1
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Chen M, Xia Y, Wang Q. Identification and molecular characterization of a novel totivirus from Mangifera indica. Arch Virol 2024; 169:58. [PMID: 38424260 DOI: 10.1007/s00705-024-06001-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/20/2024] [Indexed: 03/02/2024]
Abstract
In this study, we determined the complete genome sequence of a novel totivirus, tentatively named "Mangifera indica totivirus 1" (MiTV1), identified in 'Apple' mango in China. The double-stranded RNA genome of MiTV1 is 4800 base pairs (bp) in length and contains two open reading frames (ORFs) encoding a putative coat protein (CP) and an RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis based on RdRp and CP amino acid sequences showed that MiTV1 is closely related to members of the genus Totivirus in the family Totiviridae. To our knowledge, this is the first report of a totivirus found in Mangifera indica.
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Affiliation(s)
- Mengyi Chen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510316, China
| | - Yujia Xia
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products/ Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs of China, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, 524000, China
- South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Qihua Wang
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products/ Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs of China, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, 524000, China.
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2
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Chen B, Chen Y, Chen H, Liang Z, Chen J, Wu R, Zhang T, Zhou G, Yang X. Identification, characterization and prevalence in southern China of a new iflavirus in the leafhopper Recilia dorsalis (Hemiptera: Cicadellidae). Virus Res 2023; 323:199005. [PMID: 36410611 PMCID: PMC10194291 DOI: 10.1016/j.virusres.2022.199005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022]
Abstract
The leafhopper Recilia dorsalis (Hemiptera: Cicadellidae) is not only a significant pest in agriculture but also an important vector involved in transmitting numerous pathogens that are known to cause economic losses by affecting rice crops. Here, a new iflavirus was discovered in the leafhopper R. dorsalis by employing a transcriptomic approach. The complete viral genome was determined to be 10,711 nucleotides (nt) in length and contains a single open reading frame (ORF) encoding a putative polyprotein comprised of 3,161 amino acids (aa), which is flanked by 5' and 3' untranslated regions. The full viral genome nt and the deduced polyprotein aa sequence showed the highest similarity (71.6% and 77.8%, respectively) with Langfang leafhopper iflavirus. Phylogenetic analysis based on the RdRp domain indicated that the isolated virus, which we have tentatively named Recilia dorsalis iflavirus 2 (RdIV2), is clustered with the members of the family Iflaviridae. Moreover, the results of our surveys indicate that RdIV2 predominates in southwestern Guangdong and southeastern Guangxi, China, and was absent in the other three species of leafhoppers; Nephotettix cincticeps, N. virescens and N. nigropictus. Notably, R. dorsalis was found to be co-infected with RdIV2 and rice stripe mosaic virus (RSMV; a well-known rice-infecting virus vectored by R. dorsalis) in rice fields, although the co-infection rate is low.
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Affiliation(s)
- Biao Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yulu Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Huazhou Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Zhenyi Liang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Jiahao Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Ruifeng Wu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Tong Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China.
| | - Xin Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China.
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Adamopoulos PG, Tsiakanikas P, Stolidi I, Scorilas A. A versatile 5′ RACE-Seq methodology for the accurate identification of the 5′ termini of mRNAs. BMC Genomics 2022; 23:163. [PMID: 35219290 PMCID: PMC8881849 DOI: 10.1186/s12864-022-08386-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 02/14/2022] [Indexed: 12/12/2022] Open
Abstract
Background Technological advancements in the era of massive parallel sequencing have enabled the functional dissection of the human transcriptome. However, 5′ ends of mRNAs are significantly underrepresented in these datasets, hindering the efficient analysis of the complex human transcriptome. The implementation of the template-switching mechanism at the reverse transcription stage along with 5′ rapid amplification of cDNA ends (RACE) constitutes the most prominent and efficient strategy to specify the actual 5′ ends of cDNAs. In the current study, we developed a 5′ RACE-seq method by coupling a custom template-switching and 5′ RACE assay with targeted nanopore sequencing, to accurately unveil 5′ termini of mRNA targets. Results The optimization of the described 5′ RACE-seq method was accomplished using the human BCL2L12 as control gene. We unveiled that the selection of hybrid DNA/RNA template-switching oligonucleotides as well as the complete separation of the cDNA extension incubation from the template-switching process, significantly increase the overall efficiency of the downstream 5′ RACE. Collectively, our results support the existence of two distinct 5′ termini for BCL2L12, being in complete accordance with the results derived from both direct RNA and PCR-cDNA sequencing approaches from Oxford Nanopore Technologies. As proof of concept, we implemented the described 5′ RACE-seq methodology to investigate the 5′ UTRs of several kallikrein-related peptidases (KLKs) gene family members. Our results confirmed the existence of multiple annotated 5′ UTRs of the human KLK gene family members, but also identified novel, previously uncharacterized ones. Conclusions In this work we present an in-house developed 5′ RACE-seq method, based on the template-switching mechanism and targeted nanopore sequencing. This approach enables the broad and in-depth study of 5′ UTRs of any mRNA of interest, by offering a tremendous sequencing depth, while significantly reducing the cost-per reaction compared to commercially available kits. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08386-y.
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Stone JK, Vukadin L, Ahn EYE. eNEMAL, an enhancer RNA transcribed from a distal MALAT1 enhancer, promotes NEAT1 long isoform expression. PLoS One 2021; 16:e0251515. [PMID: 34019552 PMCID: PMC8139514 DOI: 10.1371/journal.pone.0251515] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 04/28/2021] [Indexed: 01/22/2023] Open
Abstract
Emerging evidence has shown that active enhancers are abundantly transcribed, generating long non-coding RNAs, called enhancer RNAs (eRNAs). While putative eRNAs are often observed from RNA sequencing, the roles of most eRNAs remain largely unknown. Previously, we identified putative enhancer regions at the MALAT1 locus that form chromatin-chromatin interactions under hypoxia, and one of these enhancers is located about 30 kb downstream of the NEAT1 gene and -20 kb upstream of the MALAT1 gene (MALAT1–20 kb enhancer). Here, we report that a novel eRNA, named eRNA of the NEAT1-MALAT1-Locus (eNEMAL), is transcribed from the MALAT1–20 kb enhancer and conserved in primates. We found that eNEMAL is upregulated in response to hypoxia in multiple breast cancer cell lines, but not in non-tumorigenic MCF10A cells. Overexpression and knockdown of eNEMAL revealed that alteration of eNEMAL level does not affect MALAT1 expression. Instead, we found that eNEMAL upregulates the long isoform of NEAT1 (NEAT1_2) without increasing the total NEAT1 transcript level in MCF7 breast cancer cells, suggesting that eNEMAL has a repressive effect on the 3’-end polyadenylation process required for generating the short isoform of NEAT1 (NEAT1_1). Altogether, we demonstrated that an eRNA transcribed from a MALAT1 enhancer regulates NEAT1 isoform expression, implicating the MALAT1–20 kb enhancer and its transcript eNEMAL in co-regulation of MALAT1 and NEAT1 in response to hypoxia in breast cancer cells.
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Affiliation(s)
- Joshua K. Stone
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, United States of America
| | - Lana Vukadin
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Eun-Young Erin Ahn
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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5
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Arif M, Atta S, Bashir MA, Hussain A, Khan MI, Farooq S, Hannan A, Islam SU, Umar UUD, Khan M, Lin W, Hashem M, Alamri S, Wu Z. Molecular characterization and RSV Co-infection of Nicotiana benthamiana with three distinct begomoviruses. Methods 2020; 183:43-49. [PMID: 31759050 DOI: 10.1016/j.ymeth.2019.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/10/2019] [Accepted: 11/16/2019] [Indexed: 12/31/2022] Open
Abstract
Geminiviruses constitute a family of plant viruses with characteristic twinned quasi-icosahedral virions and a small circular DNA genome. Geminiviruses, especially begomoviruses, cause substantial economic losses in tropical and subtropical regions globally. Geminiviruses use the host's transcriptional mechanisms to synthesize their mRNAs. They are considered as an attractive model to understand the transcription mechanism of their host plants. Experiments were conducted to identify transcriptional start sites (TSSs) of the three begomoviruses, i.e., Cotton leaf curl Multan virus (CLCuMuV), Corchorus yellow vein virus (CoYVV), and Ramie mosaic virus (RamV). We first rub-inoculated Rice stripe tenuivirus (RSV), a segmented negative-sense RNA virus that uses cap-snatching to produce capped viral mRNAs, into N. benthamiana. After the inoculation, RSV-infected N. benthamiana were super-infected by CoYVV, CLCuMuV, or RamV, respectively. The capped-RNA leaders snatched by RSV were obtained by determining the 5'-ends of RSV mRNA with high throughput sequencing. Afterwards, snatched capped-RNA leaders of RSV were mapped onto the genome of each begomovirus and those matching the begomoviral genome were considered to come from the 5' ends of assumed begomoviral mRNAs. In this way, TSSs of begomoviruses were obtained. After mapping these TSSs onto the genome of the respective begomovirus, it was found very commonly that a begomovirus can use many different TSSs to transcribe the same gene, producing many different mRNA isoforms containing the corresponding open reading frames (ORFs).
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Affiliation(s)
- Muhammad Arif
- Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan; Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
| | - Sagheer Atta
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Muhammad Amjad Bashir
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Ansar Hussain
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Muhammad Ifnan Khan
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Shahid Farooq
- Department of Plant Protection, Faculty of Agriculture, Harran University, Sanliurfa 63200, Turkey
| | - Abdul Hannan
- Department of Botany, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Saif Ul Islam
- Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ummad Ud Din Umar
- Department of Plant Pathology, Bahauddin Zakariya University, Multan, Punjab 60800, Pakistan
| | - Mehran Khan
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Wenzhong Lin
- Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Mohamed Hashem
- King Khalid University, College of Science, Department of Biology, Abha 61413, Saudi Arabia; Assiut University, Faculty of Science, Botany and Microbiology Department, Assiut, Egypt
| | - Saad Alamri
- King Khalid University, College of Science, Department of Biology, Abha 61413, Saudi Arabia; Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 61413, Saudi Arabia
| | - Zujian Wu
- Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
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Shiba K, Hatta C, Sasai S, Tojo M, Ohki ST, Mochizuki T. A novel toti-like virus from a plant pathogenic oomycete Globisporangium splendens. Virology 2019; 537:165-171. [DOI: 10.1016/j.virol.2019.08.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/26/2019] [Accepted: 08/26/2019] [Indexed: 02/02/2023]
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7
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Shin H, Lee J, Kim Y, Jang S, Kim M, Lee Y. Heterogeneous Sequences of Brain Cytoplasmic 200 RNA Formed by Multiple Adenine Nucleotide Insertions. Mol Cells 2019; 42:495-500. [PMID: 31250622 PMCID: PMC6602144 DOI: 10.14348/molcells.2019.0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/06/2019] [Indexed: 11/27/2022] Open
Abstract
Brain cytoplasmic 200 RNA (BC200 RNA), originally identified as a neuron-specific non-coding RNA, is also observed in various cancer cells that originate from non-neural cells. Studies have revealed diverse functions of BC200 RNA in cancer cells. Accordingly, we hypothesized that BC200 RNA might be modified in cancer cells to generate cancerous BC200 RNA responsible for its cancer-specific functions. Here, we report that BC200 RNA sequences are highly heterogeneous in cancer cells by virtue of multiple adenine nucleotide insertions in the internal A-rich region. The insertion of adenine nucleotides enhances BC200 RNAmediated translation inhibition, possibly by increasing the binding affinity of BC200 RNA for eIF4A (eukaryotic translation initiation factor 4A).
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Affiliation(s)
- Heegwon Shin
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Jungmin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Youngmi Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Seonghui Jang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Meehyein Kim
- Virus Research and Testing Group, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114,
Korea
| | - Younghoon Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
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Gaafar YZA, Richert-Pöggeler KR, Maaß C, Vetten HJ, Ziebell H. Characterisation of a novel nucleorhabdovirus infecting alfalfa (Medicago sativa). Virol J 2019; 16:55. [PMID: 31036009 PMCID: PMC6489223 DOI: 10.1186/s12985-019-1147-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/19/2019] [Indexed: 12/22/2022] Open
Abstract
Background Nucleorhabdoviruses possess bacilliform particles which contain a single-stranded negative-sense RNA genome. They replicate and mature in the nucleus of infected cells. Together with viruses of three other genera of the family Rhabdoviridae, they are known to infect plants and can be transmitted by arthropod vectors, during vegetative propagation, or by mechanical means. In 2010, an alfalfa (Medicago sativa) plant showing virus-like symptoms was collected from Stadl-Paura, Austria and sent to Julius Kühn Institute for analysis. Methods Electron microscopy (EM) of leaf extracts from infected plants revealed the presence of rhabdovirus-like particles and was further used for ultrastructural analyses of infected plant tissue. Partially-purified preparations of rhabdovirus nucleocapsids were used for raising an antiserum. To determine the virus genome sequence, high throughput sequencing (HTS) was performed. RT-PCR primers were designed to confirm virus infection and to be used as a diagnostic tool. Results EM revealed bacilliform virions resembling those of plant-infecting rhabdoviruses. HTS of ribosomal RNA-depleted total RNA extracts revealed a consensus sequence consisting of 13,875 nucleotides (nt) and containing seven open reading frames (ORFs). Homology and phylogenetic analyses suggest that this virus isolate represents a new species of the genus Nucleorhabdovirus (family Rhabdoviridae). Since the virus originated from an alfalfa plant in Austria, the name alfalfa-associated nucleorhabdovirus (AaNV) is proposed. Viroplasms (Vp) and budding virions were observed in the nuclei of infected cells by EM, thus confirming its taxonomic assignment based on sequence data. Conclusions In this study, we identified and characterised a new nucleorhabdovirus from alfalfa. It shared only 39.8% nucleotide sequence identity with its closest known relative, black currant-associated rhabdovirus 1. The virus contains an additional open reading frame (accessory gene) with unknown function, located between the matrix protein and the glycoprotein genes. Serological and molecular diagnostic assays were designed for future screening of field samples. Further studies are needed to identify other natural hosts and potential vectors. Electronic supplementary material The online version of this article (10.1186/s12985-019-1147-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yahya Z A Gaafar
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Katja R Richert-Pöggeler
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Christina Maaß
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | | | - Heiko Ziebell
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany.
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Liu X, Chen M, Zhou X, Cao Z. Identification of novel miRNAs and their target genes from Populus szechuanica infected with Melampsora larici-populina. Mol Biol Rep 2019; 46:3083-3092. [PMID: 30859446 DOI: 10.1007/s11033-019-04746-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/05/2019] [Indexed: 01/21/2023]
Abstract
Two novel miRNAs were selected from a pre-constructed RNA library of Populus szechuanica infected with the foliar rust fungus Melampsora larici-populina in order to detect the genes regulated as targets of the miRNAs novel_mir_11 and novel_mir_357. The novel miRNAs were identified from P. szechuanica using stem-loop methods and their precursors were able to fold into a complete stem loop structure. The predicted target genes of the novel miRNAs were verified with RNA ligase-mediated 5' rapid amplification of cDNA ends (RLM-5'RACE). The full-length sequences of target genes, RPM1 and RPS2/5, in P. szechuanica were obtained through rapid amplification of cDNA ends (RACE) and officially named PsRPM1 and PsRPS2/5. These genes contain nucleotide binding site-leucine-rich repeats (NBS-LRR) domains typical of resistance genes. The expression levels of miRNAs and their target genes in different periods post infection were analysed with quantitative real-time PCR (qRT-PCR). After infection with the foliar rust fungus, the expression levels of the novel miRNAs and their target genes were dynamic. Both novel_mir_11 and novel_mir_357 negatively regulated the expression of their target genes. In this study, the regulatory effects of two novel miRNAs through their target genes were characterized to provide further mechanistic information regarding the interaction between Populus and a foliar rust fungus. Results of this study improve our understanding of the defence response mechanisms of Populus and will stimulate future work to characterize strategies to prevent and control Populus diseases.
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Affiliation(s)
- Xin Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Min Chen
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xue Zhou
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhimin Cao
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Pollpeter D, Sobala A, Malim MH. Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells. J Vis Exp 2019:10.3791/58715. [PMID: 30774124 PMCID: PMC6682491 DOI: 10.3791/58715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Monitoring of nucleic acid intermediates during virus replication provides insights into the effects and mechanisms of action of antiviral compounds and host cell proteins on viral DNA synthesis. Here we address the lack of a cell-based, high-coverage, and high-resolution assay that is capable of defining retroviral reverse transcription intermediates within the physiological context of virus infection. The described method captures the 3'-termini of nascent complementary DNA (cDNA) molecules within HIV-1 infected cells at single nucleotide resolution. The protocol involves harvesting of whole cell DNA, targeted enrichment of viral DNA via hybrid capture, adaptor ligation, size fractionation by gel purification, PCR amplification, deep sequencing, and data analysis. A key step is the efficient and unbiased ligation of adaptor molecules to open 3'-DNA termini. Application of the described method determines the abundance of reverse transcripts of each particular length in a given sample. It also provides information about the (internal) sequence variation in reverse transcripts and thereby any potential mutations. In general, the assay is suitable for any questions relating to DNA 3'-extension, provided that the template sequence is known.
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Affiliation(s)
- Darja Pollpeter
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London;
| | - Andrew Sobala
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London
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11
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Tal S, Ben Izhak M, Wachtel C, Wiseman A, Braun T, Yechezkel E, Golan E, Hadas R, Turjeman A, Banet-Noach C, Bronstein M, Lublin A, Berman E, Raviv Z, Pirak M, Klement E, Louzoun Y. Evaluating methods for Avian avulavirus-1 whole genome sequencing. Gene 2019; 721S:100004. [PMID: 32550541 PMCID: PMC7285907 DOI: 10.1016/j.gene.2019.100004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/03/2019] [Indexed: 11/18/2022]
Abstract
Background Avian avulavirus-1 (AAvV-1, previously Newcastle Disease Virus) is responsible for poultry and wild birds' disease outbreaks. Numerous whole genome sequencing methods were reported for this virus. These methods included cloning, specific primers amplification, shotgun PCR approaches, Sequence Independent Single Primer Amplification and next generation sequencing platform kits. Methods Three methods were used to sequence 173 Israeli Avian avulavirus-1 field isolates and one vaccine strain (VH). The sequencing was performed on Proton and Ion Torrent Personal Genome Machine and to a lesser extent, Illumina MiSeq and NextSeq sequencers. Target specific primers (SP) and Sequence Independent Single Primer Amplification (SISPA) products sequenced via the Ion torrent sequencer had a high error rate and truncated genomes. All the next generation sequencing platform sequencing kits generated high sequence accuracy and near-complete genomic size. Results A high level of mutations was observed in the intergenic regions between the avian avulavirus-1 genes. Within genes, multiple regions are more mutated than the Fusion region currently used for typing. Conclusions Our findings suggest that the whole genome sequencing by the Ion torrent sequencing kit is sufficient. However, when higher fidelity is desired, the Illumina NextSeq and Proton torrent sequencing kits were found to be preferable.
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Affiliation(s)
- Saar Tal
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Meirav Ben Izhak
- Life Science faculty and Gonda Brain Research Center, Bar Ilan University, Israel
| | | | - Anat Wiseman
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel
| | - Tzipi Braun
- Life Science faculty and Gonda Brain Research Center, Bar Ilan University, Israel
| | - Elinor Yechezkel
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Einav Golan
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Ruth Hadas
- Kimron Veterinary Institute, Division of Avian Diseases, Israel
| | - Adi Turjeman
- The Center for Genomic Technologies, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | | | - Michal Bronstein
- The Center for Genomic Technologies, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Avishai Lublin
- Kimron Veterinary Institute, Division of Avian Diseases, Israel
| | - Elyakum Berman
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Ziv Raviv
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel
| | - Michael Pirak
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Eyal Klement
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel
| | - Yoram Louzoun
- Department of Mathematics and Gonda Brain Research Center, Bar Ilan University, Israel
- Corresponding author at: Math Department and Gonda Brain Research Center, Bar Ilan University, Ramat Gan 52900, Israel.
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Peyambari M, Warner S, Stoler N, Rainer D, Roossinck MJ. A 1,000-Year-Old RNA Virus. J Virol 2019; 93:e01188-18. [PMID: 30305356 PMCID: PMC6288340 DOI: 10.1128/jvi.01188-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/26/2018] [Indexed: 11/20/2022] Open
Abstract
Only a few RNA viruses have been discovered from archaeological samples, the oldest dating from about 750 years ago. Using ancient maize cobs from Antelope house, Arizona, dating from ca. 1,000 CE, we discovered a novel plant virus with a double-stranded RNA genome. The virus is a member of the family Chrysoviridae that infect plants and fungi in a persistent manner. The extracted double-stranded RNA from 312 maize cobs was converted to cDNA, and sequences were determined using an Illumina HiSeq 2000. Assembled contigs from many samples showed similarity to Anthurium mosaic-associated virus and Persea americana chrysovirus, putative species in the Chrysovirus genus, and nearly complete genomes were found in three ancient maize samples. We named this new virus Zea mays chrysovirus 1. Using specific primers, we were able to recover sequences of a closely related virus from modern maize and obtained the nearly complete sequences of the three genomic RNAs. Comparing the nucleotide sequences of the three genomic RNAs of the modern and ancient viruses showed 98, 96.7, and 97.4% identities, respectively. Hence, in 1,000 years of maize cultivation, this virus has undergone about 3% divergence.IMPORTANCE A virus related to plant chrysoviruses was found in numerous ancient samples of maize, with nearly complete genomes in three samples. The age of the ancient samples (i.e., about 1,000 years old) was confirmed by carbon dating. Chrysoviruses are persistent plant viruses. They infect their hosts from generation to generation by transmission through seeds and can remain in their hosts for very long time periods. When modern corn samples were analyzed, a closely related chrysovirus was found with only about 3% divergence from the ancient sequences. This virus represents the oldest known plant virus.
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Affiliation(s)
- Mahtab Peyambari
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sylvia Warner
- The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Nicholas Stoler
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Drew Rainer
- The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Marilyn J Roossinck
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, Pennsylvania, USA
- The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
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13
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Liu F, Zheng K, Chen HC, Liu ZF. Capping-RACE: a simple, accurate, and sensitive 5' RACE method for use in prokaryotes. Nucleic Acids Res 2018; 46:e129. [PMID: 30107543 PMCID: PMC6265449 DOI: 10.1093/nar/gky739] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/30/2018] [Accepted: 08/03/2018] [Indexed: 12/13/2022] Open
Abstract
Rapid amplification of cDNA ends (RACE) is a prevalent technique used to obtain the 5' ends of transcripts. Several different 5' RACE methods have been developed, and one particularly simple and efficient approach called CapFinder relies on the 5' cap-dependent template-switching that occurs in eukaryotes. However, most prokaryotic transcripts lack a 5' cap structure. Here, we report a procedure to capture primary transcripts based on capping the 5' triphosphorylated RNA in prokaryotes. Primary transcripts were first treated with vaccinia capping enzyme to add a 5' cap structure. First-strand cDNA was then synthesized using Moloney murine leukaemia virus reverse transcriptase. Finally, a template-switching oligonucleotide with a tail containing three ribonucleic acid guanines was hybridized to the cDNA 3' poly(C) and further used as template for reverse transcriptase. It is oligonucleotide sequence independent and is more sensitive compared to RLM-RACE. This approach specifically identified the transcription start sites of ompA, sodB and shiA in Escherichia coli and of ompA, rne and rppH in Brucella melitensis. Furthermore, we also successfully identified the transcription start sites of small noncoding genes ryhB and micC in E. coli and bsnc135 and bsnc149 in B. melitensis. Our findings suggest that Capping-RACE is a simple, accurate, and sensitive 5' RACE method for use in prokaryotes.
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Affiliation(s)
- Fang Liu
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Ke Zheng
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Huan-Chun Chen
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Zheng-Fei Liu
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
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14
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Analysis of RNA 5' ends: Phosphate enumeration and cap characterization. Methods 2018; 155:3-9. [PMID: 30419334 DOI: 10.1016/j.ymeth.2018.10.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/24/2018] [Accepted: 10/30/2018] [Indexed: 12/21/2022] Open
Abstract
The function and fate of cellular RNAs are often governed by the phosphorylation state at the 5' end or the identity of whatever cap may be present there. Here we describe methods for examining these important 5'-terminal features on any cellular or synthetic RNA of interest that can be detected by Northern blotting. One such method, PABLO, is a splinted ligation assay that makes it possible to accurately quantify the percentage of 5' ends that are monophosphorylated. Another, PACO, is a capping assay that reveals the percentage of 5' ends that are diphosphorylated. A third, boronate gel electrophoresis in conjunction with deoxyribozyme-mediated cleavage, enables different types of caps (e.g., m7Gppp caps versus NAD caps) to be distinguished from one another and the percentage of each to be determined. After completing all three tests, the percentage of 5' ends that are triphosphorylated can be deduced by process of elimination. Together, this battery of assays allows the 5' terminus of an RNA to be profiled in unprecedented detail.
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15
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Abstract
Knowing the exact 5'-end of a specific RNA molecule has long been of great interest, since this information can reveal transcription start sites, which subsequently pinpoints promoter regions and potential binding sites for transcriptional regulators. Mapping of the 5'-end can also identify endoribonucleolytic cleavage sites, for the maturation of ribosomal RNA or events which initiate degradation of all or parts of the RNA molecule. If the 5' nucleotide of an RNA is triphosphorylated, then the nucleotide represents the original, unaltered 5'-end of the RNA. Similarly, if an endoribonuclease cleaves the RNA with a mechanism that leaves a monophosphate on the 5'-end downstream cleavage product, then it is useful to search exclusively for monophosphorylated 5'-ends to identify the cleavage sites of the endoribonuclease. This chapter details three variations of the EMOTE (exact mapping of transcriptome ends) protocol, which can identify RNA 5'-ends on a transcriptome-wide scale, and simultaneously provide information about the phosphorylation state of the detected ends. EMOTE, TSS-EMOTE (transcription start specific EMOTE), and nEMOTE (nonphosphorylated EMOTE) reveals mono-, tri-, and nonphosphorylated 5'-ends, respectively, and the protocols can be performed individually or in parallel on the same RNA sample.
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Affiliation(s)
- Peter Redder
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Integrative, University of Toulouse, Toulouse, France.
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16
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Shiba K, Hatta C, Sasai S, Tojo M, T. Ohki S, Mochizuki T. Genome sequence of a novel partitivirus identified from the oomycete Pythium nunn. Arch Virol 2018; 163:2561-2563. [DOI: 10.1007/s00705-018-3880-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/08/2018] [Indexed: 11/30/2022]
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17
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Lin W, Qiu P, Jin J, Liu S, Ul Islam S, Yang J, Zhang J, Kormelink R, Du Z, Wu Z. The Cap Snatching of Segmented Negative Sense RNA Viruses as a Tool to Map the Transcription Start Sites of Heterologous Co-infecting Viruses. Front Microbiol 2017; 8:2519. [PMID: 29312219 PMCID: PMC5735111 DOI: 10.3389/fmicb.2017.02519] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/04/2017] [Indexed: 01/06/2023] Open
Abstract
Identification of the transcription start sites (TSSs) of a virus is of great importance to understand and dissect the mechanism of viral genome transcription but this often requires costly and laborious experiments. Many segmented negative-sense RNA viruses (sNSVs) cleave capped leader sequences from a large variety of mRNAs and use these cleaved leaders as primers for transcription in a conserved process called cap snatching. The recent developments in high-throughput sequencing have made it possible to determine most, if not all, of the capped RNAs snatched by a sNSV. Here, we show that rice stripe tenuivirus (RSV), a plant-infecting sNSV, co-infects Nicotiana benthamiana with two different begomoviruses and snatches capped leader sequences from their mRNAs. By determining the 5' termini of a single RSV mRNA with high-throughput sequencing, the 5' ends of almost all the mRNAs of the co-infecting begomoviruses could be identified and mapped on their genomes. The findings in this study provide support for the using of the cap snatching of sNSVs as a tool to map viral TSSs.
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Affiliation(s)
- Wenzhong Lin
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ping Qiu
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Jin
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shunmin Liu
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Saif Ul Islam
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinguang Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jie Zhang
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Zhenguo Du
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
| | - Zujian Wu
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
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18
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Kaur H, Sparvoli D, Osakada H, Iwamoto M, Haraguchi T, Turkewitz AP. An endosomal syntaxin and the AP-3 complex are required for formation and maturation of candidate lysosome-related secretory organelles (mucocysts) in Tetrahymena thermophila. Mol Biol Cell 2017; 28:1551-1564. [PMID: 28381425 PMCID: PMC5449153 DOI: 10.1091/mbc.e17-01-0018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/22/2017] [Accepted: 03/28/2017] [Indexed: 12/14/2022] Open
Abstract
Lysosome-related organelles (LROs) are secretory organelles formed by convergence between secretory and endosomal trafficking pathways. In Tetrahymena, secretory vesicles that resemble dense core granules are a new class of LROs whose synthesis depends on a conserved syntaxin required for heterotypic fusion and AP-3 for maturation. The ciliate Tetrahymena thermophila synthesizes large secretory vesicles called mucocysts. Mucocyst biosynthesis shares features with dense core granules (DCGs) in animal cells, including proteolytic processing of cargo proteins during maturation. However, other molecular features have suggested relatedness to lysosome-related organelles (LROs). LROs, which include diverse organelles in animals, are formed via convergence of secretory and endocytic trafficking. Here we analyzed Tetrahymena syntaxin 7-like 1 (Stx7l1p), a Qa-SNARE whose homologues in other lineages are linked with vacuoles/LROs. Stx7l1p is targeted to both immature and mature mucocysts and is essential in mucocyst formation. In STX7L1-knockout cells, the two major classes of mucocyst cargo proteins localize independently, accumulating in largely nonoverlapping vesicles. Thus initial formation of immature mucocysts involves heterotypic fusion, in which a subset of mucocyst proteins is delivered via an endolysosomal compartment. Further, we show that subsequent maturation requires AP-3, a complex widely implicated in LRO formation. Knockout of the µ-subunit gene does not impede delivery of any known mucocyst cargo but nonetheless arrests mucocyst maturation. Our data argue that secretory organelles in ciliates may represent a new class of LROs and reveal key roles of an endosomal syntaxin and AP-3 in the assembly of this complex compartment.
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Affiliation(s)
- Harsimran Kaur
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Daniela Sparvoli
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Hiroko Osakada
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Masaaki Iwamoto
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Tokuko Haraguchi
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe 651-2492, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Aaron P Turkewitz
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
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19
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Yang X, Huang J, Liu C, Chen B, Zhang T, Zhou G. Rice Stripe Mosaic Virus, a Novel Cytorhabdovirus Infecting Rice via Leafhopper Transmission. Front Microbiol 2017; 7:2140. [PMID: 28101087 PMCID: PMC5210121 DOI: 10.3389/fmicb.2016.02140] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 12/19/2016] [Indexed: 01/08/2023] Open
Abstract
A new rice viral disease exhibiting distinct symptoms-yellow stripes, mosaic and twisted tips on leaves-was found in China. Electron microscopy of infected leaf cells revealed the presence of bacilliform virions and electron-translucent granular-fibrillar viroplasm in the cytoplasm. The enveloped viral particles were 300 to 375 nm long and 45 to 55 nm wide. The leafhopper Recilia dorsalis was able to transmit the virus to rice seedlings, which subsequently exhibited symptoms similar to those observed in fields. The complete genome of the virus was obtained by small-RNA deep sequencing and reverse transcription-PCR product sequencing. The anti-genome contains seven open reading frames (ORFs). The deduced amino acids of ORF1, ORF5, and ORF7 are, respectively, homologous to the nucleocapsid protein (N), glycoprotein (G), and large polymerase protein (L) of known rhabdoviruses. The predicted product of ORF2 is identified as a phosphoprotein (P) based on its multiple potential phosphorylation sites and 12.6 to 21.0% amino acid (aa) identities with the P proteins of plant rhabdoviruses. The product of ORF4 is presumed to be the viral matrix (M) protein for it shares 10.3 to 14.3% aa identities with those of other rhabdoviruses. The above five products were confirmed as the viral structural proteins by SDS-PAGE and aa sequencing analyses of purified virus preparation. ORF3 and ORF6 are considered to encode two nonstructural proteins with unknown functions. Phylogenetic analysis based on protein N, G, and L amino acid sequences indicated that the isolated virus, which we have tentatively named Rice stripe mosaic virus (RSMV), is a new species in the genus Cytorhabdovirus. To our knowledge, RSMV is the only cytorhabdovirus naturally infecting rice and the first reported leafhopper-transmitted cytorhabdovirus. Our surveys of rice fields indicate that RSMV occurs frequently in Guangdong Province, China. Although the disease incidence is low at present, it might become serious with the vector insect population increasing.
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Affiliation(s)
- Xin Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural UniversityGuangdong, China
| | - Jilei Huang
- Instrumental Analysis and Research Center, South China Agricultural UniversityGuangdong, China
| | - Chuanhe Liu
- Instrumental Analysis and Research Center, South China Agricultural UniversityGuangdong, China
| | - Biao Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural UniversityGuangdong, China
| | - Tong Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural UniversityGuangdong, China
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural UniversityGuangdong, China
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20
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Using a Novel Partitivirus in Pseudogymnoascus destructans to Understand the Epidemiology of White-Nose Syndrome. PLoS Pathog 2016; 12:e1006076. [PMID: 28027325 PMCID: PMC5189944 DOI: 10.1371/journal.ppat.1006076] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/18/2016] [Indexed: 11/22/2022] Open
Abstract
White-nose syndrome is one of the most lethal wildlife diseases, killing over 5 million North American bats since it was first reported in 2006. The causal agent of the disease is a psychrophilic filamentous fungus, Pseudogymnoascus destructans. The fungus is widely distributed in North America and Europe and has recently been found in some parts of Asia, but interestingly, no mass mortality is observed in European or Asian bats. Here we report a novel double-stranded RNA virus found in North American isolates of the fungus and show that the virus can be used as a tool to study the epidemiology of White-nose syndrome. The virus, termed Pseudogymnoascus destructans partitivirus-pa, contains 2 genomic segments, dsRNA 1 and dsRNA 2 of 1.76 kbp and 1.59 kbp respectively, each possessing a single open reading frame, and forms isometric particles approximately 30 nm in diameter, characteristic of the genus Gammapartitivirus in the family Partitiviridae. Phylogenetic analysis revealed that the virus is closely related to Penicillium stoloniferum virus S. We were able to cure P. destructans of the virus by treating fungal cultures with polyethylene glycol. Examination of 62 isolates of P. destructans including 35 from United States, 10 from Canada and 17 from Europe showed virus infection only in North American isolates of the fungus. Bayesian phylogenetic analysis using nucleotide sequences of the viral coat protein geographically clustered North American isolates indicating fungal spread followed by local adaptation of P. destructans in different regions of the United States and Canada. This is the first demonstration that a mycovirus potentially can be used to study fungal disease epidemiology. Many species of bats in North America have been severely impacted by a fungal disease, white-nose syndrome, that has killed over 5 million bats since it was first identified in 2006. The fungus is believed to have been introduced into a cave in New York where bats hibernate, and has now spread to 29 states and 4 Canadian provinces. The fungus is nearly identical from all sites where it has been isolated; however, we discovered that the fungus harbors a virus, and the virus varies enough to be able to use it to understand how the fungus has been spreading. This study used samples from infected bats throughout Pennsylvania and New York, and New Brunswick, Canada, as well a few isolates from other northeastern states. The evolution of the virus recapitulates the spread of the virus across these geographical areas, and should be useful for studying the further spread of the fungus.
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21
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Sulthana S, Basturea GN, Deutscher MP. Elucidation of pathways of ribosomal RNA degradation: an essential role for RNase E. RNA (NEW YORK, N.Y.) 2016; 22:1163-71. [PMID: 27298395 PMCID: PMC4931109 DOI: 10.1261/rna.056275.116] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/12/2016] [Indexed: 05/26/2023]
Abstract
Although normally stable in growing cells, ribosomal RNAs are degraded under conditions of stress, such as starvation, and in response to misassembled or otherwise defective ribosomes in a process termed RNA quality control. Previously, our laboratory found that large fragments of 16S and 23S rRNA accumulate in strains lacking the processive exoribonucleases RNase II, RNase R, and PNPase, implicating these enzymes in the later steps of rRNA breakdown. Here, we define the pathways of rRNA degradation in the quality control process and during starvation, and show that the essential endoribonuclease, RNase E, is required to make the initial cleavages in both degradative processes. We also present evidence that explains why the exoribonuclease, RNase PH, is required to initiate the degradation of rRNA during starvation. The data presented here provide the first detailed description of rRNA degradation in bacterial cells.
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Affiliation(s)
- Shaheen Sulthana
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Georgeta N Basturea
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Murray P Deutscher
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
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22
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Miller E. Rapid Amplification of cDNA Ends for RNA Transcript Sequencing in Staphylococcus. Methods Mol Biol 2016; 1373:169-83. [PMID: 26187203 DOI: 10.1007/7651_2015_282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rapid amplification of cDNA ends (RACE) is a technique that was developed to swiftly and efficiently amplify full-length RNA molecules in which the terminal ends have not been characterized. Current usage of this procedure has been more focused on sequencing and characterizing RNA 5' and 3' untranslated regions. Herein is described an adapted RACE protocol to amplify bacterial RNA transcripts.
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Affiliation(s)
- Eric Miller
- Department of Microbiology and Immunology, School of Medicine, University of Nevada Reno, 1664 N. Virginia Street, Reno, NV, 89557, USA.
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23
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Zhang W, Barger CJ, Link PA, Mhawech-Fauceglia P, Miller A, Akers SN, Odunsi K, Karpf AR. DNA hypomethylation-mediated activation of Cancer/Testis Antigen 45 (CT45) genes is associated with disease progression and reduced survival in epithelial ovarian cancer. Epigenetics 2016; 10:736-48. [PMID: 26098711 PMCID: PMC4622579 DOI: 10.1080/15592294.2015.1062206] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Epithelial ovarian cancer (EOC) is a highly lethal malignancy due to a lack of early detection approaches coupled with poor outcomes for patients with clinically advanced disease. Cancer-testis (CT) or cancer-germline genes encode antigens known to generate spontaneous anti-tumor immunity in cancer patients. CT45 genes are a recently discovered 6-member family of X-linked CT genes with oncogenic function. Here, we determined CT45 expression in EOC and fully defined its epigenetic regulation by DNA methylation. CT45 was silent and hypermethylated in normal control tissues, but a large subset of EOC samples showed increased CT45 expression in conjunction with promoter DNA hypomethylation. In contrast, copy number status did not correlate with CT45 expression in the TCGA database for EOC. CT45 promoter methylation inversely correlated with both CT45 mRNA and protein expression, the latter determined using IHC staining of an EOC TMA. CT45 expression was increased and CT45 promoter methylation was decreased in late-stage and high-grade EOC, and both measures were associated with poor survival. CT45 hypomethylation was directly associated with LINE-1 hypomethylation, and CT45 was frequently co-expressed with other CT antigen genes in EOC. Decitabine treatment induced CT45 mRNA and protein expression in EOC cells, and promoter transgene analyses indicated that DNA methylation directly represses CT45 promoter activity. These data verify CT45 expression and promoter hypomethylation as possible prognostic biomarkers, and suggest CT45 as an immunological or therapeutic target in EOC. Treatment with decitabine or other epigenetic modulators could provide a means for more effective immunological targeting of CT45.
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Key Words
- CNA, copy number alteration
- CT antigen genes, cancer-testis or cancer-germline antigen genes
- CT45
- DAC, decitabine, 5-Aza-2′-deoxycytidine
- DFS, disease-free survival
- DNA methylation
- DNMT, DNA methyltransferase
- EOC, epithelial ovarian cancer
- FTE, normal fallopian tube epithelia
- HGSOC, high-grade serous ovarian cancer
- IHC, immunohistochemistry
- NO, bulk normal ovary
- OS, overall survival
- OSE, normal ovary surface epithelia
- RLM-RACE, 5′ RNA ligase-mediated rapid amplification of cDNA ends
- RNA-seq, RNA sequencing
- TCGA, The Cancer Genome Atlas
- TMA, tissue microarray
- TSS, transcription start site
- cancer germline genes
- cancer testis antigen genes
- decitabine
- epithelial ovarian cancer
- tumor antigens
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Affiliation(s)
- Wa Zhang
- a Eppley Institute; University of Nebraska Medical Center ; Omaha , NE USA
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24
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An efficient full-length cDNA amplification strategy based on bioinformatics technology and multiplexed PCR methods. Sci Rep 2016; 5:19420. [PMID: 26758040 PMCID: PMC4725349 DOI: 10.1038/srep19420] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/14/2015] [Indexed: 12/01/2022] Open
Abstract
A novel strategy for amplification full-length cDNA and promoter sequences has been developed using bioinformatics technology and multiplexed PCR methods in this study. The amplification of 3′ ends of cDNA is performed according to the modified classic 3′ RACE techniques, therein the more efficient and effective oligo(dT)-anchor primer with hairpin structure is specially designed. For the amplification of 5′ ends of cDNA, two or three-round TAIL-PCR or touch-down PCR using arbitrary degenerate (AD) and sequence-specific reverse (SPR) primers is performed until the 5′ sequence of multi-assembled fragment reaches the exon1 region identified by aligning this fragment to reference genome database. Then another TAIL-PCR or touch-down PCR using genomic DNA as template is conducted to obtain the remaining 5′ and promoter sequences. The 5′ end sites of cDNA are predicted by aligning finally assembled fragment to homologous reference genes of other species, and screening the relative locations of common characteristic cis-elements in silico on promoter. The putative 5′ ends are further validated by primers corresponding to these predicted sites in cDNAs. This method is suitable for researchers to isolate limited full-length cDNA sequences due to its operability, inexpensiveness, efficiency and speediness.
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25
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A novel long non-coding RNA in the rheumatoid arthritis risk locus TRAF1-C5 influences C5 mRNA levels. Genes Immun 2015; 17:85-92. [PMID: 26673966 DOI: 10.1038/gene.2015.54] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/06/2015] [Accepted: 11/11/2015] [Indexed: 01/05/2023]
Abstract
Long non-coding RNAs (lncRNAs) can regulate the transcript levels of genes in the same genomic region. These locally acting lncRNAs have been found deregulated in human disease and some have been shown to harbour quantitative trait loci (eQTLs) in autoimmune diseases. However, lncRNAs linked to the transcription of candidate risk genes in loci associated to rheumatoid arthritis (RA) have not yet been identified. The TRAF1 and C5 risk locus shows evidence of multiple eQTLs and transcription of intergenic non-coding sequences. Here, we identified a non-coding transcript (C5T1lncRNA) starting in the 3' untranslated region (UTR) of C5. RA-relevant cell types express C5T1lncRNA and RNA levels are further enhanced by specific immune stimuli. C5T1lncRNA is expressed predominantly in the nucleus and its expression correlates positively with C5 mRNA in various tissues (P=0.001) and in peripheral blood mononuclear cells (P=0.02) indicating transcriptional co-regulation. Knockdown results in a concurrent decrease in C5 mRNA levels but not of other neighbouring genes. Overall, our data show the identification of a novel lncRNA C5T1lncRNA that is fully located in the associated region and influences transcript levels of C5, a gene previously linked to RA pathogenesis.
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Sarkar MK, Gayen S, Kumar S, Maclary E, Buttigieg E, Hinten M, Kumari A, Harris C, Sado T, Kalantry S. An Xist-activating antisense RNA required for X-chromosome inactivation. Nat Commun 2015; 6:8564. [PMID: 26477563 PMCID: PMC4616153 DOI: 10.1038/ncomms9564] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/07/2015] [Indexed: 01/06/2023] Open
Abstract
The transcriptional imbalance due to the difference in the number of X chromosomes between male and female mammals is remedied through X-chromosome inactivation, the epigenetic transcriptional silencing of one of the two X chromosomes in females. The X-linked Xist long non-coding RNA functions as an X inactivation master regulator; Xist is selectively upregulated from the prospective inactive X chromosome and is required in cis for X inactivation. Here we discover an Xist antisense long non-coding RNA, XistAR (XistActivating RNA), which is encoded within exon 1 of the mouse Xist gene and is transcribed only from the inactive X chromosome. Selective truncation of XistAR, while sparing the overlapping Xist RNA, leads to a deficiency in Xist RNA expression in cis during the initiation of X inactivation. Thus, the Xist gene carries within its coding sequence an antisense RNA that drives Xist expression. The X-chromosome linked long non-coding RNA, Xist, is a master regulator of the X inactivation. Here, the authors report that XistAR, an Xist anti-sense long non-coding RNA encoded within the mouse Xist gene and transcribed only from the inactive X chromosome, regulates Xist expression.
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Affiliation(s)
- Mrinal K Sarkar
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Srimonta Gayen
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Surinder Kumar
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Emily Maclary
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Emily Buttigieg
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Michael Hinten
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Archana Kumari
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Clair Harris
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Takashi Sado
- Department of Advanced Bioscience, Graduate School of Agriculture, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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Archaeal Nucleic Acid Ligases and Their Potential in Biotechnology. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:170571. [PMID: 26494982 PMCID: PMC4606414 DOI: 10.1155/2015/170571] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/18/2015] [Indexed: 12/23/2022]
Abstract
With their ability to catalyse the formation of phosphodiester linkages, DNA ligases and RNA ligases are essential tools for many protocols in molecular biology and biotechnology. Currently, the nucleic acid ligases from bacteriophage T4 are used extensively in these protocols. In this review, we argue that the nucleic acid ligases from Archaea represent a largely untapped pool of enzymes with diverse and potentially favourable properties for new and emerging biotechnological applications. We summarise the current state of knowledge on archaeal DNA and RNA ligases, which makes apparent the relative scarcity of information on in vitro activities that are of most relevance to biotechnologists (such as the ability to join blunt- or cohesive-ended, double-stranded DNA fragments). We highlight the existing biotechnological applications of archaeal DNA ligases and RNA ligases. Finally, we draw attention to recent experiments in which protein engineering was used to modify the activities of the DNA ligase from Pyrococcus furiosus and the RNA ligase from Methanothermobacter thermautotrophicus, thus demonstrating the potential for further work in this area.
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Wang F, Johnson X, Cavaiuolo M, Bohne AV, Nickelsen J, Vallon O. Two Chlamydomonas OPR proteins stabilize chloroplast mRNAs encoding small subunits of photosystem II and cytochrome b6 f. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:861-73. [PMID: 25898982 DOI: 10.1111/tpj.12858] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 03/17/2015] [Accepted: 04/09/2015] [Indexed: 05/08/2023]
Abstract
In plants and algae, chloroplast gene expression is controlled by nucleus-encoded proteins that bind to mRNAs in a specific manner, stabilizing mRNAs or promoting their splicing, editing, or translation. Here, we present the characterization of two mRNA stabilization factors of the green alga Chlamydomonas reinhardtii, which both belong to the OctotricoPeptide Repeat (OPR) family. MCG1 is necessary to stabilize the petG mRNA, encoding a small subunit of the cytochrome b6 f complex, while MBI1 stabilizes the psbI mRNA, coding for a small subunit of photosystem II. In the mcg1 mutant, the small RNA footprint corresponding to the 5'-end of the petG transcript is reduced in abundance. In both cases, the absence of the small subunit perturbs assembly of the cognate complex. Whereas PetG is essential for formation of a functional cytochrome b6 f dimer, PsbI appears partly dispensable as a low level of PSII activity can still be measured in its absence. Thus, nuclear control of chloroplast gene expression is not only exerted on the major core subunits of the complexes, but also on small subunits with a single transmembrane helix. While OPR proteins have thus far been involved in translation or trans-splicing of plastid mRNAs, our results expand the potential roles of this repeat family to their stabilization.
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Affiliation(s)
- Fei Wang
- UMR 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, Paris, 75005, France
- Biozentrum Ludwig-Maximilians-Universität München, D-82152, Planegg-Martinsried, Germany
| | - Xenie Johnson
- UMR 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, Paris, 75005, France
| | - Marina Cavaiuolo
- UMR 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, Paris, 75005, France
| | - Alexandra-Viola Bohne
- Biozentrum Ludwig-Maximilians-Universität München, D-82152, Planegg-Martinsried, Germany
| | - Joerg Nickelsen
- Biozentrum Ludwig-Maximilians-Universität München, D-82152, Planegg-Martinsried, Germany
| | - Olivier Vallon
- UMR 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, Paris, 75005, France
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Whole transcriptome analysis with sequencing: methods, challenges and potential solutions. Cell Mol Life Sci 2015; 72:3425-39. [PMID: 26018601 DOI: 10.1007/s00018-015-1934-y] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/25/2015] [Accepted: 05/21/2015] [Indexed: 10/23/2022]
Abstract
Whole transcriptome analysis plays an essential role in deciphering genome structure and function, identifying genetic networks underlying cellular, physiological, biochemical and biological systems and establishing molecular biomarkers that respond to diseases, pathogens and environmental challenges. Here, we review transcriptome analysis methods and technologies that have been used to conduct whole transcriptome shotgun sequencing or whole transcriptome tag/target sequencing analyses. We focus on how adaptors/linkers are added to both 5' and 3' ends of mRNA molecules for cloning or PCR amplification before sequencing. Challenges and potential solutions are also discussed. In brief, next generation sequencing platforms have accelerated releases of the large amounts of gene expression data. It is now time for the genome research community to assemble whole transcriptomes of all species and collect signature targets for each gene/transcript, and thus use known genes/transcripts to determine known transcriptomes directly in the near future.
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Liang W, Rudd KE, Deutscher MP. A role for REP sequences in regulating translation. Mol Cell 2015; 58:431-9. [PMID: 25891074 DOI: 10.1016/j.molcel.2015.03.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/21/2015] [Accepted: 03/12/2015] [Indexed: 01/07/2023]
Abstract
Repetitive extragenic palindromic (REP) sequences are highly structured elements found downstream of ∼500 genes in Escherichia coli that result in extensive stem-loop structures in their mRNAs. However, their physiological role has remained elusive. Here, we show that REP sequences can downregulate translation, but only if they are within 15 nt of a termination codon; a spacing of 16 nt has no effect, suggesting that the REP element acts to stall ribosome movement. Ribosome stalling leads to cleavage of the mRNA and induction of the trans-translation process. Using nrdAB as a model, we find that its regulation can be partially reversed by overexpression of RNA helicases and can be fully overcome upon UV stress, emphasizing the importance of this regulatory process. Since 50% of REP-associated genes have these elements within the critical 15 nt, these findings identify a regulatory mechanism with the potential to affect translation from a large number of genes.
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Affiliation(s)
- Wenxing Liang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA; The Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China
| | - Kenneth E Rudd
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA
| | - Murray P Deutscher
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA.
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Taylor-Douglas DC, Basu A, Gardner RM, Aspelund S, Wen X, Yanovski JA. Evaluation of hypothalamic murine and human melanocortin 3 receptor transcript structure. Biochem Biophys Res Commun 2014; 454:234-8. [PMID: 25450386 DOI: 10.1016/j.bbrc.2014.10.072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 10/15/2014] [Indexed: 11/16/2022]
Abstract
The melanocortin 3 receptor (MC3R) is involved in regulation of energy homeostasis. However, its transcript structure is not well understood. We therefore studied initiation and termination sites for hypothalamic murine Mc3r and human MC3R transcripts. Rapid Amplification of cDNA Ends (RACE) was performed for the 5' and 3' ends of murine and human hypothalamic RNA. 5' RACE experiments using hypothalamic murine RNA indicated mouse hypothalamus expresses two major Mc3r transcription start sites: one with a 5' UTR approximately 368 bases in length and another previously unknown transcript with a 5' UTR approximately 440 bases in length. 5' RACE experiments using human hypothalamic RNA identified a 5' UTR beginning 533 bases upstream of the start codon with a 248 base splice. 3' RACE experiments using hypothalamic murine RNA indicated the 3' UTR terminates approximately 1286 bases after the translational stop codon, with a previously unknown 787 base splice between consensus splice donor and acceptor sites. 3' RACE experiments using human MC3R transcript indicated the 3' UTR terminates approximately 115-160 bases after the translational stop codon. These data provide insight into melanocortin 3 receptor transcript structure.
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Affiliation(s)
- Dezmond C Taylor-Douglas
- Section on Growth and Obesity, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA; Howard University College of Medicine, Department of Physiology, 520 W Street N.W., Washington, DC 20059, USA
| | - Arunabha Basu
- Section on Growth and Obesity, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Ryan M Gardner
- Section on Growth and Obesity, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Sender Aspelund
- Section on Growth and Obesity, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Xin Wen
- Section on Growth and Obesity, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Jack A Yanovski
- Section on Growth and Obesity, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA.
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Okano Y, Senshu H, Hashimoto M, Neriya Y, Netsu O, Minato N, Yoshida T, Maejima K, Oshima K, Komatsu K, Yamaji Y, Namba S. In Planta Recognition of a Double-Stranded RNA Synthesis Protein Complex by a Potexviral RNA Silencing Suppressor. THE PLANT CELL 2014; 26:2168-2183. [PMID: 24879427 PMCID: PMC4079376 DOI: 10.1105/tpc.113.120535] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 04/23/2014] [Accepted: 05/09/2014] [Indexed: 05/22/2023]
Abstract
RNA silencing plays an important antiviral role in plants and invertebrates. To counteract antiviral RNA silencing, most plant viruses have evolved viral suppressors of RNA silencing (VSRs). TRIPLE GENE BLOCK PROTEIN1 (TGBp1) of potexviruses is a well-characterized VSR, but the detailed mechanism by which it suppresses RNA silencing remains unclear. We demonstrate that transgenic expression of TGBp1 of plantago asiatica mosaic virus (PlAMV) induced developmental abnormalities in Arabidopsis thaliana similar to those observed in mutants of SUPPRESSOR OF GENE SILENCING3 (SGS3) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6) required for the trans-acting small interfering RNA synthesis pathway. PlAMV-TGBp1 inhibits SGS3/RDR6-dependent double-stranded RNA synthesis in the trans-acting small interfering RNA pathway. TGBp1 interacts with SGS3 and RDR6 and coaggregates with SGS3/RDR6 bodies, which are normally dispersed in the cytoplasm. In addition, TGBp1 forms homooligomers, whose formation coincides with TGBp1 aggregation with SGS3/RDR6 bodies. These results reveal the detailed molecular function of TGBp1 as a VSR and shed new light on the SGS3/RDR6-dependent double-stranded RNA synthesis pathway as another general target of VSRs.
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Affiliation(s)
- Yukari Okano
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroko Senshu
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masayoshi Hashimoto
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yutaro Neriya
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Osamu Netsu
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Nami Minato
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tetsuya Yoshida
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kensaku Maejima
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kenro Oshima
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ken Komatsu
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuyuki Yamaji
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shigetou Namba
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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Akimoto C, Sakashita E, Kasashima K, Kuroiwa K, Tominaga K, Hamamoto T, Endo H. Translational repression of the McKusick-Kaufman syndrome transcript by unique upstream open reading frames encoding mitochondrial proteins with alternative polyadenylation sites. Biochim Biophys Acta Gen Subj 2013; 1830:2728-38. [PMID: 23671934 DOI: 10.1016/j.bbagen.2012.12.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Upstream open reading frames (uORFs) are commonly found in the 5'-untranslated region (UTR) of many genes and function in translational control. However, little is known about the existence of the proteins encoded by uORFs, and the role of the proteins except translational control. There was no report about uORFs of the McKusick-Kaufman syndrome (MKKS) gene that causes a genetic disorder. METHODS Northern blotting, 3'-RACE, and bioinformatics were used for determining the length of transcripts and their 3' ends. Luciferase assay and in vitro translation were used for evaluation of translational regulatory activity of uORFs. Immunoblotting and immunocytochemical analyses were used for detection of uORF-derived protein products and their subcellular localization. RESULTS The MKKS gene generates two types of transcripts: a canonical long transcript that encodes both uORFs and MKKS, and a short transcript that encodes only uORFs by using alternative polyadenylation sites at the 5'-UTR. The simultaneous disruption of the uORF initiation codons increased the translation of the downstream ORF. Furthermore, both protein products from the two longest uORFs were detected in the mitochondrial membrane fraction of HeLa cells. Database searches indicated that such uORFs with active alternative polyadenylation sites at the 5'-UTR are atypical but surely exist in human transcripts. CONCLUSIONS Multiple uORFs at the 5'-UTR of the MKKS long transcript function as translational repressor for MKKS. Two uORFs are translated in vivo and imported onto the mitochondrial membrane. GENERAL SIGNIFICANCE Our findings provide unique insights into production of uORF-derived peptides and functions of uORFs.
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Affiliation(s)
- Chizuru Akimoto
- Division of Neurology, Department of Internal Medicine, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
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İnce İA, Özcan K, Vlak JM, van Oers MM. Temporal classification and mapping of non-polyadenylated transcripts of an invertebrate iridovirus. J Gen Virol 2013; 94:187-192. [DOI: 10.1099/vir.0.046359-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The temporal expression of the 54 Chilo iridescent virus (CIV) virion protein genes was investigated by combining drug treatments that inhibit protein or DNA synthesis and an RT-PCR strategy particularly suitable for non-polyadenylated mRNAs. This method generates a uniform 3′ terminus by ligation of a 5′-phosphorylated oligonucleotide to the 3′ end of the transcript that is recognized by a complementary primer during RT-PCR. This analysis showed that CIV virion proteins are encoded by genes in all three predetermined temporal classes: 23 immediate-early, 11 delayed-early and seven late virion gene transcripts were identified and assigned to ORFs. Early transcription of many virion protein genes supports the notion that virion proteins may also play essential roles in the initial stages of infection. In addition, some of the early gene products present in the virion may reflect the intracellular path that the virus follows during infection.
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Affiliation(s)
- İkbal Agah İnce
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Department of Genetics and Bioengineering, Yeditepe University, 34755, Istanbul, Turkey
- Department of Biosystems Engineering, Faculty of Engineering, Giresun University, 28100, Giresun, Turkey
| | - Kadriye Özcan
- Department of Biosystems Engineering, Faculty of Engineering, Giresun University, 28100, Giresun, Turkey
| | - Just M. Vlak
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Monique M. van Oers
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Abstract
Gene transcripts are under extensive posttranscriptional regulation, including the regulation of their stability. A major route for mRNA degradation produces uncapped mRNAs, which can be generated by decapping enzymes, endonucleases, and small RNAs. Profiling uncapped mRNA molecules is important for the understanding of the transcriptome, whose composition is determined by a balance between mRNA synthesis and degradation. In this chapter, we describe a method to profile these uncapped mRNAs at the genome scale.
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Baeza M, Bravo N, Sanhueza M, Flores O, Villarreal P, Cifuentes V. Molecular characterization of totiviruses in Xanthophyllomyces dendrorhous. Virol J 2012; 9:140. [PMID: 22838956 PMCID: PMC3561658 DOI: 10.1186/1743-422x-9-140] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 07/17/2012] [Indexed: 12/12/2022] Open
Abstract
Background Occurrence of extrachromosomal dsRNA elements has been described in the red-yeast Xanthophyllomyces dendrorhous, with numbers and sizes that are highly variable among strains with different geographical origin. The studies concerning to the encapsidation in viral-like particles and dsRNA-curing have suggested that some dsRNAs are helper viruses, while others are satellite viruses. However, the nucleotide sequences and functions of these dsRNAs are still unknown. In this work, the nucleotide sequences of four dsRNAs of the strain UCD 67–385 of X. dendrorhous were determined, and their identities and genome structures are proposed. Based on this molecular data, the dsRNAs of different strains of X. dendrorhous were analyzed. Results The complete sequences of L1, L2, S1 and S2 dsRNAs of X. dendrorhous UCD 67–385 were determined, finding two sequences for L1 dsRNA (L1A and L1B). Several ORFs were uncovered in both S1 and S2 dsRNAs, but no homologies were found for any of them when compared to the database. Instead, two ORFs were identified in each L1A, L1B and L2 dsRNAs, whose deduced amino acid sequences were homologous with a major capsid protein (5’-ORF) and a RNA-dependent RNA polymerase (3’-ORF) belonging to the Totiviridae family. The genome structures of these dsRNAs are characteristic of Totiviruses, with two overlapped ORFs (the 3’-ORF in the −1 frame with respect to the 5’-ORF), with a slippery site and a pseudoknot in the overlapped regions. These structures are essential for the synthesis of the viral polymerase as a fusion protein with the viral capsid protein through −1 ribosomal frameshifting. In the RNase protection analysis, all the dsRNAs in the four analyzed X. dendrorhous strains were protected from enzymatic digestion. The RT-PCR analysis revealed that, similar to strain UCD 67–385, the L1A and L1B dsRNAs coexist in the strains VKM Y-2059, UCD 67–202 and VKM Y-2786. Furthermore, determinations of the relative amounts of L1 dsRNAs using two-step RT-qPCR revealed a 40-fold increment of the ratio L1A/L1B in the S2 dsRNA-cured strain compared to its parental strain. Conclusions Three totiviruses, named as XdV-L1A, XdV-L1B and XdV-L2, were identified in the strain UCD 67–385 of X. dendrorhous. The viruses XdV-L1A and XdV-L1B were also found in other three X. dendrorhous strains. Our results suggest that the smaller dsRNAs (named XdRm-S1 and XdRm-S2) of strain UCD 67–385 are satellite viruses, and particularly that XdRm-S2 is a satellite of XdV-L1A.
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Affiliation(s)
- Marcelo Baeza
- Departamento de Ciencias Ecológicas, Laboratorio de Genética, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile.
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Song X, Bowen J, Miao W, Liu Y, Gorovsky MA. The nonhistone, N-terminal tail of an essential, chimeric H2A variant regulates mitotic H3-S10 dephosphorylation. Genes Dev 2012; 26:615-29. [PMID: 22426537 PMCID: PMC3315122 DOI: 10.1101/gad.182683.111] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Accepted: 02/06/2012] [Indexed: 12/21/2022]
Abstract
H2A.Y is an essential, divergent Tetrahymena thermophila histone variant. It has a long nonhistone N terminus that contains leucine-rich repeats (LRR) and an LRR cap domain with similarity to Sds22p, a regulator of yeast protein phosphatase 1 (PP1) activity in the nucleus. In growing cells, H2A.Y is incorporated into micronuclei only during S phase, which occurs immediately after micronuclear mitosis. Depletion of H2A.Y causes prolonged retention of mitosis-associated histone H3-S10 phosphorylation and mitotic abnormalities that mimic S10E mutation. In cells where H2A.Y is depleted, an inducible chimeric gene, in which the H2A.Y N terminus is attached to H2A.X, is shown to regulate micronuclear H3-S10 phosphorylation. H2A.Y can also be specifically coimmunoprecipitated with a Tetrahymena PP1 ortholog (Ppo1p). Taken together, these results argue that the N terminus of H2A.Y functions to regulate H3-S10 dephosphorylation. This striking in vivo case of "cross-talk" between a H2A variant and a specific post-translational modification of another histone demonstrates a novel function for a histone variant.
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Affiliation(s)
- Xiaoyuan Song
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Josephine Bowen
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Wei Miao
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Yifan Liu
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Martin A. Gorovsky
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
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Xu H, Fu J, Ha SW, Ju D, Zheng J, Li L, Xie Y. The CCAAT box-binding transcription factor NF-Y regulates basal expression of human proteasome genes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:818-25. [PMID: 22285817 DOI: 10.1016/j.bbamcr.2012.01.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Revised: 01/08/2012] [Accepted: 01/09/2012] [Indexed: 01/04/2023]
Abstract
Protein degradation by the proteasome plays an important role in all major cellular pathways. Aberrant proteasome activity is associated with numerous human diseases including cancer and neurological disorders, but the underlying mechanism is virtually unclear. At least part of the reason for this is due to lack of understanding of the regulation of human proteasome genes. In this study, we found that a large set of human proteasome genes carry the CCAAT box in their promoters. We further demonstrated that the basal expression of these CCAAT box-containing proteasome genes is regulated by the transcription factor NF-Y. Knockdown of NF-YA, an essential subunit of NF-Y, reduced proteasome gene expression and compromised the cellular proteasome activity. In addition, we showed that knockdown of NF-YA sensitized breast cancer cells to the proteasome inhibitor MG132. This study unveils a new role for NF-Y in the regulation of human proteasome genes and suggests that NF-Y may be a potential target for cancer therapy.
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Affiliation(s)
- Haiming Xu
- Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
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Zhuang F, Fuchs RT, Sun Z, Zheng Y, Robb GB. Structural bias in T4 RNA ligase-mediated 3'-adapter ligation. Nucleic Acids Res 2012; 40:e54. [PMID: 22241775 PMCID: PMC3326334 DOI: 10.1093/nar/gkr1263] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
T4 RNA ligases are commonly used to attach adapters to RNAs, but large differences in ligation efficiency make detection and quantitation problematic. We developed a ligation selection strategy using random RNAs in combination with high-throughput sequencing to gain insight into the differences in efficiency of ligating pre-adenylated DNA adapters to RNA 3′-ends. After analyzing biases in RNA sequence, secondary structure and RNA-adapter cofold structure, we conclude that T4 RNA ligases do not show significant primary sequence preference in RNA substrates, but are biased against structural features within RNAs and adapters. Specifically, RNAs with less than three unstructured nucleotides at the 3′-end and RNAs that are predicted to cofold with an adapter in unfavorable structures are likely to be poorly ligated. The effect of RNA-adapter cofold structures on ligation is supported by experiments where the ligation efficiency of specific miRNAs was changed by designing adapters to alter cofold structure. In addition, we show that using adapters with randomized regions results in higher ligation efficiency and reduced ligation bias. We propose that using randomized adapters may improve RNA representation in experiments that include a 3′-adapter ligation step.
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Clowney EJ, Magklara A, Colquitt BM, Pathak N, Lane RP, Lomvardas S. High-throughput mapping of the promoters of the mouse olfactory receptor genes reveals a new type of mammalian promoter and provides insight into olfactory receptor gene regulation. Genome Res 2011; 21:1249-59. [PMID: 21705439 PMCID: PMC3149492 DOI: 10.1101/gr.120162.110] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 05/16/2011] [Indexed: 11/25/2022]
Abstract
The olfactory receptor (OR) genes are the largest mammalian gene family and are expressed in a monogenic and monoallelic fashion in olfactory neurons. Using a high-throughput approach, we mapped the transcription start sites of 1085 of the 1400 murine OR genes and performed computational analysis that revealed potential transcription factor binding sites shared by the majority of these promoters. Our analysis produced a hierarchical model for OR promoter recognition in which unusually high AT content, a unique epigenetic signature, and a stereotypically positioned O/E site distinguish OR promoters from the rest of the murine promoters. Our computations revealed an intriguing correlation between promoter AT content and evolutionary plasticity, as the most AT-rich promoters regulate rapidly evolving gene families. Within the AT-rich promoter category the position of the TATA-box does not correlate with the transcription start site. Instead, a spike in GC composition might define the exact location of the TSS, introducing the concept of "genomic contrast" in transcriptional regulation. Finally, our experiments show that genomic neighborhood rather than promoter sequence correlates with the probability of different OR genes to be expressed in the same olfactory cell.
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Affiliation(s)
- E. Josephine Clowney
- Program in Biomedical Sciences, University of California, San Francisco, San Francisco, California 94158, USA
| | - Angeliki Magklara
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94158, USA
| | - Bradley M. Colquitt
- Program in Neurosciences, University of California, San Francisco, San Francisco, California 94158, USA
| | - Nidhi Pathak
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06457, USA
| | - Robert P. Lane
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06457, USA
| | - Stavros Lomvardas
- Program in Biomedical Sciences, University of California, San Francisco, San Francisco, California 94158, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94158, USA
- Program in Neurosciences, University of California, San Francisco, San Francisco, California 94158, USA
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Tao L, DeRosa AM, White TW, Valdimarsson G. Zebrafish cx30.3: identification and characterization of a gap junction gene highly expressed in the skin. Dev Dyn 2011; 239:2627-36. [PMID: 20737512 DOI: 10.1002/dvdy.22399] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
We have identified and characterized a zebrafish connexin, Cx30.3. Sequence similarity analyses suggested that Cx30.3 was orthologous to both mammalian Cx26 and Cx30, known to play important roles in the skin and inner ear of mammals. Analysis of mRNA expression showed that Cx30.3 was present in early embryos, and was highly abundant in skin, but also detected in other tissues including fins, inner ear, heart, and the retina. Injection of Cx30.3 cRNA into Xenopus oocytes elicited robust intercellular coupling with voltage gating sensitivity similar to mammalian Cx26 and Cx30. The similarities in functional properties and expression patterns suggest that Cx30.3, like mammalian Cx26 and Cx30, may play a significant role in skin development, hearing, and balance in zebrafish. Thus, zebrafish could potentially serve as an excellent model to study disorders of the skin and deafness that result from human connexin mutations.
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Affiliation(s)
- Liang Tao
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
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42
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Guo Y, Ma L, Ji Y, Pu G, Liu B, Du Z, Li G, Ye H, Wang H. Isolation of the 5'-end of plant genes from genomic DNA by TATA-box-based degenerate primers. Mol Biotechnol 2011; 47:152-6. [PMID: 20730510 DOI: 10.1007/s12033-010-9323-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We report a rapid and simple method for isolating the 5'-end of plant genes from genomic DNA by polymerase chain reaction (PCR) with TATA-box-based degenerate primers (TDPs). The TDPs were specially designed according to the TATA box, which is conserved in the promoter region of most plant genes. The unknown 5'-ends of several genes in different plants were isolated by PCR with gene-specific primers of the known core fragment and the TDPs. Our method does not require the arduous RNA manipulations and expensive enzyme treatments of the popular rapid amplification of cDNA ends (RACE) and its variants, and so could be a cheap practical alternative.
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Affiliation(s)
- Yanwu Guo
- Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, No. 20 Nanxincun, Haidian District, Beijing 100093, China
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43
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Teylaert B, Meurice E, Bobowski M, Harduin-Lepers A, Gaucher C, Fontayne A, Jorieux S, Delannoy P. Molecular cloning, characterization, genomic organization and promoter analysis of the α1,6-fucosyltransferase gene (fut8) expressed in the rat hybridoma cell line YB2/0. BMC Biotechnol 2011; 11:1. [PMID: 21208406 PMCID: PMC3022693 DOI: 10.1186/1472-6750-11-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 01/05/2011] [Indexed: 02/02/2023] Open
Abstract
Background The rat hybridoma cell line YB2/0 appears a good candidate for the large-scale production of low fucose recombinant mAbs due to its lower expression of fut8 gene than other commonly used rodent cell lines. However, important variations of the fucose content of recombinant mAbs are observed in production culture conditions. To improve our knowledge on the YB2/0 fucosylation capacity, we have cloned and characterized the rat fut8 gene. Results The cDNAs encoding the rat α1,6-fucosyltransferase (FucT VIII) were cloned from YB2/0 cells by polymerase chain reaction-based and 5' RNA-Ligase-Mediated RACE methods. The cDNAs contain an open reading frame of 1728 bp encoding a 575 amino acid sequence showing 94% and 88% identity to human and pig orthologs, respectively. The recombinant protein expressed in COS-7 cells exhibits a α1,6-fucosyltransferase activity toward human asialo-agalacto-apotransferrin. The rat fut8 gene is located on chromosome 6 q and spans over 140 kbp. It contains 9 coding exons and four 5'-untranslated exons. FISH analysis shows a heterogeneous copy number of fut8 in YB2/0 nuclei with 2.8 ± 1.4 mean copy number. The YB2/0 fut8 gene is expressed as two main transcripts that differ in the first untranslated exon by the usage of distinct promoters and alternative splicing. Luciferase assays allow defining the minimal promoting regions governing the initiation of the two transcripts, which are differentially expressed in YB2/0 as shown by duplex Taqman QPCR analysis. Bioinformatics analysis of the minimal promoter regions upstream exons E-2 and E-3, governing the transcription of T1 and T2 transcripts, respectively, evidenced several consensus sequences for potential transcriptional repressors. Transient transfections of Rat2 cells with transcription factor expression vectors allowed identifying KLF15 as a putative repressor of T1 transcript in Rat2 cells. Conclusion Altogether, these data contribute to a better knowledge of fut8 expression in YB2/0 that will be useful to better control the fucosylation of recombinant mAbs produced in these cells.
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Affiliation(s)
- Béatrice Teylaert
- Laboratoire Français du Fractionnement et des Biotechnologies, Lille, France
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Abstract
Rapid Amplification of cDNA ends (RACE) provides an inexpensive and powerful tool to quickly obtain full-length cDNA when the sequence is only partially known. Starting with an mRNA mixture, gene-specific primers generated from the known regions of the gene and non-specific anchors, full-length sequences can be identified in as little as 3 days. RACE can also be used to identify alternative transcripts of a gene when the partial or complete sequence of only one transcript is known. In the following sections, we outline details for rapid amplification of 5(') and 3(') cDNA ends using the "new RACE" technique.
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Affiliation(s)
- Oladapo Yeku
- Department of Pharmacology, Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, USA.
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45
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Jin H, Tuo W, Lian H, Liu Q, Zhu XQ, Gao H. Strategies to identify microRNA targets: new advances. N Biotechnol 2010; 27:734-8. [PMID: 20888440 DOI: 10.1016/j.nbt.2010.09.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 08/23/2010] [Accepted: 09/22/2010] [Indexed: 11/28/2022]
Abstract
MicroRNAs (miRNAs) are small regulatory RNA molecules functioning to modulate gene expression at the post-transcriptional level, and playing an important role in many developmental and physiological processes. Ten thousand miRNAs have been discovered in various organisms. Although considerable progress has been made in computational methodology to identify miRNA targets, most predicted miRNA targets may be false positive. Due to the lack of effective tools to identify miRNA targets, the study of miRNAs is seriously retarded. In recent years, some molecular cloning strategies of miRNA targets have been developed, including RT-PCR using miRNAs as endogenous primers, labeled miRNA pull-down assay (LAMP) and RNA ligase-mediated amplification of cDNA end (RLM-RACE). The identified miRNA targets should be further validated via effects of miRNA alteration on the target protein levels and bioactivity. This review summarizes advances in strategies to identify miRNA targets and methods by which miRNA targets are validated.
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Affiliation(s)
- Hongtao Jin
- Institute of Military Veterinary, Academy of Military Medical Sciences, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130062, Jilin Province, People's Republic of China
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Tandem alternative splicing of zebrafish connexin45.6. Genomics 2010; 96:112-8. [PMID: 20466054 DOI: 10.1016/j.ygeno.2010.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 04/19/2010] [Accepted: 05/04/2010] [Indexed: 11/24/2022]
Abstract
Early studies suggested that most connexin genes share a relatively simple structure with a single intron of variable length interrupting the 5' untranslated region (UTR). Here we report that zebrafish cx45.6 shows six isoforms of alternative 5'UTRs which are generated from multiple promoter usage and alternative pre-mRNA splicing. Interestingly, cx45.6 undergoes tandem alternative splicing, which produces transcripts only differing by 3 nucleotides. This is the first study that has demonstrated tandem alternative pre-mRNA splicing in the connexin gene family. Expression patterns of cx45.6 alternative transcripts were demonstrated by real-time RT-PCR during zebrafish embryonic development and in adult tissues. The complexity of 5'UTR diversity suggests complicated regulatory mechanisms for cx45.6 gene expression at both transcriptional and post-transcriptional levels, and we propose that tandem alternative splicing in cx45.6 5'UTRs could play a role in translational control. These results lay groundwork for further investigations on the regulation and function of cx45.6 gene expression.
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47
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Addo-Quaye C, Snyder JA, Park YB, Li YF, Sunkar R, Axtell MJ. Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome. RNA (NEW YORK, N.Y.) 2009; 15:2112-21. [PMID: 19850910 PMCID: PMC2779683 DOI: 10.1261/rna.1774909] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Accepted: 08/23/2009] [Indexed: 05/19/2023]
Abstract
Expression profiling of the 5' ends of uncapped mRNAs ("degradome" sequencing) can be used to empirically catalog microRNA (miRNA) targets, to probe patterns of miRNA hairpin processing, to examine mRNA decay, and to analyze accumulation of endogenous short interfering RNA (siRNA) precursors. We sequenced and analyzed the degradome of the moss Physcomitrella patens, an important model system for functional genomic analyses in plant evolution. A total of 52 target mRNAs of 27 different Physcomitrella miRNA families were identified. Many targets of both more conserved and less conserved miRNA families encoded putative regulatory proteins. Remnants of MIRNA hairpin processing also populated the degradome data and indicated an unusual "loop-first" mode of precise processing for the MIR319 gene family. Precise loop-first processing was confirmed for native Physcomitrella, rice, and Arabidopsis MIR319 hairpins, as well as an Arabidopsis artificial MIRNA (aMIRNA) based upon a MIR319 backbone. MIR319 is thus a conserved exception to the general rule of loop-last processing of MIRNA hairpins. Loop-first MIR319 processing may contribute to the high efficacy of a widely used MIR319-based strategy for aMIRNA production in plants.
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Affiliation(s)
- Charles Addo-Quaye
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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48
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Euprosterna elaeasa virus genome sequence and evolution of the Tetraviridae family: emergence of bipartite genomes and conservation of the VPg signal with the dsRNA Birnaviridae family. Virology 2009; 397:145-54. [PMID: 19954807 DOI: 10.1016/j.virol.2009.10.042] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 10/08/2009] [Accepted: 10/28/2009] [Indexed: 11/21/2022]
Abstract
The Tetraviridae is a family of non-enveloped positive-stranded RNA insect viruses that is defined by the T=4 symmetry of virions. We report the complete Euprosterna elaeasa virus (EeV) genome sequence of 5698 nt with no poly(A) tail and two overlapping open reading frames, encoding the replicase and capsid precursor, with approximately 67% amino acid identity to Thosea asigna virus (TaV). The N-terminally positioned 17 kDa protein is released from the capsid precursor by a NPGP motif. EeV has 40 nm non-enveloped isometric particles composed of 58 and 7 kDa proteins. The 3'-end of TaV/EeV is predicted to form a conserved pseudoknot. Replicases of TaV and EeV include a newly delineated VPg signal mediating the protein priming of RNA synthesis in dsRNA Birnaviridae. Results of rooted phylogenetic analysis of replicase and capsid proteins are presented to implicate recombination between monopartite tetraviruses, involving autonomization of a sgRNA, in the emergence of bipartite tetraviruses. They are also used to revise the Tetraviridae taxonomy.
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49
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Radeloff B, Nagler L, Zirra M, Ziegler A, Volz A. Specific amplification of cDNA ends (SPACE): A new tool for the analysis of rare transcripts and its application for the promoter analysis of killer cell receptor genes. ACTA ACUST UNITED AC 2009; 16:44-52. [PMID: 16040346 DOI: 10.1080/10425170400028202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The expression control of activating and inhibitory killer cell Ig-like receptors (KIR) on natural killer (NK) cells is highly relevant for the initiation of NK cell mediated cytolysis and cytokine secretion. Transcription start points of nine human KIR genes from two Caucasian donors and the NK cell line NK3.3 were investigated. To overcome sensitivity problems due to the low abundance of the respective transcripts, a novel protocol, specific amplification of cDNA ends (SPACE) with superior specificity and sensitivity was applied. A total of 235 individual SPACE clones resulting from different KIR genes were analysed and revealed a series of transcription start sites tightly clustered between 10 and 60 bp upstream of the start codon. The comparison of the adjacent putative promoter region of the human, chimpanzee and macaque KIR genes revealed a very high conservation for almost all of the KIR family members. An inter-gene and inter-species comparative approach revealed transcription factor binding sites at regions of maximal homology for all primate KIR genes analysed.
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Affiliation(s)
- Britta Radeloff
- Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Germany
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50
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Rahrmann EP, Collier LS, Knutson TP, Doyal ME, Kuslak SL, Green LE, Malinowski RL, Roethe L, Akagi K, Waknitz M, Huang W, Largaespada DA, Marker PC. Identification of PDE4D as a proliferation promoting factor in prostate cancer using a Sleeping Beauty transposon-based somatic mutagenesis screen. Cancer Res 2009; 69:4388-97. [PMID: 19401450 DOI: 10.1158/0008-5472.can-08-3901] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Retroviral and transposon-based mutagenesis screens in mice have been useful for identifying candidate cancer genes for some tumor types. However, many of the organs that exhibit the highest cancer rates in humans, including the prostate, have not previously been amenable to these approaches. This study shows for the first time that the Sleeping Beauty transposon system can be used to identify candidate prostate cancer genes in mice. Somatic mobilization of a mutagenic transposon resulted in focal epithelial proliferation and hyperplasia in the prostate. Efficient methods were established to identify transposon insertion sites in these lesions, and analysis of transposon insertions identified candidate prostate cancer genes at common insertion sites, including Pde4d. PDE4D was also overexpressed in human prostate cancer patient samples and cell lines, and changes in PDE4D mRNA isoform expression were observed in human prostate cancers. Furthermore, knockdown of PDE4D reduced the growth and migration of prostate cancer cells in vitro, and knockdown of PDE4D reduced the growth and proliferation rate of prostate cancer xenografts in vivo. These data indicate that PDE4D functions as a proliferation promoting factor in prostate cancer, and the Sleeping Beauty transposon system is a useful tool for identifying candidate prostate cancer genes.
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Affiliation(s)
- Eric P Rahrmann
- Department of Genetics, Cell Biology, and Development and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
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