study, we annotated and validated genes involved in B. tabaci RNAi. A better understanding of the building blocks of the RNAi process in B. tabaci facilitates integration of this novel biotechnology into the management of this emerging pest, either directly or indirectly. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Lixia Tian
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Zeng
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wen Xie
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingjun Wu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoli Wang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY, USA
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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9
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The Prognosis Value of PIWIL1 and PIWIL2 Expression in Pancreatic Cancer. J Clin Med 2019; 8:jcm8091275. [PMID: 31443431 PMCID: PMC6780139 DOI: 10.3390/jcm8091275] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 08/12/2019] [Accepted: 08/21/2019] [Indexed: 12/13/2022] Open
Abstract
Pancreatic cancer is a highly aggressive manifestation of cancer, and currently presents poor clinical outcome due to its late diagnosis with metastasic disease. Surgery is the only approach with a curative intend; however, the survival rates seen in this type of patient are still low. After surgery, there is a lack of predictive prognosis biomarkers to predict treatment response and survival to establish a personalized medicine. Human P-element-induced wimpy testis 1 (PIWIL1) and P-element-induced wimpy testis 2 (PIWIL2) proteins act as protectors of germline, and their aberrant expression has been described in several types of tumors. In this study, we aimed to assess an association between PIWIL1 and PIWIL2 expression and the prognosis of biliopancreatic cancer patients. For this, we analyzed protein expression in complete resected tumor samples, and found a significant association between PIWIL2 expression and both progression-free and overall survival (p = 0.036 and p = 0.012, respectively). However, PIWIL2 expression was significantly associated with progression-free survival (p = 0.029), and overall survival (p = 0.025) of such tumors originated in the pancreas, but not in the bile duct or ampulla of Vater. Further analysis revealed that PIWIL1 and PIWIL2, at both mRNA and protein expression levels, correlated positively with factors associated to the progenitor molecular subtype of pancreatic cancer. Based on these findings, PIWIL1 and PIWIL2 expression may be considered a potential prognostic biomarker for resectable pancreatic cancer and may serve to guide subsequent adjuvant treatment decisions.
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10
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Meki IK, Kariithi HM, Parker AG, Vreysen MJB, Ros VID, Vlak JM, van Oers MM, Abd-Alla AMM. RNA interference-based antiviral immune response against the salivary gland hypertrophy virus in Glossina pallidipes. BMC Microbiol 2018; 18:170. [PMID: 30470195 PMCID: PMC6251114 DOI: 10.1186/s12866-018-1298-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; Hytrosaviridae) is a non-occluded dsDNA virus that specifically infects the adult stages of the hematophagous tsetse flies (Glossina species, Diptera: Glossinidae). GpSGHV infections are usually asymptomatic, but unknown factors can result to a switch to acute symptomatic infection, which is characterized by the salivary gland hypertrophy (SGH) syndrome associated with decreased fecundity that can ultimately lead to a colony collapse. It is uncertain how GpSGHV is maintained amongst Glossina spp. populations but RNA interference (RNAi) machinery, a conserved antiviral defense in insects, is hypothesized to be amongst the host’s mechanisms to maintain the GpSGHV in asymptomatic (persistent or latent) infection state. Here, we investigated the involvement of RNAi during GpSGHV infections by comparing the expression of three key RNAi machinery genes, Dicer (DCR), Argonaute (AGO) and Drosha, in artificially virus injected, asymptomatic and symptomatic infected G. pallidipes flies compared to PBS injected (controls) individuals. We further assessed the impact of AGO2 knockdown on virus infection by RT-qPCR quantification of four selected GpSGHV genes, i.e. odv-e66, dnapol, maltodextrin glycosyltransferase (a tegument gene) and SGHV091 (a capsid gene). Results We show that in response to hemocoelic injections of GpSGHV into G. pallidipes flies, increased virus replication was accompanied by significant upregulation of the expression of three RNAi key genes; AGO1, AGO2 and DCR2, and a moderate increase in the expression of Drosha post injection compared to the PBS-injected controls. Furthermore, compared to asymptomatically infected individuals, symptomatic flies showed significant downregulation of AGO1, AGO2 and Drosha, but a moderate increase in the expression of DCR2. Compared to the controls, knockdown of AGO2 did not have a significant impact on virus infection in the flies as evidenced by unaltered transcript levels of the selected GpSGHV genes. Conclusion The upregulation of the expression of the RNAi genes implicate involvement of this machinery in controlling GpSGHV infections and the establishment of symptomatic GpSGHV infections in Glossina. These findings provide a strategic foundation to understand GpSGHV infections and to control latent (asymptomatic) infections in Glossina spp. and thereby control SGHVs in insect production facilities. Electronic supplementary material The online version of this article (10.1186/s12866-018-1298-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene K Meki
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna International Centre, P.O. Box 100, 1400, Vienna, Austria.,Laboratory of Virology, Wageningen University, 6708, PB, Wageningen, The Netherlands
| | - Henry M Kariithi
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna International Centre, P.O. Box 100, 1400, Vienna, Austria.,Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, P.O Box 57811, Loresho, Nairobi, Kenya
| | - Andrew G Parker
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna International Centre, P.O. Box 100, 1400, Vienna, Austria
| | - Marc J B Vreysen
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna International Centre, P.O. Box 100, 1400, Vienna, Austria
| | - Vera I D Ros
- Laboratory of Virology, Wageningen University, 6708, PB, Wageningen, The Netherlands
| | - Just M Vlak
- Laboratory of Virology, Wageningen University, 6708, PB, Wageningen, The Netherlands
| | - Monique M van Oers
- Laboratory of Virology, Wageningen University, 6708, PB, Wageningen, The Netherlands
| | - Adly M M Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna International Centre, P.O. Box 100, 1400, Vienna, Austria.
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11
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Camargo C, Wu K, Fishilevich E, Narva KE, Siegfried BD. Knockdown of RNA interference pathway genes in western corn rootworm, Diabrotica virgifera virgifera, identifies no fitness costs associated with Argonaute 2 or Dicer-2. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2018; 148:103-110. [PMID: 29891360 DOI: 10.1016/j.pestbp.2018.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/07/2018] [Accepted: 04/07/2018] [Indexed: 06/08/2023]
Abstract
The use of transgenic crops that induce silencing of essential genes using double-stranded RNA (dsRNA) through RNA interference (RNAi) in western corn rootworm, Diabrotica virgifera virgifera, is likely to be an important component of new technologies for the control of this important corn pest. Previous studies have demonstrated that the dsRNA response in D. v. virgifera depends on the presence of RNAi pathway genes including Dicer-2 and Argonaute 2, and that downregulation of these genes limits the lethality of environmental dsRNA. A potential resistance mechanism to lethal dsRNA may involve loss of function of RNAi pathway genes. Howver, the potential for resistance to evolve may depend on whether these pathway genes have essential functions such that the loss of function of core proteins in the RNAi pathway will have fitness costs in D. v. virgifera. Fitness costs associated with potential resistance mechanisms have a central role in determining how resistance can evolve to RNAi technologies in western corn rootworm. We evaluated the effect of dsRNA and microRNA pathway gene knockdown on the development of D. v. virgifera larvae through short-term and long-term exposures to dsRNA for Dicer and Argonaute genes. Downregulation of Argonaute 2, Dicer-2, Dicer-1 did not significantly affect larval survivorship or development through short and long-term exposure to dsRNA. However, downregulation of Argonaute 1 reduced larval survivorship and delayed development. The implications of these results as they relate to D. v. virgifera resistance to lethal dsRNA are discussed.
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Affiliation(s)
- Carolina Camargo
- Department of Entomology and Nematology, University of Florida, 1881 Natural Area Drive, Steinmetz Hall, Gainesville, FL 32611, United States
| | - Ke Wu
- Department of Entomology and Nematology, University of Florida, 1881 Natural Area Drive, Steinmetz Hall, Gainesville, FL 32611, United States
| | - Elane Fishilevich
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN 46268, United States
| | - Kenneth E Narva
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN 46268, United States
| | - Blair D Siegfried
- Department of Entomology and Nematology, University of Florida, 1881 Natural Area Drive, Steinmetz Hall, Gainesville, FL 32611, United States.
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12
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MacLeod AR, Crooke ST. RNA Therapeutics in Oncology: Advances, Challenges, and Future Directions. J Clin Pharmacol 2018; 57 Suppl 10:S43-S59. [PMID: 28921648 DOI: 10.1002/jcph.957] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 05/08/2017] [Indexed: 12/18/2022]
Abstract
RNA-based therapeutic technologies represent a rapidly expanding class of therapeutic opportunities with the power to modulate cellular biology in ways never before possible. With RNA-targeted therapeutics, inhibitors of previously undruggable proteins, gene expression modulators, and even therapeutic proteins can be rationally designed based on sequence information alone, something that is not possible with other therapeutic modalities. The most advanced RNA therapeutic modalities are antisense oligonucleotides (ASOs) and small interfering RNAs. Particularly with ASOs, recent clinical data have demonstrated proof of mechanism and clinical benefit with these approaches across several nononcology disease areas by multiple routes of administration. In cancer, next-generation ASOs have recently demonstrated single-agent activity in patients with highly refractory cancers. Here we discuss advances in RNA therapeutics for the treatment of cancer and the challenges that remain to solidify these as mainstay therapeutic modalities to bridge the pharmacogenomic divide that remains in cancer drug discovery.
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Affiliation(s)
- A Robert MacLeod
- Vice President, Oncology Discovery, Ionis Pharmaceuticals, Carlsbad, CA, USA
| | - Stanley T Crooke
- CEO and Chairman of the Board, Ionis Pharmaceuticals, Carlsbad, CA, USA
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Abstract
Evolution of bacteria and archaea involves an incessant arms race against an enormous diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most bacteria and archaea are dedicated to antiparasite defense. The functions of these defense systems follow several distinct strategies, including innate immunity; adaptive immunity; and dormancy induction, or programmed cell death. Recent comparative genomic studies taking advantage of the expanding database of microbial genomes and metagenomes, combined with direct experiments, resulted in the discovery of several previously unknown defense systems, including innate immunity centered on Argonaute proteins, bacteriophage exclusion, and new types of CRISPR-Cas systems of adaptive immunity. Some general principles of function and evolution of defense systems are starting to crystallize, in particular, extensive gain and loss of defense genes during the evolution of prokaryotes; formation of genomic defense islands; evolutionary connections between mobile genetic elements and defense, whereby genes of mobile elements are repeatedly recruited for defense functions; the partially selfish and addictive behavior of the defense systems; and coupling between immunity and dormancy induction/programmed cell death.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894;
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894;
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894;
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Koonin EV. Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence. Biol Direct 2017; 12:5. [PMID: 28187792 PMCID: PMC5303251 DOI: 10.1186/s13062-017-0177-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/06/2017] [Indexed: 12/18/2022] Open
Abstract
Abstract Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation. The nucleic acid-guided defense systems include prokaryotic Argonaute (pAgo)-centered innate immunity and CRISPR-Cas adaptive immunity as well as diverse branches of RNA interference (RNAi) in eukaryotes. The archaeal pAgo machinery is the direct ancestor of eukaryotic RNAi that, however, acquired additional components, such as Dicer, and enormously diversified through multiple duplications. In contrast, eukaryotes lack any heritage of the CRISPR-Cas systems, conceivably, due to the cellular toxicity of some Cas proteins that would get activated as a result of operon disruption in eukaryotes. The adaptive immunity function in eukaryotes is taken over partly by the PIWI RNA branch of RNAi and partly by protein-based immunity. In this review, I briefly discuss the interplay between homology and analogy in the evolution of RNA- and DNA-guided immunity, and attempt to formulate some general evolutionary principles for this ancient class of defense systems. Reviewers This article was reviewed by Mikhail Gelfand and Bojan Zagrovic.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
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15
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Sharma C, Mohanty D. Sequence- and structure-based analysis of proteins involved in miRNA biogenesis. J Biomol Struct Dyn 2017; 36:139-151. [DOI: 10.1080/07391102.2016.1269687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Chhaya Sharma
- Bioinformatics Center, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Debasisa Mohanty
- Bioinformatics Center, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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16
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Knockdown of RNA Interference Pathway Genes in Western Corn Rootworms (Diabrotica virgifera virgifera Le Conte) Demonstrates a Possible Mechanism of Resistance to Lethal dsRNA. PLoS One 2016; 11:e0157520. [PMID: 27310918 PMCID: PMC4911125 DOI: 10.1371/journal.pone.0157520] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 06/01/2016] [Indexed: 01/28/2023] Open
Abstract
RNA interference (RNAi) is being developed as a potential tool for insect pest management. Increased understanding of the RNAi pathway in target insect pests will provide information to use this technology effectively and to inform decisions related to resistant management strategies for RNAi based traits. Dicer 2 (Dcr2), an endonuclease responsible for formation of small interfering RNA’s and Argonaute 2 (Ago2), an essential catalytic component of the RNA-induced silencing complex (RISC) have both been associated with the RNAi pathway in a number of different insect species including the western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae). We identified both genes from a transcriptome library generated from different tissues and developmental stages of the western corn rootworm, an important target pest for transgenic plants expressing dsRNA targeting essential genes. The expression of these genes was suppressed by more than 90% after injecting gene specific dsRNA into adult rootworms. The injected beetles were then fed vATPase A dsRNA which has previously been demonstrated to cause mortality in western corn rootworm adults. The suppression of both RNAi pathway genes resulted in reduced mortality after subsequent exposure to lethal concentrations of vATPase A dsRNA as well as increased vATPase A expression relative to control treatments. Injections with dsRNA for a non-lethal target sequence (Laccase 2) did not affect mortality or expression caused by vATPase A dsRNA indicating that the results observed with Argo and Dicer dsRNA were not caused by simple competition among different dsRNA’s. These results confirm that both genes play an important role in the RNAi pathway for western corn rootworms and indicate that selection pressures that potentially affect the expression of these genes may provide a basis for future studies to understand potential mechanisms of resistance.
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Zhou YR, Li LY, Li JM, Sun ZT, Xie L, Chen JP. ARGONAUTE SUBFAMILY GENES IN THE SMALL BROWN PLANTHOPPER, Laodelphax striatellus (HEMIPTERA: DELPHACIDAE). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2016; 91:37-51. [PMID: 26446351 DOI: 10.1002/arch.21307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Argonaute (AGO) proteins are essential catalytic components of the RNA-induced silencing complex and play central roles in RNA interference. Using a combination of bioinformatics and rapid amplification of cDNA ends (RACE) methods, putative AGO subfamily members, ls-AGO1 and ls-AGO2, were cloned and characterized from the small brown planthopper, Laodelphax striatellus. The open reading frame (ORF) of ls-AGO1 is 2,820 bp long, encoding a putative protein of 939 amino acid residues, and ls-AGO2 contains an ORF of 2,490 bp, encoding 829 amino acid residues. The expected conserved PAZ and PIWI domains, and the conserved Asp-Asp-His (DDH) catalytic triad motif in the PIWI domain were observed in both ls-AGO1 and ls-AGO2. Reverse transcription-qPCR (RT-qPCR) results showed that both ls-AGO1 and ls-AGO2 were expressed in all developmental stages of L. striatellus with highest mRNA abundance in eggs. Expression of ls-AGO1 and ls-AGO2 was significantly decreased in adult insects in response to acquisition of rice black-streaked dwarf virus by second instar nymphs. mRNA expression of ls-AGO1 was significantly downregulated in response to low and high temperatures, but expression of ls-AGO2 was only affected by low temperature. ls-AGO1 and ls-AGO2 were initially downregulated when insects were transferred from rice to maize and to the wild grass Brachypodium distachyon, but expression showed partial or complete recovery 7 days after transfer. These results document that AGO subfamily members of L. striatellus are ubiquitously expressed at different developmental stages and respond to various stresses. Thus, AGO subfamily may act in regulating the stress-response of L. striatellus by controlling related gene expression.
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Affiliation(s)
- Yan-Ru Zhou
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lin-Ying Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jun-Min Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zong-Tao Sun
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Li Xie
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jian-Ping Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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18
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Luo LF, Hou CC, Yang WX. Small non-coding RNAs and their associated proteins in spermatogenesis. Gene 2015; 578:141-57. [PMID: 26692146 DOI: 10.1016/j.gene.2015.12.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/30/2015] [Accepted: 12/08/2015] [Indexed: 12/26/2022]
Abstract
The importance of the gene regulation roles of small non-coding RNAs and their protein partners is of increasing focus. In this paper, we reviewed three main small RNA species which appear to affect spermatogenesis. MicroRNAs (miRNAs) are single stand RNAs derived from transcripts containing stem-loops and hairpins which target corresponding mRNAs and affect their stability or translation. Many miRNA species have been found to be related to normal male germ cell development. The biogenesis of piRNAs is still largely unknown but several models have been proposed. Some piRNAs and PIWIs target transposable elements and it is these that may be active in regulating translation or stem cell maintenance. endo-siRNAs may also participate in sperm development. Some possible interactions between different kinds of small RNAs have even been suggested. We also show that male germ granules are seen to have a close relationship with a considerable number of mRNAs and small RNAs. Those special structures may also participate in sperm development.
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Affiliation(s)
- Ling-Feng Luo
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Cong-Cong Hou
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Wan-Xi Yang
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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19
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Guo WC, Fu KY, Yang S, Li XX, Li GQ. Instar-dependent systemic RNA interference response in Leptinotarsa decemlineata larvae. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2015; 123:64-73. [PMID: 26267054 DOI: 10.1016/j.pestbp.2015.03.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/28/2015] [Accepted: 03/15/2015] [Indexed: 06/04/2023]
Abstract
RNA interference (RNAi) is a promising approach to control Leptinotarsa decemlineata. In this study, RNAi efficiency by double-stranded RNA (dsRNA) targeting S-adenosyl-L-homocysteine hydrolase (LdSAHase) was compared among L. decemlineata first- to fourth-instar larvae. Ingesting dsLdSAHase successfully decreased the target gene expression, caused lethality, inhibited growth and impaired pupation in an instar- and concentration-dependent manner. To study the role of Dicer2 and Argonaute2 genes in RNAi efficiency, we identified LdDcr2a, LdDcr2b, LdAgo2a and LdAgo2b. Their expression levels were higher in young larvae than those in old ones. Exposure to dsegfp for 6 h significantly elevated LdDcr2a, LdDcr2b, LdAgo2a and LdAgo2b mRNA levels in the first-, second-, third- and fourth-instar larvae. When the exposure periods were extended, however, the expression levels were gradually reduced. Continuous exposure for 72 h significantly repressed the expression of LdAgo2a and LdAgo2b in the first, second and third larval instars, and the four genes in final instars. Moreover, we found that dsLdSAHase-caused LdSAHase suppressions and larval mortalities were influenced by previous dsegfp exposure: 12 h of previous exposure increased LdSAHase silencing and mortality of the final instar larvae, whereas 72 h of exposure reduced LdSAHase silencing and mortality. Thus, it seems the activities of core RNAi-machinery proteins affect RNAi efficiency in L. decemlineata.
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Affiliation(s)
- Wen-Chao Guo
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Department of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Kai-Yun Fu
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Yang
- Department of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Xiao-Xu Li
- Department of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Guo-Qing Li
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
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20
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Xiong HL, Zhou SW, Sun AH, He Y, Li J, Yuan X. MicroRNA‑197 reverses the drug resistance of fluorouracil‑induced SGC7901 cells by targeting mitogen‑activated protein kinase 1. Mol Med Rep 2015; 12:5019-25. [PMID: 26151540 PMCID: PMC4581796 DOI: 10.3892/mmr.2015.4052] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/10/2015] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are a group of small non‑coding RNA molecules, which serve an important function in the development of multidrug resistance in cancer through the post‑transcriptional regulation of gene expression and RNA silencing. In the present study, the functional effects of miR‑197 were analyzed in chemo‑resistant gastric cancer cells. Low expression levels of miR‑197 were observed in the fluorouracil (5‑FU)‑resistant gastric cell line SGC7901/5‑FU when compared with those in the parental gastric cell line SGC7901. Overexpression of miR‑197 in SGC7901/5‑FU cells was identified to partially restore 5‑FU sensitivity. miRNA target prediction algorithms suggested that mitogen‑activated protein kinase 1 (MAPK1) is a candidate target gene for miR‑197. A luciferase reporter assay confirmed that miR‑197 led to silencing of the MAPK1 gene by recognizing and then specifically binding to the predicted site of the MAPK1 mRNA 3'‑untranslated region. When miR‑197 was overexpressed in SGC7901 cells, the protein levels of MAPK1 were downregulated. Furthermore, MAPK1 knockdown significantly increased the growth inhibition rate of the SGC7901/5‑FU cells compared with those in the control group. These results indicated that miR‑197 may influence the sensitivity of 5‑FU treatment in a gastric cancer cell line by targeting MAPK1.
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Affiliation(s)
- Hai-Lin Xiong
- Department of Medical Oncology, Huizhou Municipal Central Hospital of Guangdong Province, Huizhou, Guangdong 516000, P.R. China
| | - Si-Wei Zhou
- Department of Medical Oncology, Huizhou Municipal Central Hospital of Guangdong Province, Huizhou, Guangdong 516000, P.R. China
| | - Ai-Hua Sun
- Department of Medical Oncology, Huizhou Municipal Central Hospital of Guangdong Province, Huizhou, Guangdong 516000, P.R. China
| | - Ying He
- Department of Medical Oncology, Huizhou Municipal Central Hospital of Guangdong Province, Huizhou, Guangdong 516000, P.R. China
| | - Jun Li
- Department of Medical Oncology, Huizhou Municipal Central Hospital of Guangdong Province, Huizhou, Guangdong 516000, P.R. China
| | - Xia Yuan
- Department of Medical Oncology, Huizhou Municipal Central Hospital of Guangdong Province, Huizhou, Guangdong 516000, P.R. China
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21
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Yang G, Jiang O, Ling D, Jiang X, Yuan P, Zeng G, Zhu J, Tian J, Weng Y, Wu D. MicroRNA-522 reverses drug resistance of doxorubicin-induced HT29 colon cancer cell by targeting ABCB5. Mol Med Rep 2015; 12:3930-3936. [PMID: 26043974 DOI: 10.3892/mmr.2015.3890] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 04/16/2015] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs, which are important in the development of multidrug resistance in cancer by regulating gene expression at the post‑transcriptional level. The present study investigated the functional effects of miR‑522 in chemoresistant colon cancer cells. The results demonstrated that miR‑522 was significantly downregulated in doxorubicin (DOX) resistant colon cell line, HT29/DOX, compared with the parental HT29 colon cancer cell line. Overexpression of miR‑522 in the HT29/DOX cells partially restored DOX sensitivity. miRNA target prediction algorithms suggested that ABCB5 was a target gene for miR‑522. A fluorescent reporter assay confirmed that miR‑522 was able to specifically bind to the predicted site of the ABCB5 mRNA 3'‑untranslated region. When miR‑522 was overexpressed in the HT29/DOX cells, the protein expression levels of ABCB5 were downregulated. Furthermore, knockdown of ABCB5 significantly increased the growth inhibition rate of the HT29/DOX cells, compared with the control group. These results suggested that miR‑522 may affect the sensitivity of colon cancer cell lines to DOX treatment by targeting ABCB5.
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Affiliation(s)
- Ge Yang
- Clinical Laboratory, Affiliated Second People's Hospital of Luzhou Medical College, Neijiang, Sichuan 641000, P.R. China
| | - Ou Jiang
- Clinical Laboratory, Affiliated Second People's Hospital of Luzhou Medical College, Neijiang, Sichuan 641000, P.R. China
| | - Daiqiong Ling
- Clinical Laboratory, Affiliated Second People's Hospital of Luzhou Medical College, Neijiang, Sichuan 641000, P.R. China
| | - Xiaoyue Jiang
- Clinical Laboratory, Affiliated Second People's Hospital of Luzhou Medical College, Neijiang, Sichuan 641000, P.R. China
| | - Pingzong Yuan
- Clinical Laboratory, Affiliated Second People's Hospital of Luzhou Medical College, Neijiang, Sichuan 641000, P.R. China
| | - Guang Zeng
- Clinical Laboratory, Affiliated Second People's Hospital of Luzhou Medical College, Neijiang, Sichuan 641000, P.R. China
| | - Jing Zhu
- Key Laboratory of Diagnostic Medicine Designated by the Chinese Ministry of Education and School of Diagnostic Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Jie Tian
- Key Laboratory of Diagnostic Medicine Designated by the Chinese Ministry of Education and School of Diagnostic Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yaguang Weng
- Key Laboratory of Diagnostic Medicine Designated by the Chinese Ministry of Education and School of Diagnostic Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Daoquan Wu
- Clinical Laboratory, Affiliated Second People's Hospital of Luzhou Medical College, Neijiang, Sichuan 641000, P.R. China
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22
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Zhang Z, Zhang G, Kong C, Bi J, Gong D, Yu X, Shi D, Zhan B, Ye P. EIF2C, Dicer, and Drosha are up-regulated along tumor progression and associated with poor prognosis in bladder carcinoma. Tumour Biol 2015; 36:5071-9. [PMID: 25656609 DOI: 10.1007/s13277-015-3158-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 01/26/2015] [Indexed: 12/13/2022] Open
Abstract
EIF2C, Dicer, and Drosha are microRNA-regulating machinery components, which participate in microRNA intracellular process and transfer. Our research demonstrated the expression and clinical role of the microRNA-regulating machinery in bladder cancer. EIF2C1, EIF2C2, Dicer, and Drosha mRNA and protein levels were analyzed in 100 bladder carcinomas and 50 normal bladder tissues using quantitative polymerase chain reaction and Western blotting. EIF2C2, Dicer, and Drosha mRNAs and proteins were overexpressed in carcinoma compared with normal tissues, whereas EIF2C1 mRNA and protein were not obviously different. Moreover, immunohistochemistry was used to detect the expressions of EIF2C2, Dicer, and Drosha in 100 bladder carcinomas. There were higher EIF2C2, Dicer, and Drosha expressions in carcinomas than in the adjacent normal tissues, positive correlations being noted with clinical stage, histopathologic grade, and recurrence. Higher EIF2C2, Dicer, and Drosha expressions were related to shorter cancer-specific survival and shorter recurrence-free survival. Multivariate Cox analysis showed that EIF2C2 was an important risk factor in bladder cancer. In conclusion, EIF2C2, Dicer, and Drosha are more highly expressed in bladder carcinoma, promote the development of bladder cancer, and suggested a poor prognosis. Their clinical role in bladder carcinoma merits further research.
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Affiliation(s)
- Zhe Zhang
- Department of Urology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang City, Liaoning Province, 110001, People's Republic of China,
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23
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Zhang L, Liu W, Shao C, Zhang N, Li H, Liu K, Dong Z, Qi Q, Zhao W, Chen S. Cloning, expression and methylation analysis of piwil2 in half-smooth tongue sole (Cynoglossus semilaevis). Mar Genomics 2014; 18 Pt A:45-54. [DOI: 10.1016/j.margen.2014.04.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 04/17/2014] [Accepted: 04/18/2014] [Indexed: 12/25/2022]
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Expression profiles of PIWIL2 short isoforms differ in testicular germ cell tumors of various differentiation subtypes. PLoS One 2014; 9:e112528. [PMID: 25384072 PMCID: PMC4226551 DOI: 10.1371/journal.pone.0112528] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 09/13/2014] [Indexed: 01/22/2023] Open
Abstract
PIWI family proteins have recently emerged as essential contributors in numerous biological processes including germ cell development, stem cell maintenance and epigenetic reprogramming. Expression of some of the family members has been shown to be elevated in tumors. In particular, PIWIL2 has been probed as a potential neoplasia biomarker in many cancers in humans. Previously, PIWIL2 was shown to be expressed in most tumours as a set of its shorter isoforms. In this work, we demonstrated the presence of its 60 kDa (PL2L60A) and 80 kDa (PL2L80A) isoforms in testicular cancer cell lines. We also ascertained the transcriptional boundaries of mRNAs and alternative promoter regions for these PIWIL2 isoforms. Further, we probed a range of testicular germ cell tumor (TGCT) samples and found PIWIL2 to be predominantly expressed as PL2L60A in most of them. Importantly, the levels of both PL2L60A mRNA and protein products were found to vary depending on the differentiation subtype of TGCTs, i.e., PL2L60A expression is significantly higher in undifferentiated seminomas and appears to be substantially decreased in mixed and nonseminomatous TGCTs. The higher level of PL2L60A expression in undifferentiated TGCTs was further validated in the model system of retinoic acid induced differentiation in NT2/D1 cell line. Therefore, both PL2L60A mRNA and protein abundance could serve as an additional marker distinguishing between seminomas and nonseminomatous tumors with different prognosis and therapy approaches.
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25
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In silico identification, phylogenetic and bioinformatic analysis of argonaute genes in plants. Int J Genomics 2014; 2014:967461. [PMID: 25309901 PMCID: PMC4181786 DOI: 10.1155/2014/967461] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/03/2014] [Accepted: 08/05/2014] [Indexed: 11/26/2022] Open
Abstract
Argonaute protein family is the key players in pathways of gene silencing and small regulatory RNAs in different organisms. Argonaute proteins can bind small noncoding RNAs and control protein synthesis, affect messenger RNA stability, and even participate in the production of new forms of small RNAs. The aim of this study was to characterize and perform bioinformatic analysis of Argonaute proteins in 32 plant species that their genome was sequenced. A total of 437 Argonaute genes were identified and were analyzed based on lengths, gene structure, and protein structure. Results showed that Argonaute proteins were highly conserved across plant kingdom. Phylogenic analysis divided plant Argonautes into three classes. Argonaute proteins have three conserved domains PAZ, MID and PIWI. In addition to three conserved domains namely, PAZ, MID, and PIWI, we identified few more domains in AGO of some plant species. Expression profile analysis of Argonaute proteins showed that expression of these genes varies in most of tissues, which means that these proteins are involved in regulation of most pathways of the plant system. Numbers of alternative transcripts of Argonaute genes were highly variable among the plants. A thorough analysis of large number of putative Argonaute genes revealed several interesting aspects associated with this protein and brought novel information with promising usefulness for both basic and biotechnological applications.
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Cora E, Pandey RR, Xiol J, Taylor J, Sachidanandam R, McCarthy AA, Pillai RS. The MID-PIWI module of Piwi proteins specifies nucleotide- and strand-biases of piRNAs. RNA (NEW YORK, N.Y.) 2014; 20:773-81. [PMID: 24757166 PMCID: PMC4024632 DOI: 10.1261/rna.044701.114] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Piwi-interacting RNAs (piRNAs) guide Piwi Argonautes to suppress transposon activity in animal gonads. Known piRNA populations are extremely complex, with millions of individual sequences present in a single organism. Despite this complexity, specific Piwi proteins incorporate piRNAs with distinct nucleotide- and transposon strand-biases (antisense or sense) of unknown origin. Here, we examined the contribution of structural domains in Piwi proteins toward defining these biases. We report the first crystal structure of the MID domain from a Piwi Argonaute and use docking experiments to show its ability to specify recognition of 5' uridine (1U-bias) of piRNAs. Mutational analyses reveal the importance of 5' end-recognition within the MID domain for piRNA biogenesis in vivo. Finally, domain-swapping experiments uncover an unexpected role for the MID-PIWI module of a Piwi protein in dictating the transposon strand-orientation of its bound piRNAs. Our work identifies structural features that allow distinguishing individual Piwi members during piRNA biogenesis.
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Affiliation(s)
- Elisa Cora
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
| | - Radha R. Pandey
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
| | - Jordi Xiol
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
| | - Josh Taylor
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
| | - Ravi Sachidanandam
- Department of Oncological Sciences, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
| | - Ramesh S. Pillai
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
- Corresponding authorE-mail
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Upadhyay SK, Dixit S, Sharma S, Singh H, Kumar J, Verma PC, Chandrashekar K. siRNA machinery in whitefly (Bemisia tabaci). PLoS One 2013; 8:e83692. [PMID: 24391810 PMCID: PMC3877088 DOI: 10.1371/journal.pone.0083692] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 11/06/2013] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND RNA interference has been emerged as an utmost tool for the control of sap sucking insect pests. Systemic response is necessary to control them in field condition. Whitefly is observed to be more prone to siRNA in recent studies, however the siRNA machinery and mechanism is not well established. METHODOLOGY/PRINCIPAL FINDINGS To identify the core siRNA machinery, we curated transcriptome data of whitefly from NCBI database. Partial mRNA sequences encoding Dicer2, R2D2, Argonaute2 and Sid1 were identified by tblastn search of homologous sequences from Aphis glycines and Tribolium castaneum. Complete encoding sequences were obtained by RACE, protein sequences derived by Expasy translate tool and confirmed by blastp analysis. Conserved domain search and Prosite-Scan showed similar domain architecture as reported in homologs from related insects. We found helicase, PAZ, RNaseIIIa, RNaseIIIb and double-stranded RNA-binding fold (DSRBF) in Dicer2; DsRBD in R2D2; and PAZ and PIWI domains in Argonaute2. Eleven transmembrane domains were detected in Sid1. Sequence homology and phylogenetic analysis revealed that RNAi machinery of whitefly is close to Aphids. Real-time PCR analysis showed similar expression of these genes in different developmental stages as reported in A. glycines and T. castaneum. Further, the expression level of above genes was quite similar to the housekeeping gene actin. CONCLUSIONS/SIGNIFICANCE Availability of core siRNA machinery including the Sid1 and their universal expression in reasonable quantity indicated significant response of whitefly towards siRNA. Present report opens the way for controlling whitefly, one of the most destructive crop insect pest.
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Affiliation(s)
- Santosh Kumar Upadhyay
- National Agri-Food Biotechnology Institute, (Department of Biotechnology, Government of India), Mohali, Punjab, India
- * E-mail: (SKU); (PCV); (KC)
| | - Sameer Dixit
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research, RanaPratapMarg, Lucknow, India
| | - Shailesh Sharma
- National Agri-Food Biotechnology Institute, (Department of Biotechnology, Government of India), Mohali, Punjab, India
| | - Harpal Singh
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research, RanaPratapMarg, Lucknow, India
| | - Jitesh Kumar
- National Agri-Food Biotechnology Institute, (Department of Biotechnology, Government of India), Mohali, Punjab, India
| | - Praveen C. Verma
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research, RanaPratapMarg, Lucknow, India
- * E-mail: (SKU); (PCV); (KC)
| | - K. Chandrashekar
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research, RanaPratapMarg, Lucknow, India
- Indian Agricultural Research Institute-Regional Station, Agricultural College Estate, Shivaji Nagar, Pune, Maharashtra, India
- * E-mail: (SKU); (PCV); (KC)
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Xu HJ, Chen T, Ma XF, Xue J, Pan PL, Zhang XC, Cheng JA, Zhang CX. Genome-wide screening for components of small interfering RNA (siRNA) and micro-RNA (miRNA) pathways in the brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae). INSECT MOLECULAR BIOLOGY 2013; 22:635-47. [PMID: 23937246 DOI: 10.1111/imb.12051] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The brown planthopper (BPH), Nilaparvata lugens, is a major rice pest in Asia, and accumulated evidence indicates that this species is susceptible to RNA interference (RNAi); however, the mechanism underlying RNAi and parental RNAi has not yet been determined. We comprehensively investigated the repertoire of core genes involved in small interfering RNA (siRNA) and micro-RNA (miRNA) pathways in the BPH by comparing its newly assembled transcriptome and genome with those of Drosophila melanogaster, Tribolium castaneum and Caenorhabditis elegans. Our analysis showed that the BPH possesses one drosha and two Dicer (dcr) genes, three dsRNA-binding motif protein genes, two Argonaute (ago) genes, two Eri-1-like genes (eri-1), and a Sid-1-like gene (sid-1). Additionally, we report for first time that parental RNAi might occur in this species, and siRNA pathway and Sid-1 were required for high efficiency of systemic RNAi triggered by exogenous dsRNA. Furthermore, our results also demonstrated that the miRNA pathway was involved in BPH metamorphosis as depletion of the ago1 or dcr1 gene severely impaired ecdysis. The BPH might be a good model system to study the molecular mechanism of systemic RNAi in hemimetabolous insects, and RNAi has potential to be developed to control this pest in agricultural settings.
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Affiliation(s)
- H-J Xu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Science, Zhejiang University, Hangzhou, China
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Govan JM, Young DD, Lusic H, Liu Q, Lively MO, Deiters A. Optochemical control of RNA interference in mammalian cells. Nucleic Acids Res 2013; 41:10518-28. [PMID: 24021631 PMCID: PMC3905849 DOI: 10.1093/nar/gkt806] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Short interfering RNAs (siRNAs) and microRNAs (miRNAs) have been widely used in mammalian tissue culture and model organisms to selectively silence genes of interest. One limitation of this technology is the lack of precise external control over the gene-silencing event. The use of photocleavable protecting groups installed on nucleobases is a promising strategy to circumvent this limitation, providing high spatial and temporal control over siRNA or miRNA activation. Here, we have designed, synthesized and site-specifically incorporated new photocaged guanosine and uridine RNA phosphoramidites into short RNA duplexes. We demonstrated the applicability of these photocaged siRNAs in the light-regulation of the expression of an exogenous green fluorescent protein reporter gene and an endogenous target gene, the mitosis motor protein, Eg5. Two different approaches were investigated with the caged RNA molecules: the light-regulation of catalytic RNA cleavage by RISC and the light-regulation of seed region recognition. The ability to regulate both functions with light enables the application of this optochemical methodology to a wide range of small regulatory RNA molecules.
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Affiliation(s)
- Jeane M Govan
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA, Department of Chemistry, College of William & Mary, Williamsburg, VA 32187, USA, Center for Structural Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA and Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Shao F, Lu S. Genome-wide identification, molecular cloning, expression profiling and posttranscriptional regulation analysis of the Argonaute gene family in Salvia miltiorrhiza, an emerging model medicinal plant. BMC Genomics 2013; 14:512. [PMID: 23889895 PMCID: PMC3750313 DOI: 10.1186/1471-2164-14-512] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 07/27/2013] [Indexed: 12/27/2022] Open
Abstract
Background Argonaute (AGO) is the core component of RNA-induced silencing complex. The AGO gene family has been analyzed in various plant species; however, there is no report about AGOs in the well-known Traditional Chinese Medicine (TCM) plant, Salvia miltiorrhiza. Results Through a genome-wide analysis, we identified ten SmAGO genes in S. miltiorrhiza. Full-length cDNAs of all SmAGOs were subsequently cloned and sequenced. These SmAGOs were characterized using a comprehensive approach. Sequence features, gene structures and conserved domains were analyzed by the comparison of SmAGOs and AtAGOs. Phylogenetic relationships among AGO proteins from S. miltiorrhiza, Arabidopsis and rice were revealed. The expression levels of SmAGO genes in various tissues of S. miltiorrhiza were investigated. The results implied that some SmAGOs, such as SmAGO1, SmAGO2, SmAGO3, SmAGO7 and SmAGO10, probably played similar roles as their counterparts in Arabidopsis; whereas the others could be more species-specialized. It suggests the conservation and diversity of AGOs in plants. Additionally, we identified a total of 24 hairpin structures, representing six miRNA gene families, to be miRNA precursors. Using the modified 5′-RACE method, we confirmed that SmAGO1 and SmAGO2 were targeted by S. miltiorrhiza miR168a/b and miR403, respectively. It suggests the conservation of AGO1-miR168 and AGO2-miR403 regulatory modules in S. miltiorrhiza and Arabidopsis. Conclusions This is the first attempt to explore SmAGOs and miRNAs in S. miltiorrhiza. The results provide useful information for further elucidation of gene silencing pathways in S. miltiorrhiza.
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Affiliation(s)
- Fenjuan Shao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No 151, Malianwa North Road, Haidian District, Beijing 100193, China
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Golbabapour S, Majid NA, Hassandarvish P, Hajrezaie M, Abdulla MA, Hadi AHA. Gene silencing and Polycomb group proteins: an overview of their structure, mechanisms and phylogenetics. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 17:283-96. [PMID: 23692361 PMCID: PMC3662373 DOI: 10.1089/omi.2012.0105] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
DNA methylation, histone modifications, and chromatin configuration are crucially important in the regulation of gene expression. Among these epigenetic mechanisms, silencing the expression of certain genes depending on developmental stage and tissue specificity is a key repressive system in genome programming. Polycomb (Pc) proteins play roles in gene silencing through different mechanisms. These proteins act in complexes and govern the histone methylation profiles of a large number of genes that regulate various cellular pathways. This review focuses on two main Pc complexes, Pc repressive complexes 1 and 2, and their phylogenetic relationship, structures, and function. The dynamic roles of these complexes in silencing will be discussed herein, with a focus on the recruitment of Pc complexes to target genes and the key factors involved in their recruitment.
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Affiliation(s)
- Shahram Golbabapour
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
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Wang GH, Jiang L, Zhu L, Cheng TC, Niu WH, Yan YF, Xia QY. Characterization of Argonaute family members in the silkworm, Bombyx mori. INSECT SCIENCE 2013; 20:78-91. [PMID: 23955828 DOI: 10.1111/j.1744-7917.2012.01555.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The Argonaute protein family is a highly conserved group of proteins, which have been implicated in RNA silencing in both plants and animals. Here, four members of the Argonaute family were systemically identified based on the genome sequence of Bombyx mori. Based on their sequence similarity, BmAgo1 and BmAgo2 belong to the Ago subfamily, while BmAgo3 and BmPiwi are in the Piwi subfamily. Phylogenetic analysis reveals that silkworm Argonaute family members are conserved in insects. Conserved amino acid residues involved in recognition of the 5' end of the small RNA guide strand and of the conserved (aspartate, aspartate and histidine [DDH]) motif present in their PIWI domains suggest that these four Argonaute family members may have conserved slicer activities. The results of microarray expression analysis show that there is a low expression level for B. mori Argonaute family members in different tissues and different developmental stages, except for BmPiwi. All four B. mori Argonaute family members are upregulated upon infection with B. mori nucleopolyhedrovirus. The complete coding sequence of BmPiwi, the homolog of Drosophila piwi, was cloned and its expression occurred mainly in the area where spermatogonia and spermatocytes appear. Our results provide an overview of the B. mori Argonaute family members and suggest that they may have multiple roles. In addition, this is also the first report, to our knowledge, of the response of RNA silencing machinery to DNA virus infection in insects.
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Affiliation(s)
- Gen-Hong Wang
- State Key Laboratory of Silkworm Genome Biology, School of Biotechnology, Southwest, Chongqing, China
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Abstract
One of the most important and evolutionarily conserved strategies to control gene expression in higher metazoa is posttranscriptional regulation via small regulatory RNAs such as microRNAs (miRNAs), endogenous small interfering RNAs (endo-siRNAs), and piwi-interacting RNAs (piRNAs). Primordial germ cells, which are defined by their totipotent potential and noted for their dependence on posttranscriptional regulation by RNA-binding proteins, rely on these small regulatory RNAs for virtually every aspect of their development, including specification, migration, and differentiation into competent gametes. Here, we review current knowledge of the roles miRNAs, endo-siRNAs, and piRNAs play at all stages of germline development in various organisms, focusing on studies in the mouse.
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Affiliation(s)
- Matthew S Cook
- Department of Urology, University of California, San Francisco, California, USA.
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Bifunctional short hairpin RNA (bi-shRNA): design and pathway to clinical application. Methods Mol Biol 2013; 942:259-78. [PMID: 23027056 DOI: 10.1007/978-1-62703-119-6_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The discovery of RNA interference (RNAi) engendered great excitement and raised expectations regarding its potential applications in biomedical research and clinical usage. Over the ensuing years, expanded understanding of RNAi and preliminary results from early clinical trials tempered enthusiasm with realistic appraisal resulting in cautious optimism and a better understanding of necessary research and clinical directions. As a result, data from more recent trials are beginning to show encouraging positive clinical outcomes. The capability of delivering a pharmacologically effective dose to the target site while avoiding adverse host reactions still remains a challenge although the delivery technology continues to improve. We have developed a novel vector-driven bifunctional short hairpin RNA (bi-shRNA) technology that harnesses both cleavage-dependent and cleavage-independent RISC loading pathways to enhance knockdown potency. Consequent advantages provided by the bi-shRNA include a lower effective systemic dose than comparator siRNA/shRNA to minimize the potential for off-target side effects, due to its ability to induce both a rapid (inhibition of protein translation) and delayed (mRNA cleavage and degradation) targeting effect depending on protein and mRNA kinetics, and a longer duration of effectiveness for clinical applications. Here, we provide an overview of key molecular methods for the design, construction, quality control, and application of bi-shRNA that we believe will be useful for others interested in utilizing this technology.
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Padmanabhan PK, Dumas C, Samant M, Rochette A, Simard MJ, Papadopoulou B. Novel features of a PIWI-like protein homolog in the parasitic protozoan Leishmania. PLoS One 2012; 7:e52612. [PMID: 23285111 PMCID: PMC3528672 DOI: 10.1371/journal.pone.0052612] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 11/19/2012] [Indexed: 11/22/2022] Open
Abstract
In contrast to nearly all eukaryotes, the Old World Leishmania species L. infantum and L. major lack the bona fide RNAi machinery genes. Interestingly, both Leishmania genomes code for an atypical Argonaute-like protein that possesses a PIWI domain but lacks the PAZ domain found in Argonautes from RNAi proficient organisms. Using sub-cellular fractionation and confocal fluorescence microscopy, we show that unlike other eukaryotes, the PIWI-like protein is mainly localized in the single mitochondrion in Leishmania. To predict PIWI function, we generated a knockout mutant for the PIWI gene in both L. infantum (Lin) and L. major species by double-targeted gene replacement. Depletion of PIWI has no effect on the viability of insect promastigote forms but leads to an important growth defect of the mammalian amastigote lifestage in vitro and significantly delays disease pathology in mice, consistent with a higher expression of the PIWI transcript in amastigotes. Moreover, amastigotes lacking PIWI display a higher sensitivity to apoptosis inducing agents than wild type parasites, suggesting that PIWI may be a sensor for apoptotic stimuli. Furthermore, a whole-genome DNA microarray analysis revealed that loss of LinPIWI in Leishmania amastigotes affects mostly the expression of specific subsets of developmentally regulated genes. Several transcripts encoding surface and membrane-bound proteins were found downregulated in the LinPIWI(−/−) mutant whereas all histone transcripts were upregulated in the null mutant, supporting the possibility that PIWI plays a direct or indirect role in the stability of these transcripts. Although our data suggest that PIWI is not involved in the biogenesis or the stability of small noncoding RNAs, additional studies are required to gain further insights into the role of this protein on RNA regulation and amastigote development in Leishmania.
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Affiliation(s)
- Prasad K. Padmanabhan
- Research Centre in Infectious Diseases, CHUL Research Centre (CHUQ) and Department of Microbiology and Immunology, Faculty of Medicine, Laval University, Quebec, Canada
| | - Carole Dumas
- Research Centre in Infectious Diseases, CHUL Research Centre (CHUQ) and Department of Microbiology and Immunology, Faculty of Medicine, Laval University, Quebec, Canada
| | - Mukesh Samant
- Research Centre in Infectious Diseases, CHUL Research Centre (CHUQ) and Department of Microbiology and Immunology, Faculty of Medicine, Laval University, Quebec, Canada
| | | | - Martin J. Simard
- Laval University Cancer Research Centre, Hôtel-Dieu de Québec (CHUQ), Quebec, Canada
| | - Barbara Papadopoulou
- Research Centre in Infectious Diseases, CHUL Research Centre (CHUQ) and Department of Microbiology and Immunology, Faculty of Medicine, Laval University, Quebec, Canada
- * E-mail:
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Chen J, Zhang W. Kinetic analysis of the effects of target structure on siRNA efficiency. J Chem Phys 2012; 137:225102. [DOI: 10.1063/1.4769821] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Miller SC, Miyata K, Brown SJ, Tomoyasu Y. Dissecting systemic RNA interference in the red flour beetle Tribolium castaneum: parameters affecting the efficiency of RNAi. PLoS One 2012; 7:e47431. [PMID: 23133513 PMCID: PMC3484993 DOI: 10.1371/journal.pone.0047431] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 09/17/2012] [Indexed: 11/29/2022] Open
Abstract
The phenomenon of RNAi, in which the introduction of dsRNA into a cell triggers the destruction of the corresponding mRNA resulting in a gene silencing effect, is conserved across a wide array of plant and animal phyla. However, the mechanism by which the dsRNA enters a cell, allowing the RNAi effect to occur throughout a multicellular organism (systemic RNAi), has only been studied extensively in certain plants and the nematode Caenorhabditis elegans. In recent years, RNAi has become a popular reverse genetic technique for gene silencing in many organisms. Although many RNAi techniques in non-traditional model organisms rely on the systemic nature of RNAi, little has been done to analyze the parameters required to obtain a robust systemic RNAi response. The data provided here show that the concentration and length of dsRNA have profound effects on the efficacy of the RNAi response both in regard to initial efficiency and duration of the effect in Tribolium castaneum. In addition, our analyses using a series of short dsRNAs and chimeric dsRNA provide evidence that dsRNA cellular uptake (and not the RNAi response itself) is the major step affected by dsRNA size in Tribolium. We also demonstrate that competitive inhibition of dsRNA can occur when multiple dsRNAs are injected together, influencing the effectiveness of RNAi. These data provide specific information essential to the design and implementation of RNAi based studies, and may provide insight into the molecular basis of the systemic RNAi response in insects.
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Affiliation(s)
- Sherry C. Miller
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
- K-State Arthropod Genomics Center, Kansas State University, Manhattan, Kansas, United States of America
| | - Keita Miyata
- Department of Zoology, Miami University, Oxford, Ohio, United States of America
| | - Susan J. Brown
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
- K-State Arthropod Genomics Center, Kansas State University, Manhattan, Kansas, United States of America
| | - Yoshinori Tomoyasu
- Department of Zoology, Miami University, Oxford, Ohio, United States of America
- * E-mail:
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Suzuki R, Honda S, Kirino Y. PIWI Expression and Function in Cancer. Front Genet 2012; 3:204. [PMID: 23087701 PMCID: PMC3472457 DOI: 10.3389/fgene.2012.00204] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 09/23/2012] [Indexed: 12/13/2022] Open
Abstract
PIWI proteins, a subclade of the Argonaute family proteins, are expressed predominantly in the germline and bind to PIWI-interacting RNAs (piRNAs), which are 25–31 nucleotides in length. The PIWI/piRNA pathway plays critical roles in germline development by regulating transposons and other targets to maintain genome integrity. While the functions of PIWI in the germline have been extensively investigated, recent studies have accumulated evidence that the human PIWI proteins, HIWI and HILI, are aberrantly expressed in a variety of cancers. This review summarizes our knowledge of PIWI expression in cancer and discusses its possible role in tumorigenesis.
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Affiliation(s)
- Ryusuke Suzuki
- Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center Los Angeles, CA, USA
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Jahandideh S, Srinivasasainagendra V, Zhi D. Comprehensive comparative analysis and identification of RNA-binding protein domains: multi-class classification and feature selection. J Theor Biol 2012; 312:65-75. [PMID: 22884576 DOI: 10.1016/j.jtbi.2012.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 07/09/2012] [Accepted: 07/13/2012] [Indexed: 01/11/2023]
Abstract
RNA-protein interaction plays an important role in various cellular processes, such as protein synthesis, gene regulation, post-transcriptional gene regulation, alternative splicing, and infections by RNA viruses. In this study, using Gene Ontology Annotated (GOA) and Structural Classification of Proteins (SCOP) databases an automatic procedure was designed to capture structurally solved RNA-binding protein domains in different subclasses. Subsequently, we applied tuned multi-class SVM (TMCSVM), Random Forest (RF), and multi-class ℓ1/ℓq-regularized logistic regression (MCRLR) for analysis and classifying RNA-binding protein domains based on a comprehensive set of sequence and structural features. In this study, we compared prediction accuracy of three different state-of-the-art predictor methods. From our results, TMCSVM outperforms the other methods and suggests the potential of TMCSVM as a useful tool for facilitating the multi-class prediction of RNA-binding protein domains. On the other hand, MCRLR by elucidating importance of features for their contribution in predictive accuracy of RNA-binding protein domains subclasses, helps us to provide some biological insights into the roles of sequences and structures in protein-RNA interactions.
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Affiliation(s)
- Samad Jahandideh
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Vinodh Srinivasasainagendra
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Degui Zhi
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA.
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Kong WQ, Bai R, Liu T, Cai CL, Liu M, Li X, Tang H. MicroRNA-182 targets cAMP-responsive element-binding protein 1 and suppresses cell growth in human gastric adenocarcinoma. FEBS J 2012; 279:1252-60. [PMID: 22325466 DOI: 10.1111/j.1742-4658.2012.08519.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) constitute a class of noncoding RNAs that post-transcriptionally regulate gene expression. Recent evidence indicates that many miRNAs function as oncogenes or tumor suppressors by negatively regulating their target genes. In our previous study, using miRNA microarray analysis, we found that miRNA-182 (miR-182) was significantly downregulated in human gastric adenocarcinoma tissue samples. Here, we confirmed the downregulation of miR-182 in a larger sample of gastric tissue samples. Overexpression of miR-182 suppressed the proliferation and colony formation of gastric cancer cells. An oncogene, encoding cAMP-responsive element binding protein 1 (CREB1), serves as a direct target gene of miR-182. A fluorescent reporter assay confirmed that miR-182 binds specifically to the predicted site of the CREB1 mRNA 3'-UTR. When miR-182 was overexpressed in gastric cancer cell lines, both the mRNA and protein levels of CREB1 were depressed. Furthermore, CREB1 was present at a high level in human gastric adenocarcinoma tissues, and this was inversely correlated with miR-182 expression. Ectopic expression of CREB1 overcame the suppressive phenotypes of gastric cancer cells caused by miR-182. These results indicate that miR-182 targets the CREB1 gene and suppresses gastric adenocarcinoma cell growth, suggesting that miR-182 shows tumor-suppressive activity in human gastric cancer.
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Affiliation(s)
- Wei-Qing Kong
- Tianjin Life Science Research Center and Basic Medical School, Tianjin Medical University, Tianjin, China
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Takada S, Asahara H. Current strategies for microRNA research. Mod Rheumatol 2012; 22:645-53. [PMID: 22237764 DOI: 10.1007/s10165-011-0583-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 12/16/2011] [Indexed: 10/14/2022]
Abstract
The short ribonucleic acid molecules (20-24 nucleotides) known as microRNAs (miRNAs) are non-coding RNAs that disrupt translation or degrade target mRNAs posttranscriptionally in a sequence-specific manner, and the miRNA may not be completely complementary to its targets. This class of RNAs is thought to be functionally important because many individual miRNAs are evolutionally conserved across widely diverse phyla. Further, miRNAs are associated with diverse biological phenomena, such as cell growth, apoptosis, development, differentiation, cancer, and arthritis. MicroRNA research is one of a number of rapidly evolving fields of basic and biomedical science, with many new techniques being developed. However, miRNA experiments require modifications of preexisting molecular techniques or specialized methods, given the difficulties stemming from their small size. In this review, we summarize current in-silico and biochemical strategies for miRNA research to outline the current status of the research techniques now being employed to find a new direction in the field.
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Affiliation(s)
- Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan.
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Pillai RS, Chuma S. piRNAs and their involvement in male germline development in mice. Dev Growth Differ 2012; 54:78-92. [PMID: 22221002 DOI: 10.1111/j.1440-169x.2011.01320.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs expressed in the animal gonads. They are implicated in silencing the genome instability threat posed by mobile genetic elements called transposons. Unlike other small RNAs, which use double-stranded precursors, piRNAs seem to arise from long single-stranded precursor transcripts expressed from discrete genomic regions. In mice, the Piwi pathway is essential for male fertility, and its loss-of-function mutations affect several distinct stages of spermatogenesis. While this small RNA pathway primarily operates post-transcriptionally, it also impacts DNA methylation of target retrotransposon loci, representing an intriguing model of RNA-directed epigenetic control in mammals. Remarkably the Piwi pathway components are specifically localized at germinal granule/nuage, an evolutionarily conserved but still enigmatic ribonucleoprotein compartment in the germline. The inaccessibility of the germline for easy experimental manipulation has meant that this class of RNAs has remained enigmatic. However, recent advances in the use of cell culture models and cell-free systems have greatly advanced our understanding. In this review, we briefly summarize our current understanding of the Piwi pathway, focusing on its developmental regulation, piRNA biogenesis and key function in male germline development from fetal spermatogonial stem cell stage to postnatal haploid spermiogenesis in mice.
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Affiliation(s)
- Ramesh S Pillai
- European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181 CNRS-UJF-EMBL International Unit (UMI 3265) for Virus Host Cell Interactions (UVHCI), 38042 Grenoble, France.
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Abstract
Given the widespread impact of RNA silencing on the Arabidopsis thaliana genome, it is indeed remarkable that this means of gene regulation went undiscovered for so long. Since the publication of landmark papers in 1998 (Fire et al., Nature 391:806-811, 1998; Waterhouse et al., Proc Natl Acad Sci U S A 95:13959-13964, 1998), intense research efforts have resulted in much progress from the speculation of Mello and colleagues that "the mechanisms underlying RNA interference probably exist for a biological purpose" (Fire et al., Nature 391:806-811, 1998). Across the eukaryotic kingdom, with the notable exception of Saccharomyces cerevisiae (Moazed, Science 326:544-550, 2009), the importance of small RNA-driven gene regulation has been recognized and implicated in central developmental processes as well as in aberrant and diseased states. Plants have by far the most complex RNA-based control of gene expression (Wang et al., Floriculture, ornamental and plant biotechnology, vol. III, 2006). Four distinct RNA silencing pathways have been recognized in plants, albeit with considerable conservation of the molecular components. These pathways are directed by various small RNA species, including microRNAs (miRNAs), trans-acting small interfering RNAs (siRNA) (ta-siRNAs), repeat-associated siRNAs (ra-siRNAs), and natural antisense transcript siRNAs (nat-siRNAs). The effective functionality of each of these pathways appear to be fundamental to the integrity of A. thaliana. Furthermore, in response to viral invasion, plants synthesize viral sRNAs as a means of defense. This process may in fact reflect the ancient origins of RNA silencing: plants may have evolved RNA silencing pathways as a defense mechanism against foreign nucleic acid species in the absence of an immune system (Wang and Metzlaff, Curr Opin Plant Biol 8:216-222, 2005). The generation of viral siRNAs is a particularly interesting illustration of RNA silencing as it provides a context to explore the potential to harness a naturally occurring system to the end goal of artificially engineering viral resistance.
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Drpiwi-1 is essential for germline cell formation during sexualization of the planarian Dugesia ryukyuensis. Dev Biol 2011; 361:167-76. [PMID: 22024321 DOI: 10.1016/j.ydbio.2011.10.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Revised: 07/28/2011] [Accepted: 10/07/2011] [Indexed: 11/23/2022]
Abstract
A piwi homolog is required for the regulation of stem cells, formation and maintenance of germline stem cells, and gametogenesis in many metazoans. Planarians can change their reproductive mode seasonally, both asexually and sexually, and develop and maintain germ cells and sexual organs. They have many pluripotent stem cells (neoblasts) that can differentiate into both somatic and germline stem cells. Thus, we searched for a piwi subfamily in the planarian Dugesia ryukyuensis. Four piwi homologs, identified as Drpiwi-1, -2, -3, and -4, were expressed in sexually reproductive worms. We then selectively destroyed the neoblasts by irradiating the worms with X-rays. In such worms, Drpiwi-1, -2, and -3 were not expressed at all, whereas Drpiwi-4 was expressed to the same degree as that in non-irradiated controls, indicating that Drpiwi-1, -2, and -3, but not Drpiwi-4, are expressed in neoblasts. During the regeneration process, Drpiwi-2(RNAi) and -3(RNAi) worms failed to regenerate after ablation, but Drpiwi-1 and -4(RNAi) worms regenerated. During the sexualizing process, Drpiwi-1(RNAi) worms failed to develop ovaries and testes, but somatic sexual organs were unaffected. Germ cell development was normal in Drpiwi-4(RNAi) worms. Therefore, Drpiwi-2 and -3 may be related to the regulation of neoblasts important for maintaining homeostasis, and Drpiwi-1 is essential for the development of germ cells but not somatic sexual organs. DrPiwi-1 is localized in the cytoplasm of stem cells and germline cells and may be involved in regulating some gene expression. We suggest that planarian Piwi controls germline formation via RNA silencing mechanisms.
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Azimzadeh Jamalkandi S, Masoudi-Nejad A. RNAi pathway integration in Caenorhabditis elegans development. Funct Integr Genomics 2011; 11:389-405. [DOI: 10.1007/s10142-011-0236-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Revised: 06/12/2011] [Accepted: 06/28/2011] [Indexed: 01/07/2023]
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Barth S, Meister G, Grässer FA. EBV-encoded miRNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:631-40. [PMID: 21640213 DOI: 10.1016/j.bbagrm.2011.05.010] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 05/14/2011] [Accepted: 05/16/2011] [Indexed: 12/12/2022]
Abstract
The Epstein-Barr virus (EBV) is an oncogenic Herpes virus involved in the induction of a variety of human tumours. It was the first virus found to encode microRNAs (miRNAs). MiRNAs are short, non-coding RNAs that in most cases negatively regulate gene expression at the post-transcriptional level. EBV-transformed cells express at least 44 mature viral miRNAs that target viral and cellular genes. In addition, EBV-infection severely deregulates the miRNA profile of the host cell. The presently available information indicates that the virus uses its miRNAs to inhibit the apoptotic response of the infected cell as a means to establish a latent infection. Likewise, EBV-encoded miRNAs interfere in the expression of viral genes in order to mask the infected cell from the immune response. Cellular targets of viral miRNAs are involved in protein traffic within the cell and regulate innate immunity. MiRNA profiling of diffuse large B-cell lymphoma (DLBCL) and nasal NK/T-cell lymphoma (NKTL) showed that only 2% of the miRNAs are derived from the virus, while viral miRNAs comprise up to 20% of the total miRNA in nasopharyngeal carcinoma (NPC) and probably contribute to the formation or maintenance of NPC. The presence of viral miRNAs in exosomes raises the fascinating possibility that virus-infected cells regulate gene expression in the surrounding tissue to avert destruction by the immune system. This article is part of a Special Issue entitled: MicroRNAs in viral gene regulation.
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Affiliation(s)
- Stephanie Barth
- Universitätsklinikum des Saarlandes, Institut für Virologie, Homburg/Saar, Germany
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Whitfield AE, Rotenberg D, Aritua V, Hogenhout SA. Analysis of expressed sequence tags from Maize mosaic rhabdovirus-infected gut tissues of Peregrinus maidis reveals the presence of key components of insect innate immunity. INSECT MOLECULAR BIOLOGY 2011; 20:225-242. [PMID: 21199018 DOI: 10.1111/j.1365-2583.2010.01060.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The corn planthopper, Peregrinus maidis, causes direct feeding damage to plants and transmits Maize mosaic rhabdovirus (MMV) in a persistent-propagative manner. MMV must cross several insect tissue layers for successful transmission to occur, and the gut serves as an important barrier for rhabdovirus transmission. In order to facilitate the identification of proteins that may interact with MMV either by facilitating acquisition or responding to virus infection, we generated and analysed the gut transcriptome of P. maidis. From two normalized cDNA libraries, we generated a P. maidis gut transcriptome composed of 20,771 expressed sequence tags (ESTs). Assembly of the sequences yielded 1860 contigs and 14,032 singletons, and biological roles were assigned to 5793 (36%). Comparison of P. maidis ESTs with other insect amino acid sequences revealed that P. maidis shares greatest sequence similarity with another hemipteran, the brown planthopper Nilaparvata lugens. We identified 202 P. maidis transcripts with putative homology to proteins associated with insect innate immunity, including those implicated in the Toll, Imd, JAK/STAT, Jnk and the small-interfering RNA-mediated pathways. Sequence comparisons between our P. maidis gut EST collection and the currently available National Center for Biotechnology Information EST database collection for Ni. lugens revealed that a pathogen recognition receptor in the Imd pathway, peptidoglycan recognition protein-long class (PGRP-LC), is present in these two members of the family Delphacidae; however, these recognition receptors are lacking in the model hemipteran Acyrthosiphon pisum. In addition, we identified sequences in the P. maidis gut transcriptome that share significant amino acid sequence similarities with the rhabdovirus receptor molecule, acetylcholine receptor (AChR), found in other hosts. This EST analysis sheds new light on immune response pathways in hemipteran guts that will be useful for further dissecting innate defence response pathways to rhabdovirus infection.
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Affiliation(s)
- A E Whitfield
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
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Kim BS, Jung JS, Jang JH, Kang KS, Kang SK. Nuclear Argonaute 2 regulates adipose tissue-derived stem cell survival through direct control of miR10b and selenoprotein N1 expression. Aging Cell 2011; 10:277-91. [PMID: 21241449 DOI: 10.1111/j.1474-9726.2011.00670.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Argonaute 2 (Ago2) has a leading function in miRNA-induced RNA silencing, a conserved gene regulatory mechanism in cells and organisms. miRNAs are critical for stem cell self-renewal, development, and other functions. Here, we report that nuclear Ago2, by binding to a specific region of functional genes, directly controls adipose tissue-derived stem cell (ATSC) survival in response to a critical dose of reactive oxygen species (ROS)-mediated oxidative cell damage or senescence. The role of nuclear Ago2 has not been previously reported. Here, we show that human ATSCs in which Ago2 was downregulated underwent apoptosis. Silencing of Ago2 in ATSCs significantly induces upregulation of miR10b and miR23b expression. These miRNAs directly interfere with ROS-scavenging gene expression, such as TXNL1 and GPX3. Upregulation of miR10b and miR23b is sufficient to induce ATSC cell apoptosis via p38 MAPK phosphorylation and caspase 3 activation. In addition, Ago2 overexpression or interference by miR10b and miR23b expression in ATSCs partially rescued H(2) O(2) /ROS-mediated apoptotic cell death by upregulating the expression of TXNL2, JUNK, caspase-3, and cytochrome C. Nuclear Ago2-mediated miR10b and miR23b downregulation also allows cells to escape senescence, which results in telomerase reverse transcriptase, stemness overexpression, and improved self-renewal and differentiation through Wnt5a/β-catenin activation. Argonaute 2 expression is critical for stem cells to escape senescence by downregulating miR10b and miR23b. The Ago2-binding gene selenoprotein N1 (SEPN1) was also effectively involved in ATSC survival and self-renewal through ROS-mediated p38 MAPK inactivation.
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Affiliation(s)
- Bong Sun Kim
- Department of Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, Korea
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