1
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Naim D, Ahsan A, Imtiaj A, Mollah NH. Genome-wide identification and in silico characterization of major RNAi gene families in date palm (Phoenix dactylifera). BMC Genom Data 2024; 25:31. [PMID: 38491426 PMCID: PMC10943882 DOI: 10.1186/s12863-024-01217-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Dates contain various minerals that are essential for good health. The major RNA interference (RNAi) gene families play a vital role in plant growth and development by controlling the expression of protein-coding genes against different biotic and abiotic stresses. However, these gene families for date palm are not yet studied. Therefore, this study has explored major RNAi genes and their characteristics in date palm. RESULTS We have identified 4 PdDCLs, 7 PdAGOs, and 3 PdRDRs as RNAi proteins from the date palm genome by using AtRNAi genes as query sequences in BLASTp search. Domain analysis of predicted RNAi genes has revealed the Helicase_C, Dicer_dimer, PAZ, RNase III, and Piwi domains that are associated with the gene silencing mechanisms. Most PdRNAi proteins have been found in the nucleus and cytosol associated with the gene silencing actions. The gene ontology (GO) enrichment analysis has revealed some important GO terms including RNA interference, dsRNA fragmentation, and ribonuclease_III activity that are related to the protein-coding gene silencing mechanisms. Gene regulatory network (GRN) analysis has identified PAZ and SNF2 as the transcriptional regulators of PdRNAi genes. Top-ranked 10 microRNAs including Pda-miR156b, Pda-miR396a, Pda-miR166a, Pda-miR167d, and Pda-miR529a have been identified as the key post-transcriptional regulators of PdRNAi genes that are associated with different biotic/abiotic stresses. The cis-acting regulatory element analysis of PdRNAi genes has detected some vital cis-acting elements including ABRE, MBS, MYB, MYC, Box-4, G-box, I-box, and STRE that are linked with different abiotic stresses. CONCLUSION The results of this study might be valuable resources for the improvement of different characteristics in date palm by further studies in wet-lab.
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Affiliation(s)
- Darun Naim
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Asif Ahsan
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Ahmed Imtiaj
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh.
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2
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Cabrera GT, Meijboom KE, Abdallah A, Tran H, Foster Z, Weiss A, Wightman N, Stock R, Gendron T, Gruntman A, Giampetruzzi A, Petrucelli L, Brown RH, Mueller C. Artificial microRNA suppresses C9ORF72 variants and decreases toxic dipeptide repeat proteins in vivo. Gene Ther 2024; 31:105-118. [PMID: 37752346 DOI: 10.1038/s41434-023-00418-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 05/28/2023] [Accepted: 08/11/2023] [Indexed: 09/28/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that affects motor neurons, causing progressive muscle weakness and respiratory failure. The presence of an expanded hexanucleotide repeat in chromosome 9 open reading frame 72 (C9ORF72) is the most frequent mutation causing familial ALS and frontotemporal dementia (FTD). To determine if suppressing expression of C9ORF72 gene products can reduce toxicity, we designed a set of artificial microRNAs (amiRNA) targeting the human C9ORF72 gene. Here we report that an AAV9-mediated amiRNA significantly suppresses expression of the C9ORF72 mRNA, protein, and toxic dipeptide repeat proteins generated by the expanded repeat in the brain and spinal cord of C9ORF72 transgenic mice.
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Affiliation(s)
- Gabriela Toro Cabrera
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Katharina E Meijboom
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Abbas Abdallah
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Helene Tran
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Zachariah Foster
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Alexandra Weiss
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Nicholas Wightman
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Rachel Stock
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Tania Gendron
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd., Jacksonville, FL, 32224, USA
| | - Alisha Gruntman
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Anthony Giampetruzzi
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd., Jacksonville, FL, 32224, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA.
| | - Christian Mueller
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA.
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3
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Zhong C, Smith NA, Zhang D, Gou X, Greaves IK, Millar AA, Walsh TK, Shan W, Wang MB. G-U base-paired hpRNA confers potent inhibition of small RNA function in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1206-1222. [PMID: 38038953 DOI: 10.1111/tpj.16555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
MicroRNA (miRNA) target mimicry technologies, utilizing naturally occurring miRNA decoy molecules, represent a potent tool for analyzing miRNA function. In this study, we present a highly efficient small RNA (sRNA) target mimicry design based on G-U base-paired hairpin RNA (hpG:U), which allows for the simultaneous targeting of multiple sRNAs. The hpG:U constructs consistently generate high amounts of intact, polyadenylated stem-loop (SL) RNA outside the nuclei, in contrast to traditional hairpin RNA designs with canonical base pairing (hpWT), which were predominantly processed resulting in a loop. By incorporating a 460-bp G-U base-paired double-stranded stem and a 312-576 nt loop carrying multiple miRNA target mimicry sites (GUMIC), the hpG:U construct displayed effective repression of three Arabidopsis miRNAs, namely miR165/166, miR157, and miR160, both individually and in combination. Additionally, a GUMIC construct targeting a prominent cluster of siRNAs derived from cucumber mosaic virus (CMV) Y-satellite RNA (Y-Sat) effectively inhibited Y-Sat siRNA-directed silencing of the chlorophyll biosynthetic gene CHLI, thereby reducing the yellowing symptoms in infected Nicotiana plants. Therefore, the G-U base-paired hpRNA, characterized by differential processing compared to traditional hpRNA, acts as an efficient decoy for both miRNAs and siRNAs. This technology holds great potential for sRNA functional analysis and the management of sRNA-mediated diseases.
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Affiliation(s)
- Chengcheng Zhong
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Neil A Smith
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Daai Zhang
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Xiuhong Gou
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ian K Greaves
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, 2601, ACT, Australia
| | - Tom K Walsh
- CSIRO Environment, Canberra, 2601, ACT, Australia
| | - Weixing Shan
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ming-Bo Wang
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
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4
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DeMell A, Mendoza MR, Scholthof HB. A tomato bushy stunt virus-based vector for simultaneous editing and sensing to survey the host antiviral RNA silencing machinery. PNAS NEXUS 2024; 3:pgad436. [PMID: 38264147 PMCID: PMC10805433 DOI: 10.1093/pnasnexus/pgad436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/06/2023] [Indexed: 01/25/2024]
Abstract
A tomato bushy stunt virus (TBSV)-derived vector system was applied for the delivery of CRISPR/Cas9 gene editing materials, to facilitate rapid, transient assays of host-virus interactions involved in the RNA silencing pathway. Toward this, single guide RNAs designed to target key components of the virus-induced host RNA silencing pathway (AGO2, DCL2, HEN1) were inserted into TBSV-based GFP-expressing viral vectors TBSV-GFP (TG) and its P19 defective mutant TGΔP19. This produced rapid, efficient, and specific gene editing in planta. Targeting AGO2, DCL2, or HEN1 partially rescued the lack of GFP accumulation otherwise associated with TGΔP19. Since the rescue phenotypes are normally only observed in the presence of the P19 silencing suppressor, the results support that the DCL2, HEN1, and AGO2 proteins are involved in anti-TBSV RNA silencing. Additionally, we show that knockdown of the RNA silencing machinery increases cargo expression from a nonviral binary Cas9 vector. The TBSV-based gene editing technology described in this study can be adapted for transient heterologous expression, rapid gene function screens, and molecular interaction studies in many plant species considering the wide host range of TBSV. In summary, we demonstrate that a plant virus can be used to establish gene editing while simultaneously serving as an accumulation sensor for successful targeting of its homologous antiviral silencing machinery components.
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Affiliation(s)
- April DeMell
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
- Present address: Plant Biology, UC Davis, Davis, CA, USA
| | - Maria R Mendoza
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
- Present address: Fujifilm Diosynth Biotechnologies Texas, College Station, TX, USA
| | - Herman B Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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5
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Hasan MN, Mosharaf MP, Uddin KS, Das KR, Sultana N, Noorunnahar M, Naim D, Mollah MNH. Genome-Wide Identification and Characterization of Major RNAi Genes Highlighting Their Associated Factors in Cowpea ( Vigna unguiculata (L.) Walp.). BIOMED RESEARCH INTERNATIONAL 2023; 2023:8832406. [PMID: 38046903 PMCID: PMC10691899 DOI: 10.1155/2023/8832406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/07/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
In different regions of the world, cowpea (Vigna unguiculata (L.) Walp.) is an important vegetable and an excellent source of protein. It lessens the malnutrition of the underprivileged in developing nations and has some positive effects on health, such as a reduction in the prevalence of cancer and cardiovascular disease. However, occasionally, certain biotic and abiotic stresses caused a sharp fall in cowpea yield. Major RNA interference (RNAi) genes like Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are essential for the synthesis of their associated factors like domain, small RNAs (sRNAs), transcription factors, micro-RNAs, and cis-acting factors that shield plants from biotic and abiotic stresses. In this study, applying BLASTP search and phylogenetic tree analysis with reference to the Arabidopsis RNAi (AtRNAi) genes, we discovered 28 VuRNAi genes, including 7 VuDCL, 14 VuAGO, and 7 VuRDR genes in cowpea. We looked at the domains, motifs, gene structures, chromosomal locations, subcellular locations, gene ontology (GO) terms, and regulatory factors (transcription factors, micro-RNAs, and cis-acting elements (CAEs)) to characterize the VuRNAi genes and proteins in cowpea in response to stresses. Predicted VuDCL1, VuDCL2(a, b), VuAGO7, VuAGO10, and VuRDR6 genes might have an impact on cowpea growth, development of the vegetative and flowering stages, and antiviral defense. The VuRNAi gene regulatory features miR395 and miR396 might contribute to grain quality improvement, immunity boosting, and pathogen infection resistance under salinity and drought conditions. Predicted CAEs from the VuRNAi genes might play a role in plant growth and development, improving grain quality and production and protecting plants from biotic and abiotic stresses. Therefore, our study provides crucial information about the functional roles of VuRNAi genes and their associated components, which would aid in the development of future cowpeas that are more resilient to biotic and abiotic stress. The manuscript is available as a preprint at this link: doi:10.1101/2023.02.15.528631v1.
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Affiliation(s)
- Mohammad Nazmol Hasan
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Md Parvez Mosharaf
- School of Business, Faculty of Business, Education, Law and Arts, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Khandoker Saif Uddin
- Department of Quantitative Science (Statistics), International University of Business Agriculture and Technology (IUBAT), Uttara, Bangladesh
| | - Keya Rani Das
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Nasrin Sultana
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Mst. Noorunnahar
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Darun Naim
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
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6
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Augspach A, Drake KD, Roma L, Qian E, Lee SR, Clarke D, Kumar S, Jaquet M, Gallon J, Bolis M, Triscott J, Galván JA, Chen Y, Thalmann GN, Kruithof-de Julio M, Theurillat JPP, Wuchty S, Gerstein M, Piscuoglio S, Kanadia RN, Rubin MA. Minor intron splicing is critical for survival of lethal prostate cancer. Mol Cell 2023; 83:1983-2002.e11. [PMID: 37295433 PMCID: PMC10637423 DOI: 10.1016/j.molcel.2023.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 03/29/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023]
Abstract
The evolutionarily conserved minor spliceosome (MiS) is required for protein expression of ∼714 minor intron-containing genes (MIGs) crucial for cell-cycle regulation, DNA repair, and MAP-kinase signaling. We explored the role of MIGs and MiS in cancer, taking prostate cancer (PCa) as an exemplar. Both androgen receptor signaling and elevated levels of U6atac, a MiS small nuclear RNA, regulate MiS activity, which is highest in advanced metastatic PCa. siU6atac-mediated MiS inhibition in PCa in vitro model systems resulted in aberrant minor intron splicing leading to cell-cycle G1 arrest. Small interfering RNA knocking down U6atac was ∼50% more efficient in lowering tumor burden in models of advanced therapy-resistant PCa compared with standard antiandrogen therapy. In lethal PCa, siU6atac disrupted the splicing of a crucial lineage dependency factor, the RE1-silencing factor (REST). Taken together, we have nominated MiS as a vulnerability for lethal PCa and potentially other cancers.
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Affiliation(s)
- Anke Augspach
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Kyle D Drake
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Luca Roma
- Institute of Pathology and Medical Genetics, University Hospital Basel, 4056 Basel, Switzerland
| | - Ellen Qian
- Department of Computer Science, Yale University, New Haven, CT 06520, USA; Yale College, New Haven, CT 06520, USA
| | - Se Ri Lee
- Department of Computer Science, Yale University, New Haven, CT 06520, USA; Yale College, New Haven, CT 06520, USA
| | - Declan Clarke
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Sushant Kumar
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Muriel Jaquet
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - John Gallon
- Institute of Pathology and Medical Genetics, University Hospital Basel, 4056 Basel, Switzerland
| | - Marco Bolis
- Institute of Oncology Research, 6500 Bellinzona, Switzerland; Computational Oncology Unit, Department of Oncology, Istituto di Ricerche Farmacologiche "Mario Negri" IRCCS, 20156 Milano, Italy
| | - Joanna Triscott
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - José A Galván
- Institute of Pathology, University of Bern, Bern 3008, Switzerland
| | - Yu Chen
- Human Oncology and Pathogenesis Program (HOPP), Memorial Sloan Kettering, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - George N Thalmann
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland; Department of Urology, Inselspital, Bern University Hospital, 3008 Bern, Switzerland
| | - Marianna Kruithof-de Julio
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland; Department of Urology, Inselspital, Bern University Hospital, 3008 Bern, Switzerland; Bern Center for Precision Medicine, University of Bern and Inselspital, 3008 Bern, Switzerland
| | - Jean-Philippe P Theurillat
- Institute of Oncology Research, 6500 Bellinzona, Switzerland; Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Coral Gables, FL 33146, USA; Sylvester Comprehensive Cancer Center, University of Miami, Coral Gables, FL 33136, USA; Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Mark Gerstein
- Department of Computer Science, Yale University, New Haven, CT 06520, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Salvatore Piscuoglio
- Institute of Pathology and Medical Genetics, University Hospital Basel, 4056 Basel, Switzerland; Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
| | - Mark A Rubin
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland; Bern Center for Precision Medicine, University of Bern and Inselspital, 3008 Bern, Switzerland.
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7
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Di Serio F, Owens RA, Navarro B, Serra P, Martínez de Alba ÁE, Delgado S, Carbonell A, Gago-Zachert S. Role of RNA silencing in plant-viroid interactions and in viroid pathogenesis. Virus Res 2023; 323:198964. [PMID: 36223861 PMCID: PMC10194176 DOI: 10.1016/j.virusres.2022.198964] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Viroids are small, single-stranded, non-protein coding and circular RNAs able to infect host plants in the absence of any helper virus. They may elicit symptoms in their hosts, but the underlying molecular pathways are only partially known. Here we address the role of post-transcriptional RNA silencing in plant-viroid-interplay, with major emphasis on the involvement of this sequence-specific RNA degradation mechanism in both plant antiviroid defence and viroid pathogenesis. This review is a tribute to the memory of Dr. Ricardo Flores, who largely contributed to elucidate this and other molecular mechanisms involved in plant-viroid interactions.
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Affiliation(s)
- Francesco Di Serio
- Institute for Sustainable Plant Protection, National Research Council, Bari 70122, Italy.
| | - Robert A Owens
- Molecular Plant Pathology Laboratory, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Beatriz Navarro
- Institute for Sustainable Plant Protection, National Research Council, Bari 70122, Italy
| | - Pedro Serra
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), Valencia 46022, Spain
| | - Ángel Emilio Martínez de Alba
- Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor 37185, Salamanca, Spain
| | - Sonia Delgado
- Instituto Agroforestal Mediterráneo (IAM-UPV), Camino de Vera, s/n 46022, Valencia, Spain
| | - Alberto Carbonell
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), Valencia 46022, Spain
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
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8
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Tabara M, Yamanashi R, Kuriyama K, Koiwa H, Fukuhara T. The dicing activity of DCL3 and DCL4 is negatively affected by flavonoids. PLANT MOLECULAR BIOLOGY 2023; 111:107-116. [PMID: 36219366 DOI: 10.1007/s11103-022-01314-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The dicing activities of DCL3 and DCL4 are inhibited by accumulated metabolites in soybean leaves. Epicatechin and 7,4'-dihydroxyflavone inhibited Arabidopsis DCL3 and DCL4 in vitro. Flavonoids are major secondary metabolites in plants, and soybean (Glycine max L.) is a representative plant that accumulates flavonoids, including isoflavonoids, to high levels. Naturally-occurring RNA interference (RNAi) against the chalcone synthase (CHS) gene represses flavonoid (anthocyanin) biosynthesis in an organ-specific manner, resulting in a colorless (yellow) seed coat in many soybean cultivars. To better understand seed coat-specific naturally-occurring RNAi in soybean, we characterized soybean Dicer-like (DCL) 3 and 4, which play critical roles in RNAi. Using a previously established dicing assay, two dicing activities producing 24- and 21-nt siRNAs, corresponding to DCL3 and DCL4, respectively, were detected in soybean. Dicing activity was detected in colorless seed coats where RNAi against CHS genes was found, but no dicing activity was detected in leaves where CHS expression was prevalent. Biochemical analysis revealed that soybean leaves contained two types of inhibitors effective for Arabidopsis Dicers (AtDCL3 and AtDCL4), one of which was a heat-labile high molecular weight compound of 50 to 100 kD while another was a low molecular weight substance. We found that some flavonoids, such as epicatechin and 7,4'-dihydroxyflavone, inhibited both AtDCL3 and AtDCL4, but AtDCL4 was more sensitive to these flavonoids than AtDCL3. These results suggest that flavonoids inhibit the dicing activity of DCL4 and thereby attenuate RNAi in soybean leaves.
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Affiliation(s)
- Midori Tabara
- Ritsumeikan-Global Innovation Research Organization, Ritsumeikan University, 1-1-1, Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan.
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
| | - Riho Yamanashi
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Kazunori Kuriyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Hisashi Koiwa
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
- Vegetable and Fruit Improvement Center and Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Toshiyuki Fukuhara
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
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9
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Yang MC, Wu ZC, Huang LL, Abbas F, Wang HC. Systematic Methods for Isolating High Purity Nuclei from Ten Important Plants for Omics Interrogation. Cells 2022; 11:cells11233919. [PMID: 36497177 PMCID: PMC9740283 DOI: 10.3390/cells11233919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/23/2022] [Accepted: 12/01/2022] [Indexed: 12/07/2022] Open
Abstract
Recent advances in developmental biology have been made possible by using multi-omic studies at single cell resolution. However, progress in plants has been slowed, owing to the tremendous difficulty in protoplast isolation from most plant tissues and/or oversize protoplasts during flow cytometry purification. Surprisingly, rapid innovations in nucleus research have shed light on plant studies in single cell resolution, which necessitates high quality and efficient nucleus isolation. Herein, we present efficient nuclei isolation protocols from the leaves of ten important plants including Arabidopsis, rice, maize, tomato, soybean, banana, grape, citrus, apple, and litchi. We provide a detailed procedure for nucleus isolation, flow cytometry purification, and absolute nucleus number quantification. The nucleus isolation buffer formula of the ten plants tested was optimized, and the results indicated a high nuclei yield. Microscope observations revealed high purity after flow cytometry sorting, and the DNA and RNA quality extract from isolated nuclei were monitored by using the nuclei in cell division cycle and single nucleus RNA sequencing (snRNA-seq) studies, with detailed procedures provided. The findings indicated that nucleus yield and quality meet the requirements of snRNA-seq, cell division cycle, and likely other omic studies. The protocol outlined here makes it feasible to perform plant omic studies at single cell resolution.
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Affiliation(s)
- Ming-Chao Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Litchi Engineering Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zi-Chen Wu
- Becton Dickinson Medical Devices (Shanghai) Co., Ltd., Guangzhou 510180, China
| | - Liang-Liang Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Litchi Engineering Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Farhat Abbas
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Litchi Engineering Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Hui-Cong Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Litchi Engineering Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
- Department of Life Sciences and Technology, Yangtze Normal University, Chongqing 408100, China
- Correspondence:
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10
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Feng Z, Li X, Fan B, Zhu C, Chen Z. Maximizing the Production of Recombinant Proteins in Plants: From Transcription to Protein Stability. Int J Mol Sci 2022; 23:13516. [PMID: 36362299 PMCID: PMC9659199 DOI: 10.3390/ijms232113516] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/07/2023] Open
Abstract
The production of therapeutic and industrial recombinant proteins in plants has advantages over established bacterial and mammalian systems in terms of cost, scalability, growth conditions, and product safety. In order to compete with these conventional expression systems, however, plant expression platforms must have additional economic advantages by demonstrating a high protein production yield with consistent quality. Over the past decades, important progress has been made in developing strategies to increase the yield of recombinant proteins in plants by enhancing their expression and reducing their degradation. Unlike bacterial and animal systems, plant expression systems can utilize not only cell cultures but also whole plants for the production of recombinant proteins. The development of viral vectors and chloroplast transformation has opened new strategies to drastically increase the yield of recombinant proteins from plants. The identification of promoters for strong, constitutive, and inducible promoters or the tissue-specific expression of transgenes allows for the production of recombinant proteins at high levels and for special purposes. Advances in the understanding of RNAi have led to effective strategies for reducing gene silencing and increasing recombinant protein production. An increased understanding of protein translation, quality control, trafficking, and degradation has also helped with the development of approaches to enhance the synthesis and stability of recombinant proteins in plants. In this review, we discuss the progress in understanding the processes that control the synthesis and degradation of gene transcripts and proteins, which underlie a variety of developed strategies aimed at maximizing recombinant protein production in plants.
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Affiliation(s)
- Ziru Feng
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xifeng Li
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Baofang Fan
- Department of Botany and Plant Pathology, Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907-2054, USA
| | - Cheng Zhu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhixiang Chen
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- Department of Botany and Plant Pathology, Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907-2054, USA
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11
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Hajieghrari B, Farrokhi N. Plant RNA-mediated gene regulatory network. Genomics 2021; 114:409-442. [PMID: 34954000 DOI: 10.1016/j.ygeno.2021.12.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/21/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022]
Abstract
Not all transcribed RNAs are protein-coding RNAs. Many of them are non-protein-coding RNAs in diverse eukaryotes. However, some of them seem to be non-functional and are resulted from spurious transcription. A lot of non-protein-coding transcripts have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several non-protein-coding RNAs regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. They include a significant part of the gene expression regulatory network. RNA-mediated gene regulation machinery is evolutionarily ancient. They well-evolved during the evolutionary time and are becoming much more complex than had been expected. In this review, we are trying to summarizing the current knowledge in the field of RNA-mediated gene silencing.
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Affiliation(s)
- Behzad Hajieghrari
- Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, Jahrom, Iran.
| | - Naser Farrokhi
- Department of Cell, Molecular Biology Faculty of Life Sciences, Biotechnology, Shahid Beheshti University, G. C Evin, Tehran, Iran.
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12
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Ravelonandro M, Briard P, Scorza R, Callahan A, Zagrai I, Kundu JK, Dardick C. Robust Response to Plum pox virus Infection via Plant Biotechnology. Genes (Basel) 2021; 12:genes12060816. [PMID: 34071769 PMCID: PMC8227089 DOI: 10.3390/genes12060816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 12/23/2022] Open
Abstract
Our goal was to target silencing of the Plum pox virus coat protein (PPV CP) gene independently expressed in plants. Clone C-2 is a transgenic plum expressing CP. We introduced and verified, in planta, the effects of the inverse repeat of CP sequence split by a hairpin (IRSH) that was characterized in the HoneySweet plum. The IRSH construct was driven by two CaMV35S promoter sequences flanking the CP sequence and had been introduced into C1738 plum. To determine if this structure was enough to induce silencing, cross-hybridization was made with the C1738 clone and the CP expressing but PPV-susceptible C2 clone. In total, 4 out of 63 clones were silenced. While introduction of the IRSH is reduced due to the heterozygous character in C1738 plum, the silencing induced by the IRSH PPV CP is robust. Extensive studies, in greenhouse containment, demonstrated that the genetic resource of C1738 clone can silence the CP production. In addition, these were verified through the virus transgene pyramiding in the BO70146 BlueByrd cv. plum that successfully produced resistant BlueByrd BO70146 × C1738 (HybC1738) hybrid plums.
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Affiliation(s)
- Michel Ravelonandro
- UMR-BFP-1332, INRAE-Bordeaux, Bordeaux-UniversityII, 71 Avenue Bourleaux, 33883 Villenave d’Ornon, France;
- Correspondence:
| | - Pascal Briard
- UMR-BFP-1332, INRAE-Bordeaux, Bordeaux-UniversityII, 71 Avenue Bourleaux, 33883 Villenave d’Ornon, France;
| | - Ralph Scorza
- USDA-ARS Fruit Station, 2217 Wiltshire Road, Kearneysville, WV 25430, USA; (R.S.); (A.C.); (C.D.)
| | - Ann Callahan
- USDA-ARS Fruit Station, 2217 Wiltshire Road, Kearneysville, WV 25430, USA; (R.S.); (A.C.); (C.D.)
| | - Ioan Zagrai
- Fruit Research and Development Station Bistrita, Drumul Dumitrei Nou street, 420127 Bistrita, Romania;
| | - Jiban K. Kundu
- Crop Research Institute, Drnovska 507/73, 161 06 Praha, Czech Republic;
| | - Chris Dardick
- USDA-ARS Fruit Station, 2217 Wiltshire Road, Kearneysville, WV 25430, USA; (R.S.); (A.C.); (C.D.)
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13
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Viroids as a Tool to Study RNA-Directed DNA Methylation in Plants. Cells 2021; 10:cells10051187. [PMID: 34067940 PMCID: PMC8152041 DOI: 10.3390/cells10051187] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
Viroids are plant pathogenic, circular, non-coding, single-stranded RNAs (ssRNAs). Members of the Pospiviroidae family replicate in the nucleus of plant cells through double-stranded RNA (dsRNA) intermediates, thus triggering the host’s RNA interference (RNAi) machinery. In plants, the two RNAi pillars are Post-Transcriptional Gene Silencing (PTGS) and RNA-directed DNA Methylation (RdDM), and the latter has the potential to trigger Transcriptional Gene Silencing (TGS). Over the last three decades, the employment of viroid-based systems has immensely contributed to our understanding of both of these RNAi facets. In this review, we highlight the role of Pospiviroidae in the discovery of RdDM, expound the gradual elucidation through the years of the diverse array of RdDM’s mechanistic details and propose a revised RdDM model based on the cumulative amount of evidence from viroid and non-viroid systems.
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14
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Gong M, Zhang X, Wang Y, Mao G, Ou Y, Wei C, Hu X, Xiang S. DDX21 interacts with nuclear AGO2 and regulates the alternative splicing of SMN2. Biosci Biotechnol Biochem 2021; 85:272-279. [PMID: 33604619 DOI: 10.1093/bbb/zbaa029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/17/2020] [Indexed: 01/30/2023]
Abstract
AGO2 is the only member of mammalian Ago protein family that possesses the catalytic activity and plays a central role in gene silencing. Recently researches reported that multiple gene silencing factors, including AGO2, function in the nuclei. The molecular mechanisms of the gene silencing factors functioning in nuclei are conducive to comprehend the roles of gene silencing in pretranslational regulation of gene expression. Here, we report that AGO2 interacts with DDX21 indirectly in an RNA-dependent manner by Co-IP and GST-Pulldown assays and the 2 proteins present nuclei foci in the immunofluorescence experiments. We found that DDX21 up-regulated the protein level of AGO2 and participated in target gene, SNM2, alternative splicing involved in AGO2 by the indirect interaction with AGO2, which produced different transcripts of SMN2 in discrepant expression level. This study laid important experiment foundation for the further analysis of the nuclear functions of gene silencing components.
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Affiliation(s)
- Mengting Gong
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China.,College of Physical Education, Hunan University of Finance and Economics, Changsha, China
| | - Xi Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yaru Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Guiyan Mao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yangqi Ou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Chenxi Wei
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xiang Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shuanglin Xiang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
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15
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Čermák V, Tyč D, Přibylová A, Fischer L. Unexpected variations in posttranscriptional gene silencing induced by differentially produced dsRNAs in tobacco cells. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194647. [PMID: 33127485 DOI: 10.1016/j.bbagrm.2020.194647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 11/17/2022]
Abstract
In plants, posttranscriptional gene silencing (PTGS) is induced by small RNAs (sRNAs) generated from various dsRNA precursors. To assess the impact of dsRNA origin, we compared downregulation of GFP expression triggered by inverted repeat (IR), antisense (AS) and unterminated sense (UT) transcripts transiently expressed from the estradiol-inducible promoter. The use of homogeneously responding tobacco BY-2 cell lines allowed monitoring the onset of silencing and its reversibility. In this system, IR induced the strongest and fastest silencing accompanied by dense DNA methylation. At low induction, silencing in individual cells was binary (either strong or missing), suggesting that a certain threshold sRNA level had to be exceeded. The AS variant specifically showed a deviated sRNA-strand ratio shifted in favor of antisense orientation. In AS lines and weakly induced IR lines, only the silencer DNA was methylated, but the same target GFP sequence was not, showing that DNA methylation accompanying PTGS was influenced both by the level and origin of sRNAs, and possibly also by the epigenetic state of the locus. UT silencing appeared to be the least effective and resembled classical sense PTGS. The best responding UT lines behaved relatively heterogeneously possibly due to complexly arranged T-DNA insertions. Unlike IR and AS variants that fully restored GFP expression upon removal of the inducer, only partial reactivation was observed in some UT lines. Our results pointed out several not yet described phenomena and differences between the long-known silencer variants that may direct further research and affect selection of proper silencer variants for specific applications.
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Affiliation(s)
- Vojtěch Čermák
- Charles University, Faculty of Science, Department of Experimental Plant Biology, Viničná 5, Prague 2 128 44, Czech Republic
| | - Dimitrij Tyč
- Charles University, Faculty of Science, Department of Experimental Plant Biology, Viničná 5, Prague 2 128 44, Czech Republic
| | - Adéla Přibylová
- Charles University, Faculty of Science, Department of Experimental Plant Biology, Viničná 5, Prague 2 128 44, Czech Republic
| | - Lukáš Fischer
- Charles University, Faculty of Science, Department of Experimental Plant Biology, Viničná 5, Prague 2 128 44, Czech Republic.
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16
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Zhang Y, Wu X, Yuan L. Distinct non-coding RNAs confer root-dependent sense transgene-induced post-transcriptional gene silencing and nitrogen-dependent post-transcriptional regulation to AtAMT1;1 transcripts in Arabidopsis roots. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:823-837. [PMID: 31901180 DOI: 10.1111/tpj.14667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
High-affinity ammonium uptake in roots mediate by AMT1-type ammonium transporters, which are tightly controlled at multiple regulatory levels for adapting various nitrogen availability. For Arabidopsis AtAMT1;1 gene, in addition to the transcriptional and post-translational controls, an organ-dependent and N-dependent post-transcriptional regulation was suggested as an additional regulatory step for fine tuning ammonium uptake, but the underlying mechanisms remain to be elucidated. Here, we showed that degradation of AtAMT1;1 transcript in roots of Pro35s:AtAMT1;1-transformed atamt1;1-1 Arabidopsis plants resulted from RDR6-dependent sense transgene-induced post-transcriptional gene silencing (S-PTGS). The siRNAs for S-PTGS may derive from the aberrant RNA, of which the production was co-determined by sequence feature and excessive expression of AtAMT1;1. Switching to the expression of AtAMT1;1 driven by ProAtUBQ10 or of AtAMT1;1 mutated at two siRNA-targeted hotspots reduced AtAMT1;1-specific siRNAs and overcame S-PTGS in roots. In roots of these lines, however, the steady-state transcript levels of AtAMT1;1 still significantly decreased under conditions of N-sufficiency compared with N-deficiency, confirming a N-dependent post-transcriptional regulatory manner. A crucial role of the 207-bp 3'-end sequence of AtAMT1;1 was further demonstrated by N-dependent accumulation of chimeric-AtAMT1;1 transcript in T-DNA insertion lines and of GFP-tagged chimeric-AtAMT1;1 transcript in transgenic lines. A novel non-coding RNA (ncRNA), which was highly abundant in N-sufficient roots, may target the above-identified 3'-end region for the degrading AtAMT1;1 transcript. This degradation could be prevented by a mutation on the AtAMT1;1 transcript at a potential cleavage site (+1458). These results suggested two distinct mechanisms of regulating AtAMT1;1 mRNA turnover by ncRNA for strictly control of ammonium uptake in roots.
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Affiliation(s)
- Yongjian Zhang
- Key Laboratory of Plant-Soil Interaction, MOE, College of Resources and Environmental Sciences, China Agricultural University, 100193, Beijing, China
| | - Xiangyu Wu
- Key Laboratory of Plant-Soil Interaction, MOE, College of Resources and Environmental Sciences, China Agricultural University, 100193, Beijing, China
| | - Lixing Yuan
- Key Laboratory of Plant-Soil Interaction, MOE, College of Resources and Environmental Sciences, China Agricultural University, 100193, Beijing, China
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17
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Wei J, Dong Z, Ow DW. Spontaneous reactivation of a site-specifically placed transgene independent of copy number or DNA methylation. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1574-1584. [PMID: 31740977 DOI: 10.1093/jxb/erz514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
As millions of seeds are produced from a breeding line, the long-term stability of transgene expression is vital for commercial-scale production of seeds with transgenic traits. Transgenes can be silenced by epigenetic mechanisms, but reactivation of expression can occur as a result of treatment with chromatin modification inhibitors such as 5-azacytidine, from stress such as heat or UV-B, or in mutants that have acquired a defect in gene silencing. Previously, we targeted a gfp reporter gene into the tobacco (Nicotiana tabacum) genome by site-specific recombination but still found some silenced lines among independent integration events. One such line also had a second random copy and both copies showed DNA hypermethylation. To test whether removing the second copy would reactivate gfp expression, two T1 plants were backcrossed to the wild type. Whereas the silenced status was maintained in the progenies from one backcross, spontaneous partial reactivation of gfp expression was found among progenies from a second backcross. However, this reactivation did not correlate with loss of the second random copy or with a significant change in the pattern or amount of DNA hypermethylation. This finding supports the suggestion that gene reactivation does not necessarily involve loss of DNA homology or methylation.
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Affiliation(s)
- Junjie Wei
- Plant Gene Engineering Center; Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement; Guangdong Key Laboratory of Applied Botany. South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhicheng Dong
- Plant Gene Engineering Center; Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement; Guangdong Key Laboratory of Applied Botany. South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - David W Ow
- Plant Gene Engineering Center; Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement; Guangdong Key Laboratory of Applied Botany. South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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18
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Dalakouras A, Lauter A, Bassler A, Krczal G, Wassenegger M. Transient expression of intron-containing transgenes generates non-spliced aberrant pre-mRNAs that are processed into siRNAs. PLANTA 2019; 249:457-468. [PMID: 30251012 DOI: 10.1007/s00425-018-3015-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/20/2018] [Indexed: 05/10/2023]
Abstract
MAIN CONCLUSION In this study, we show that aberrant pre-mRNAs from non-spliced and non-polyadenylated intron-containing transgenes are channelled to the RNA silencing pathway. In plants, improperly processed transcripts are called aberrant RNAs (ab-RNAs) and are eliminated by either RNA silencing or RNA decay mechanisms. Ab-RNAs transcribed from intronless genes are copied by RNA-directed RNA polymerases (RDRs) into double-stranded RNAs which are subsequently cleaved by DICER-LIKE endonucleases into small RNAs (sRNAs). In contrast, ab-RNAs from intron-containing genes are suggested to be channelled post-splicing to exonucleolytic degradation. Yet, it is not clear how non-spliced aberrant pre-mRNAs are eliminated. We reasoned that transient expression of agroinfiltrated intron-containing transgenes in Nicotiana benthamiana would allow us to study the steady-state levels of non-spliced pre-mRNAs. SRNA deep sequencing of the agroinfiltrated transgenes revealed the presence of sRNAs mapping to the entire non-spliced pre-mRNA suggesting that RDRs (most likely RDR6) processed aberrant non-spliced pre-mRNAs. Primary and secondary sRNAs with lengths of 18-25 nucleotides (nt) were detected, with the most prominent sRNA size class of 22 nt. SRNAs also mapped to the terminator sequence, indicating that RDR substrates also comprised read-through transcripts devoid of polyadenylation tail. Importantly, the occurring sRNAs efficiently targeted cognate mRNA for degradation but failed to cleave the non-spliced pre-mRNA, corroborating the notion that sRNAs are not triggering RNA cleavage in the nucleus.
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Affiliation(s)
- Athanasios Dalakouras
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, 67435, Neustadt, Germany.
- Institute of Plant Breeding and Genetic Resources ELGO-DEMETER, 57001, Thessaloniki, Greece.
| | - Anja Lauter
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, 67435, Neustadt, Germany
| | - Alexandra Bassler
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, 67435, Neustadt, Germany
| | - Gabi Krczal
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, 67435, Neustadt, Germany
| | - Michael Wassenegger
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, 67435, Neustadt, Germany.
- Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, 69120, Heidelberg, Germany.
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19
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Ma Z, Castillo-González C, Wang Z, Sun D, Hu X, Shen X, Potok ME, Zhang X. Arabidopsis Serrate Coordinates Histone Methyltransferases ATXR5/6 and RNA Processing Factor RDR6 to Regulate Transposon Expression. Dev Cell 2018; 45:769-784.e6. [PMID: 29920280 DOI: 10.1016/j.devcel.2018.05.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 04/04/2018] [Accepted: 05/20/2018] [Indexed: 12/25/2022]
Abstract
Serrate (SE) is a key component in RNA metabolism. Little is known about whether and how it can regulate epigenetic silencing. Here, we report histone methyltransferases ATXR5 and ATXR6 (ATXR5/6) as novel partners of SE. ATXR5/6 deposit histone 3 lysine 27 monomethylation (H3K27me1) to promote heterochromatin formation, repress transposable elements (TEs), and control genome stability in Arabidopsis. SE binds to ATXR5/6-regulated TE loci and promotes H3K27me1 accumulation in these regions. Furthermore, SE directly enhances ATXR5 enzymatic activity in vitro. Unexpectedly, se mutation suppresses the TE reactivation and DNA re-replication phenotypes in the atxr5 atxr6 mutant. The suppression of TE expression results from triggering RNA-dependent RNA polymerase 6 (RDR6)-dependent RNA silencing in the se atxr5 atxr6 mutant. We propose that SE facilitates ATXR5/6-mediated deposition of the H3K27me1 mark while inhibiting RDR6-mediated RNA silencing to protect TE transcripts. Hence, SE coordinates epigenetic silencing and RNA processing machineries to fine-tune the TE expression.
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Affiliation(s)
- Zeyang Ma
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Zhiye Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Di Sun
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Xiaomei Hu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Xuefeng Shen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA; College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Magdalena E Potok
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
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20
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Montavon T, Kwon Y, Zimmermann A, Hammann P, Vincent T, Cognat V, Michel F, Dunoyer P. A specific dsRNA-binding protein complex selectively sequesters endogenous inverted-repeat siRNA precursors and inhibits their processing. Nucleic Acids Res 2017; 45:1330-1344. [PMID: 28180322 PMCID: PMC5388410 DOI: 10.1093/nar/gkw1264] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/01/2016] [Accepted: 12/06/2016] [Indexed: 01/03/2023] Open
Abstract
In plants, several dsRNA-binding proteins (DRBs) have been shown to play important roles in various RNA silencing pathways, mostly by promoting the efficiency and/or accuracy of Dicer-like proteins (DCL)-mediated small RNA production. Among the DRBs encoded by the Arabidopsis genome, we recently identified DRB7.2 whose function in RNA silencing was unknown. Here, we show that DRB7.2 is specifically involved in siRNA production from endogenous inverted-repeat (endoIR) loci. This function requires its interacting partner DRB4, the main cofactor of DCL4 and is achieved through specific sequestration of endoIR dsRNA precursors, thereby repressing their access and processing by the siRNA-generating DCLs. The present study also provides multiple lines of evidence showing that DRB4 is partitioned into, at least, two distinct cellular pools fulfilling different functions, through mutually exclusive binding with either DCL4 or DRB7.2. Collectively, these findings revealed that plants have evolved a specific DRB complex that modulates selectively the production of endoIR-siRNAs. The existence of such a complex and its implication regarding the still elusive biological function of plant endoIR-siRNA will be discussed.
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Affiliation(s)
- Thomas Montavon
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000 Strasbourg, France
| | - Yerim Kwon
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000 Strasbourg, France
| | - Aude Zimmermann
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000 Strasbourg, France
| | - Philippe Hammann
- Université de Strasbourg, CNRS, IBMC FRC1589, Plateforme Protéomique Strasbourg - Esplanade, F-67000 Strasbourg, France
| | - Timothée Vincent
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000 Strasbourg, France
| | - Valérie Cognat
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000 Strasbourg, France
| | - Fabrice Michel
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000 Strasbourg, France
| | - Patrice Dunoyer
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000 Strasbourg, France
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21
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Kwarteng A, Ahuno ST, Kwakye-Nuako G. The therapeutic landscape of HIV-1 via genome editing. AIDS Res Ther 2017; 14:32. [PMID: 28705213 PMCID: PMC5513397 DOI: 10.1186/s12981-017-0157-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 05/30/2017] [Indexed: 12/31/2022] Open
Abstract
Current treatment for HIV-1 largely relies on chemotherapy through the administration of antiretroviral drugs. While the search for anti-HIV-1 vaccine remain elusive, the use of highly active antiretroviral therapies (HAART) have been far-reaching and has changed HIV-1 into a manageable chronic infection. There is compelling evidence, including several side-effects of ARTs, suggesting that eradication of HIV-1 cannot depend solely on antiretrovirals. Gene therapy, an expanding treatment strategy, using RNA interference (RNAi) and programmable nucleases such as meganuclease, zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR-Cas9) are transforming the therapeutic landscape of HIV-1. TALENS and ZFNS are structurally similar modular systems, which consist of a FokI endonuclease fused to custom-designed effector proteins but have been largely limited, particularly ZFNs, due to their complexity and cost of protein engineering. However, the newly developed CRISPR-Cas9 system, consists of a single guide RNA (sgRNA), which directs a Cas9 endonuclease to complementary target sites, and serves as a superior alternative to the previous protein-based systems. The techniques have been successfully applied to the development of better HIV-1 models, generation of protective mutations in endogenous/host cells, disruption of HIV-1 genomes and even reactivating latent viruses for better detection and clearance by host immune response. Here, we focus on gene editing-based HIV-1 treatment and research in addition to providing perspectives for refining these techniques.
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Affiliation(s)
- Alexander Kwarteng
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), PMB, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Samuel Terkper Ahuno
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), PMB, Kumasi, Ghana
| | - Godwin Kwakye-Nuako
- Department of Biomedical Sciences, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
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22
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Barton DA, Roovers EF, Gouil Q, da Fonseca GC, Reis RS, Jackson C, Overall RL, Fusaro AF, Waterhouse PM. Live Cell Imaging Reveals the Relocation of dsRNA Binding Proteins Upon Viral Infection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:435-443. [PMID: 28296575 DOI: 10.1094/mpmi-02-17-0035-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Viral infection triggers a range of plant responses such as the activation of the RNA interference (RNAi) pathway. The double-stranded RNA binding (DRB) proteins DRB3 and DRB4 are part of this pathway and aid in defending against DNA and RNA viruses, respectively. Using live cell imaging, we show that DRB2, DRB3, and DRB5 relocate from their uniform cytoplasmic distribution to concentrated accumulation in nascent viral replication complexes (VRC) that develop following cell invasion by viral RNA. Inactivation of the DRB3 gene in Arabidopsis by T-DNA insertion rendered these plants less able to repress RNA viral replication. We propose a model for the early stages of virus defense in which DRB2, DRB3, and DRB5 are invasion sensors that relocate to nascent VRC, where they bind to viral RNA and inhibit virus replication.
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Affiliation(s)
| | - Elke F Roovers
- 1 University of Sydney, Sydney, NSW, 2006, Australia
- 2 Institute of Molecular Biology, Mainz, Germany
| | - Quentin Gouil
- 1 University of Sydney, Sydney, NSW, 2006, Australia
- 3 Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Victoria 3086
| | - Guilherme C da Fonseca
- 1 University of Sydney, Sydney, NSW, 2006, Australia
- 4 Universidade Federal do Rio Grande do Sul, RS, Brazil; and
| | | | - Craig Jackson
- 1 University of Sydney, Sydney, NSW, 2006, Australia
| | | | | | - Peter M Waterhouse
- 1 University of Sydney, Sydney, NSW, 2006, Australia
- 5 Queensland University of Technology, Brisbane, QLD, Australia
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23
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Pumplin N, Sarazin A, Jullien PE, Bologna NG, Oberlin S, Voinnet O. DNA Methylation Influences the Expression of DICER-LIKE4 Isoforms, Which Encode Proteins of Alternative Localization and Function. THE PLANT CELL 2016; 28:2786-2804. [PMID: 27956586 PMCID: PMC5155348 DOI: 10.1105/tpc.16.00554] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/21/2016] [Accepted: 11/12/2016] [Indexed: 05/08/2023]
Abstract
Plant RNA silencing operates via RNA-directed DNA-methylation (RdDM) to repress transcription or by targeting mRNAs via posttranscriptional gene silencing (PTGS). These pathways rely on distinct Dicer-like (DCL) proteins that process double-stranded RNA (dsRNA) into small-interfering RNAs (siRNAs). Here, we explored the expression and subcellular localization of Arabidopsis thaliana DCL4. DCL4 expression predominates as a transcription start site isoform encoding a cytoplasmic protein, which also represents the ancestral form in plants. A longer DCL4 transcript isoform encoding a nuclear localization signal, DCL4NLS, is present in Arabidopsis, but DNA methylation normally suppresses its expression. Hypomethylation caused by mutation, developmental reprogramming, and biotic stress correlates with enhanced DCL4NLS expression, while hypermethylation of a DCL4 transgene causes a reduction in DCL4NLS expression. DCL4NLS functions in a noncanonical siRNA pathway, producing a unique set of 21-nucleotide-long "disiRNAs," for DCL4NLS isoform-dependent siRNAs, through the nuclear RdDM dsRNA synthesis pathway. disiRNAs originate mostly from transposable elements (TEs) and TE-overlapping/proximal genes, load into the PTGS effector ARGONAUTE1 (AGO1), and display a subtle effect on transcript accumulation together with overlapping 24-nucleotide siRNAs. We propose that, via PTGS, disiRNAs could help to tighten the expression of epigenetically activated TEs and genes using the methylation-state-responsive DCL4NLS.
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Affiliation(s)
- Nathan Pumplin
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Alexis Sarazin
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | | | | | - Stefan Oberlin
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
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24
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Guo Q, Liu Q, Smith NA, Liang G, Wang MB. RNA Silencing in Plants: Mechanisms, Technologies and Applications in Horticultural Crops. Curr Genomics 2016; 17:476-489. [PMID: 28217004 PMCID: PMC5108043 DOI: 10.2174/1389202917666160520103117] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 11/30/2015] [Accepted: 12/03/2015] [Indexed: 12/20/2022] Open
Abstract
Understanding the fundamental nature of a molecular process or a biological pathway is often a catalyst for the development of new technologies in biology. Indeed, studies from late 1990s to early 2000s have uncovered multiple overlapping but functionally distinct RNA silencing pathways in plants, including the posttranscriptional microRNA and small interfering RNA pathways and the transcriptional RNA-directed DNA methylation pathway. These findings have in turn been exploited for developing artificial RNA silencing technologies such as hairpin RNA, artificial microRNA, intrinsic direct repeat, 3' UTR inverted repeat, artificial trans-acting siRNA, and virus-induced gene silencing technologies. Some of these RNA silencing technologies, such as the hairpin RNA technology, have already been widely used for genetic improvement of crop plants in agriculture. For horticultural plants, RNA silencing technologies have been used to increase disease and pest resistance, alter plant architecture and flowering time, improve commercial traits of fruits and flowers, enhance nutritional values, remove toxic compounds and allergens, and develop high-value industrial products. In this article we aim to provide an overview of the RNA silencing pathways in plants, summarize the existing RNA silencing technologies, and review the current progress in applying these technologies for the improvement of agricultural crops particularly horticultural crops.
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Affiliation(s)
- Qigao Guo
- College of Horticulture & Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Qing Liu
- Commonwealth Scientific and Industrial Research Organisation Agriculture (CSIRO), ACT 2601, Australia
| | - Neil A Smith
- Commonwealth Scientific and Industrial Research Organisation Agriculture (CSIRO), ACT 2601, Australia
| | - Guolu Liang
- College of Horticulture & Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Ming-Bo Wang
- Commonwealth Scientific and Industrial Research Organisation Agriculture (CSIRO), ACT 2601, Australia
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25
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Weinheimer I, Haikonen T, Ala-Poikela M, Moser M, Streng J, Rajamäki ML, Valkonen JPT. Viral RNase3 Co-Localizes and Interacts with the Antiviral Defense Protein SGS3 in Plant Cells. PLoS One 2016; 11:e0159080. [PMID: 27391019 PMCID: PMC4938523 DOI: 10.1371/journal.pone.0159080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/27/2016] [Indexed: 11/23/2022] Open
Abstract
Sweet potato chlorotic stunt virus (SPCSV; family Closteroviridae) encodes a Class 1 RNase III endoribonuclease (RNase3) that suppresses post-transcriptional RNA interference (RNAi) and eliminates antiviral defense in sweetpotato plants (Ipomoea batatas). For RNAi suppression, RNase3 cleaves double-stranded small interfering RNAs (ds-siRNA) and long dsRNA to fragments that are too short to be utilized in RNAi. However, RNase3 can suppress only RNAi induced by sense RNA. Sense-mediated RNAi involves host suppressor of gene silencing 3 (SGS3) and RNA–dependent RNA polymerase 6 (RDR6). In this study, subcellular localization and host interactions of RNase3 were studied in plant cells. RNase3 was found to interact with SGS3 of sweetpotato and Arabidopsis thaliana when expressed in leaves, and it localized to SGS3/RDR6 bodies in the cytoplasm of leaf cells and protoplasts. RNase3 was also detected in the nucleus. Co-expression of RNase3 and SGS3 in leaf tissue enhanced the suppression of RNAi, as compared with expression of RNase3 alone. These results suggest additional mechanisms needed for efficient RNase3-mediated suppression of RNAi and provide new information about the subcellular context and phase of the RNAi pathway in which RNase3 realizes RNAi suppression.
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Affiliation(s)
- Isabel Weinheimer
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Tuuli Haikonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Marjo Ala-Poikela
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | | | - Janne Streng
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Minna-Liisa Rajamäki
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Jari P. T. Valkonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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26
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Liu L, Chen X. RNA Quality Control as a Key to Suppressing RNA Silencing of Endogenous Genes in Plants. MOLECULAR PLANT 2016; 9:826-36. [PMID: 27045817 PMCID: PMC5123867 DOI: 10.1016/j.molp.2016.03.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 05/19/2023]
Abstract
RNA quality control of endogenous RNAs is an integral part of eukaryotic gene expression and often relies on exonucleolytic degradation to eliminate dysfunctional transcripts. In parallel, exogenous and selected endogenous RNAs are degraded through RNA silencing, which is a genome defense mechanism used by many eukaryotes. In plants, RNA silencing is triggered by the production of double-stranded RNAs (dsRNAs) by RNA-DEPENDENT RNA POLYMERASEs (RDRs) and proceeds through small interfering (si) RNA-directed, ARGONAUTE (AGO)-mediated cleavage of homologous transcripts. Many studies revealed that plants avert inappropriate posttranscriptional gene silencing of endogenous coding genes by using RNA surveillance mechanisms as a safeguard to protect their transcriptome profiles. The tug of war between RNA surveillance and RNA silencing ensures the appropriate partitioning of endogenous RNA substrates among these degradation pathways. Here we review recent advances on RNA quality control and its role in the suppression of RNA silencing at endogenous genes and discuss the mechanisms underlying the crosstalk among these pathways.
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Affiliation(s)
- Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Howard Hughes Medical Institute, University of California, Riverside, CA 92521, USA.
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27
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Design, simplified cloning, and in-silico analysis of multisite small interfering RNA-targeting cassettes. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2016; 5:31-43. [PMID: 27844018 PMCID: PMC5019331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Multiple gene silencing is being required to target and tangle metabolic pathways in eukaryotes and researchers have to develop a subtle method for construction of RNA interference (RNAi) cassettes. Although, several vectors have been developed due to different screening and cloning strategies but still some potential limitations remain to be dissolved. Here, we worked out a simple cloning strategy to develop multisite small interfering RNA (siRNA) cassette from different genes by two cloning steps. In this method, effective siRNA sites in the target messenger RNAs (mRNAs) were determined using in silico analysis and consecutively arranged to reduce length of inverted repeats. Here, we used one-step (polymerase chain reaction) PCR by designed long primer sets covering the selected siRNA sites. Rapid screening, cost-effective and shorten procedure are advantages of this method compare to PCR classic cloning. Validity of constructs was confirmed by optimal centroid secondary structures with high stability in plants.
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28
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Kotakis C. Non-coding RNAs' partitioning in the evolution of photosynthetic organisms via energy transduction and redox signaling. RNA Biol 2015; 12:101-4. [PMID: 25826417 DOI: 10.1080/15476286.2015.1017201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Ars longa, vita brevis -Hippocrates Chloroplasts and mitochondria are genetically semi-autonomous organelles inside the plant cell. These constructions formed after endosymbiosis and keep evolving throughout the history of life. Experimental evidence is provided for active non-coding RNAs (ncRNAs) in these prokaryote-like structures, and a possible functional imprinting on cellular electrophysiology by those RNA entities is described. Furthermore, updated knowledge on RNA metabolism of organellar genomes uncovers novel inter-communication bridges with the nucleus. This class of RNA molecules is considered as a unique ontogeny which transforms their biological role as a genetic rheostat into a synchronous biochemical one that can affect the energetic charge and redox homeostasis inside cells. A hypothesis is proposed where such modulation by non-coding RNAs is integrated with genetic signals regulating gene transfer. The implications of this working hypothesis are discussed, with particular reference to ncRNAs involvement in the organellar and nuclear genomes evolution since their integrity is functionally coupled with redox signals in photosynthetic organisms.
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Affiliation(s)
- Christos Kotakis
- a Agro-environmental cooperative BioNet West Hellas ; Gastouni Ileias, Hellas , Greece
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29
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Machida C, Nakagawa A, Kojima S, Takahashi H, Machida Y. The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 4:655-71. [PMID: 26108442 PMCID: PMC4744985 DOI: 10.1002/wdev.196] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/23/2015] [Accepted: 05/12/2015] [Indexed: 01/17/2023]
Abstract
Leaf primordia are born around meristem‐containing stem cells at shoot apices, grow along three axes (proximal–distal, adaxial–abaxial, medial–lateral), and develop into flat symmetric leaves with adaxial–abaxial polarity. Axis development and polarity specification of Arabidopsis leaves require a network of genes for transcription factor‐like proteins and small RNAs. Here, we summarize present understandings of adaxial‐specific genes, ASYMMETRIC LEAVES1 (AS1) and AS2. Their complex (AS1–AS2) functions in the regulation of the proximal–distal leaf length by directly repressing class 1 KNOX homeobox genes (BP, KNAT2) that are expressed in the meristem periphery below leaf primordia. Adaxial–abaxial polarity specification involves antagonistic interaction of adaxial and abaxial genes including AS1 and AS2 for the development of two respective domains. AS1–AS2 directly represses the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3) and indirectly represses ETT/ARF3 and ARF4 through tasiR‐ARF. Modifier mutations have been identified that abolish adaxialization and enhance the defect in the proximal–distal patterning in as1 and as2. AS1–AS2 and its modifiers synergistically repress both ARFs and class 1 KNOXs. Repression of ARFs is critical for establishing adaxial–abaxial polarity. On the other hand, abaxial factors KANADI1 (KAN1) and KAN2 directly repress AS2 expression. These data delineate a molecular framework for antagonistic gene interactions among adaxial factors, AS1, AS2, and their modifiers, and the abaxial factors ARFs as key regulators in the establishment of adaxial–abaxial polarity. Possible AS1–AS2 epigenetic repression and activities downstream of ARFs are discussed. WIREs Dev Biol 2015, 4:655–671. doi: 10.1002/wdev.196 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Ayami Nakagawa
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Chiba, Japan
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30
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Kumar S, Bhatia S. Isolation of Catharanthus roseus (L.) G. Don Nuclei and Measurement of Rate of Tryptophan decarboxylase Gene Transcription Using Nuclear Run-On Transcription Assay. PLoS One 2015; 10:e0127892. [PMID: 26024519 PMCID: PMC4449189 DOI: 10.1371/journal.pone.0127892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 04/21/2015] [Indexed: 11/27/2022] Open
Abstract
Background An accurate assessment of transcription ‘rate’ is often desired to describe the promoter activity. In plants, isolation of transcriptionally active nuclei and their subsequent use in nuclear run-on assays has been challenging and therefore limit an accurate measurement of gene transcription ‘rate’. Catharanthus roseus has emerged as a model medicinal plant as it exhibits an unsurpassed spectrum of chemodiversity, producing over 130 alkaloids through the terpenoid indole alkaloid (TIA) pathway and therefore serves as a ‘molecular hub’ to understand gene expression profiles. Results The protocols presented here streamline, adapt and optimize the existing methods of nuclear run-on assay for use in C. roseus. Here, we fully describe all the steps to isolate transcriptionally active nuclei from C. roseus leaves and utilize them to perform nuclear run-on transcription assay. Nuclei isolated by this method transcribed at a level consistent with their response to external stimuli, as transcription rate of TDC gene was found to be higher in response to external stimuli i.e. when seedlings were subjected to UV-B light or to methyl jasmonate (MeJA). However, the relative transcript abundance measured parallel through qRT-PCR was found to be inconsistent with the synthesis rate indicating that some post transcriptional events might have a role in transcript stability in response to stimuli. Conclusions Our study provides an optimized, efficient and inexpensive method of isolation of intact nuclei and nuclear ‘run-on’ transcription assay to carry out in-situ measurement of gene transcription rate in Catharanthus roseus. This would be valuable in investigating the transcriptional and post transcriptional response of other TIA pathway genes in C. roseus. Isolated nuclei may also provide a resource that could be used for performing the chip assay as well as serve as the source of nuclear proteins for in-vitro EMSA studies. Moreover, nascent nuclear run-on transcript could be further subjected to RNA-Seq for global nuclear run-on assay (GNRO-Seq) for genome wide in-situ measurement of transcription rate of plant genes.
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Affiliation(s)
- Santosh Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi, 110067, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi, 110067, India
- * E-mail:
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31
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García R, Nistal JF, Merino D, Price NL, Fernández-Hernando C, Beaumont J, González A, Hurlé MA, Villar AV. p-SMAD2/3 and DICER promote pre-miR-21 processing during pressure overload-associated myocardial remodeling. Biochim Biophys Acta Mol Basis Dis 2015; 1852:1520-30. [PMID: 25887159 DOI: 10.1016/j.bbadis.2015.04.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 03/23/2015] [Accepted: 04/07/2015] [Indexed: 12/21/2022]
Abstract
Transforming growth factor-β (TGF-β) induces miR-21 expression which contributes to fibrotic events in the left ventricle (LV) under pressure overload. SMAD effectors of TGF-β signaling interact with DROSHA to promote primary miR-21 processing into precursor miR-21 (pre-miR-21). We hypothesize that p-SMAD-2 and -3 also interact with DICER1 to regulate the processing of pre-miR-21 to mature miR-21 in cardiac fibroblasts under experimental and clinical pressure overload. The subjects of the study were mice undergoing transverse aortic constriction (TAC) and patients with aortic stenosis (AS). In vitro, NIH-3T3 fibroblasts transfected with pre-miR-21 responded to TGF-β1 stimulation by overexpressing miR-21. Overexpression and silencing of SMAD2/3 resulted in higher and lower production of mature miR-21, respectively. DICER1 co-precipitated along with SMAD2/3 and both proteins were up-regulated in the LV from TAC-mice. Pre-miR-21 was isolated bound to the DICER1 maturation complex. Immunofluorescence analysis revealed co-localization of p-SMAD2/3 and DICER1 in NIH-3T3 and mouse cardiac fibroblasts. DICER1-p-SMAD2/3 protein-protein interaction was confirmed by in situ proximity ligation assay. Myocardial up-regulation of DICER1 constituted a response to pressure overload in TAC-mice. DICER mRNA levels correlated directly with those of TGF-β1, SMAD2 and SMAD3. In the LV from AS patients, DICER mRNA was up-regulated and its transcript levels correlated directly with TGF-β1, SMAD2, and SMAD3. Our results support that p-SMAD2/3 interacts with DICER1 to promote pre-miR-21 processing to mature miR-21. This new TGFβ-dependent regulatory mechanism is involved in miR-21 overexpression in cultured fibroblasts, and in the pressure overloaded LV of mice and human patients.
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Affiliation(s)
- Raquel García
- Departamento de Fisiología y Farmacología, Facultad de Medicina, Universidad de Cantabria, Santander, Spain; Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - J Francisco Nistal
- Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain; Servicio de Cirugía Cardiovascular, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - David Merino
- Departamento de Fisiología y Farmacología, Facultad de Medicina, Universidad de Cantabria, Santander, Spain; Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Nathan L Price
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA; Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Carlos Fernández-Hernando
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA; Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Javier Beaumont
- Programa de Enfermedades Cardiovasculares, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
| | - Arantxa González
- Programa de Enfermedades Cardiovasculares, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
| | - María A Hurlé
- Departamento de Fisiología y Farmacología, Facultad de Medicina, Universidad de Cantabria, Santander, Spain; Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain.
| | - Ana V Villar
- Departamento de Fisiología y Farmacología, Facultad de Medicina, Universidad de Cantabria, Santander, Spain; Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
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32
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Dalakouras A, Dadami E, Bassler A, Zwiebel M, Krczal G, Wassenegger M. Replicating Potato spindle tuber viroid mediates de novo methylation of an intronic viroid sequence but no cleavage of the corresponding pre-mRNA. RNA Biol 2015; 12:268-75. [PMID: 25826660 PMCID: PMC4615544 DOI: 10.1080/15476286.2015.1017216] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 01/05/2015] [Accepted: 01/05/2015] [Indexed: 10/23/2022] Open
Abstract
In plants, Potato spindle tuber viroid (PSTVd) replication triggers post-transcriptional gene silencing (PTGS) and RNA-directed DNA methylation (RdDM) of homologous RNA and DNA sequences, respectively. PTGS predominantly occurs in the cytoplasm, but nuclear PTGS has been also reported. In this study, we investigated whether the nuclear replicating PSTVd is able to trigger nuclear PTGS. Transgenic tobacco plants carrying cytoplasmic and nuclear PTGS sensor constructs were PSTVd-infected resulting in the generation of abundant PSTVd-derived small interfering RNAs (vd-siRNAs). Northern blot analysis revealed that, in contrast to the cytoplasmic sensor, the nuclear sensor transcript was not targeted for RNA degradation. Bisulfite sequencing analysis showed that the nuclear PTGS sensor transgene was efficiently targeted for RdDM. Our data suggest that PSTVd fails to trigger nuclear PTGS, and that RdDM and nuclear PTGS are not necessarily coupled.
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Affiliation(s)
| | - Elena Dadami
- RLP AgroScience GmbH; AlPlanta-Institute for Plant Research; Neustadt, Germany
| | - Alexandra Bassler
- RLP AgroScience GmbH; AlPlanta-Institute for Plant Research; Neustadt, Germany
| | - Michele Zwiebel
- RLP AgroScience GmbH; AlPlanta-Institute for Plant Research; Neustadt, Germany
| | - Gabi Krczal
- RLP AgroScience GmbH; AlPlanta-Institute for Plant Research; Neustadt, Germany
| | - Michael Wassenegger
- RLP AgroScience GmbH; AlPlanta-Institute for Plant Research; Neustadt, Germany
- Centre for Organismal Studies (COS) Heidelberg; University of Heidelberg; Heidelberg, Germany
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Wroblewski T, Matvienko M, Piskurewicz U, Xu H, Martineau B, Wong J, Govindarajulu M, Kozik A, Michelmore RW. Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways in Arabidopsis. RNA (NEW YORK, N.Y.) 2014; 20:1987-99. [PMID: 25344399 PMCID: PMC4238362 DOI: 10.1261/rna.046532.114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The experimental induction of RNA silencing in plants often involves expression of transgenes encoding inverted repeat (IR) sequences to produce abundant dsRNAs that are processed into small RNAs (sRNAs). These sRNAs are key mediators of post-transcriptional gene silencing (PTGS) and determine its specificity. Despite its application in agriculture and broad utility in plant research, the mechanism of IR-PTGS is incompletely understood. We generated four sets of 60 Arabidopsis plants, each containing IR transgenes expressing different configurations of uidA and CHALCONE Synthase (At-CHS) gene fragments. Levels of PTGS were found to depend on the orientation and position of the fragment in the IR construct. Deep sequencing and mapping of sRNAs to corresponding transgene-derived and endogenous transcripts identified distinctive patterns of differential sRNA accumulation that revealed similarities among sRNAs associated with IR-PTGS and endogenous sRNAs linked to uncapped mRNA decay. Detailed analyses of poly-A cleavage products from At-CHS mRNA confirmed this hypothesis. We also found unexpected associations between sRNA accumulation and the presence of predicted open reading frames in the trigger sequence. In addition, strong IR-PTGS affected the prevalence of endogenous sRNAs, which has implications for the use of PTGS for experimental or applied purposes.
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Affiliation(s)
- Tadeusz Wroblewski
- The Genome Center, University of California, Davis, Davis, California 95616, USA
| | - Marta Matvienko
- The Genome Center, University of California, Davis, Davis, California 95616, USA
| | - Urszula Piskurewicz
- The Genome Center, University of California, Davis, Davis, California 95616, USA
| | - Huaqin Xu
- The Genome Center, University of California, Davis, Davis, California 95616, USA
| | - Belinda Martineau
- The Genome Center, University of California, Davis, Davis, California 95616, USA
| | - Joan Wong
- The Genome Center, University of California, Davis, Davis, California 95616, USA
| | | | - Alexander Kozik
- The Genome Center, University of California, Davis, Davis, California 95616, USA
| | - Richard W Michelmore
- The Genome Center, University of California, Davis, Davis, California 95616, USA Department of Plant Science, University of California, Davis, Davis, California 95616, USA Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616, USA Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California 95616, USA
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Abstract
The study of epigenetics in plants has a long and rich history, from initial descriptions of non-Mendelian gene behaviors to seminal discoveries of chromatin-modifying proteins and RNAs that mediate gene silencing in most eukaryotes, including humans. Genetic screens in the model plant Arabidopsis have been particularly rewarding, identifying more than 130 epigenetic regulators thus far. The diversity of epigenetic pathways in plants is remarkable, presumably contributing to the phenotypic plasticity of plant postembryonic development and the ability to survive and reproduce in unpredictable environments.
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Affiliation(s)
- Craig S Pikaard
- Department of Biology, Department of Molecular and Cellular Biochemistry, and Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana 47405
| | - Ortrun Mittelsten Scheid
- Gregor Mendel-Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
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Abstract
The study of epigenetics in plants has a long and rich history, from initial descriptions of non-Mendelian gene behaviors to seminal discoveries of chromatin-modifying proteins and RNAs that mediate gene silencing in most eukaryotes, including humans. Genetic screens in the model plant Arabidopsis have been particularly rewarding, identifying more than 130 epigenetic regulators thus far. The diversity of epigenetic pathways in plants is remarkable, presumably contributing to the phenotypic plasticity of plant postembryonic development and the ability to survive and reproduce in unpredictable environments.
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Affiliation(s)
- Craig S Pikaard
- Department of Biology, Department of Molecular and Cellular Biochemistry, and Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana 47405
| | - Ortrun Mittelsten Scheid
- Gregor Mendel-Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
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Dang TVT, Windelinckx S, Henry IM, De Coninck B, Cammue BPA, Swennen R, Remy S. Assessment of RNAi-induced silencing in banana (Musa spp.). BMC Res Notes 2014; 7:655. [PMID: 25230584 PMCID: PMC4177175 DOI: 10.1186/1756-0500-7-655] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 09/11/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND In plants, RNA- based gene silencing mediated by small RNAs functions at the transcriptional or post-transcriptional level to negatively regulate target genes, repetitive sequences, viral RNAs and/or transposon elements. Post-transcriptional gene silencing (PTGS) or the RNA interference (RNAi) approach has been achieved in a wide range of plant species for inhibiting the expression of target genes by generating double-stranded RNA (dsRNA). However, to our knowledge, successful RNAi-application to knock-down endogenous genes has not been reported in the important staple food crop banana. RESULTS Using embryogenic cell suspension (ECS) transformed with ß-glucuronidase (GUS) as a model system, we assessed silencing of gusAINT using three intron-spliced hairpin RNA (ihpRNA) constructs containing gusAINT sequences of 299-nt, 26-nt and 19-nt, respectively. Their silencing potential was analysed in 2 different experimental set-ups. In the first, Agrobacterium-mediated co-transformation of banana ECS with a gusAINT containing vector and an ihpRNA construct resulted in a significantly reduced GUS enzyme activity 6-8 days after co-cultivation with either the 299-nt and 19-nt ihpRNA vectors. In the second approach, these ihpRNA constructs were transferred to stable GUS-expressing ECS and their silencing potential was evaluated in the regenerated in vitro plants. In comparison to control plants, transgenic plants transformed with the 299-nt gusAINT targeting sequence showed a 4.5 fold down-regulated gusA mRNA expression level, while GUS enzyme activity was reduced by 9 fold. Histochemical staining of plant tissues confirmed these findings. Northern blotting used to detect the expression of siRNA in the 299-nt ihpRNA vector transgenic in vitro plants revealed a negative relationship between siRNA expression and GUS enzyme activity. In contrast, no reduction in GUS activity or GUS mRNA expression occurred in the regenerated lines transformed with either of the two gusAINT oligo target sequences (26-nt and 19-nt). CONCLUSIONS RNAi-induced silencing was achieved in banana, both at transient and stable level, resulting in significant reduction of gene expression and enzyme activity. The success of silencing was dependent on the targeted region of the target gene. The successful generation of transgenic ECS for second transformation with (an)other construct(s) can be of value for functional genomics research in banana.
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MESH Headings
- Cell Line, Transformed
- Feasibility Studies
- Gene Expression Regulation, Plant
- Gene Knockdown Techniques
- Glucuronidase/genetics
- Glucuronidase/metabolism
- Musa/embryology
- Musa/enzymology
- Musa/genetics
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plants, Genetically Modified/embryology
- Plants, Genetically Modified/enzymology
- Plants, Genetically Modified/genetics
- RNA Interference
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Time Factors
- Transfection
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Affiliation(s)
- Tuong Vi T Dang
- />Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Saskia Windelinckx
- />Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Isabelle M Henry
- />Department of Plant Biology and Genome Center, U.C.Davis, 451 E. Health Sciences Drive, Davis, CA 95616 USA
| | - Barbara De Coninck
- />Center of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- />Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium
| | - Bruno PA Cammue
- />Center of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- />Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium
| | - Rony Swennen
- />Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- />Bioversity International, Willem de Croylaan 42 bus 2455, 3001 Leuven, Belgium
- />International Institute of Tropical Agriculture, P.O. Box 10, Duluti, Arusha, Tanzania
| | - Serge Remy
- />Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
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Import routes and nuclear functions of Argonaute and other small RNA-silencing proteins. Trends Biochem Sci 2014; 39:420-31. [DOI: 10.1016/j.tibs.2014.07.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/16/2014] [Accepted: 07/16/2014] [Indexed: 02/06/2023]
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38
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Connecting the dots of RNA-directed DNA methylation in Arabidopsis thaliana. Chromosome Res 2014; 22:225-40. [PMID: 24846724 DOI: 10.1007/s10577-014-9425-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Noncoding RNAs are the rising stars of genome regulation and are crucial to an organism's metabolism, development, and defense. One of their most notable functions is its ability to direct epigenetic modifications through small RNA molecules to specific genomic regions, ensuring transcriptional regulation, proper genome organization, and maintenance of genome integrity. Here, we review the current knowledge of the spatial organization of the Arabidopsis thaliana RNA-directed DNA methylation pathway within the cell nucleus, which, while known to be essential for the proper establishment of epigenetic modifications, remains poorly understood. We will also discuss possible future cytological approaches that have the potential of unveiling functional insights into how small RNA-directed epigenetics is regulated through the spatiotemporal regulation of its major components within the cell.
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Butt H, Graner S, Luschnig C. Expression analysis of Arabidopsis XH/XS-domain proteins indicates overlapping and distinct functions for members of this gene family. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1217-27. [PMID: 24574485 PMCID: PMC3935573 DOI: 10.1093/jxb/ert480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
RNA-directed DNA methylation (RdDM) is essential for de novo DNA methylation in higher plants, and recent reports established novel elements of this silencing pathway in the model organism Arabidopsis thaliana. Involved in de novo DNA methylation 2 (IDN2) and the closely related factor of DNA methylation (FDM) are members of a plant-specific family of dsRNA-binding proteins characterized by conserved XH/XS domains and implicated in the regulation of RdDM at chromatin targets. Genetic analyses have suggested redundant as well as non-overlapping activities for different members of the gene family. However, detailed insights into the function of XH/XS-domain proteins are still elusive. By the generation and analysis of higher-order mutant combinations affected in IDN2 and further members of the gene family, we have provided additional evidence for their redundant activity. Distinct roles for members of the XH/XS-domain gene family were indicated by differences in their expression and subcellular localization. Fluorescent protein-tagged FDM genes were expressed either in nuclei or in the cytoplasm, suggestive of activities of XH/XS-domain proteins in association with chromatin as well as outside the nuclear compartment. In addition, we observed altered location of a functional FDM1-VENUS reporter from the nucleus into the cytoplasm under conditions when availability of further FDM proteins was limited. This is suggestive of a mechanism by which redistribution of XH/XS-domain proteins could compensate for the loss of closely related proteins.
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Affiliation(s)
- Haroon Butt
- * Present Address: Department of Biological Sciences, Forman Christian College, Ferozepur Road, Lahore 54600, Pakistan
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40
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Shin MR, Natsuume M, Matsumoto T, Hanaoka M, Imai M, Iijima K, Oka SI, Adachi E, Kodama H. Sense transgene-induced post-transcriptional gene silencing in tobacco compromises the splicing of endogenous counterpart genes. PLoS One 2014; 9:e87869. [PMID: 24586294 PMCID: PMC3931610 DOI: 10.1371/journal.pone.0087869] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 12/31/2013] [Indexed: 11/23/2022] Open
Abstract
Sense transgene-induced post-transcriptional gene silencing (S-PTGS) is thought to be a type of RNA silencing in which ARGONAUTE1 directs the small interfering RNA (siRNA)-mediated cleavage of a target mRNA in the cytoplasm. Here, we report that the altered splicing of endogenous counterpart genes is a main cause for the reduction of their mature mRNA levels. After the S-PTGS of a tobacco endoplasmic reticulum ω-3 fatty acid desaturase (NtFAD3) gene, 3'-truncated, polyadenylated endo-NtFAD3 transcripts and 5'-truncated, intron-containing endo-NtFAD3 transcripts were detected in the total RNA fraction. Although transcription proceeded until the last exon of the endogenous NtFAD3 gene, intron-containing NtFAD3 transcripts accumulated in the nucleus of the S-PTGS plants. Several intron-containing NtFAD3 transcripts harboring most of the exon sequences were generated when an endogenous silencing suppressor gene, rgs-CaM, was overexpressed in the S-PTGS plants. These intron-containing NtFAD3 splice variants were generated in the presence of NtFAD3 siRNAs that are homologous to the nucleotide sequences of these splice variants. The results of this study indicate that the inhibition of endo-NtFAD3 gene expression is primarily directed via the alteration of splicing and not by cytoplasmic slicer activity. Our results suggest that the transgene and intron-containing endogenous counterpart genes are differentially suppressed in S-PTGS plants.
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Affiliation(s)
- Mi-Rae Shin
- Graduate School of Advanced Integration Science, Chiba University, Inage-ku, Chiba, Japan
| | - Masaya Natsuume
- Graduate School of Horticulture, Chiba University, Chiba, Japan
| | - Takashi Matsumoto
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | | | - Misaki Imai
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Ken Iijima
- Department of Applied Biology and Chemistry, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Shin-ichiro Oka
- Graduate School of Horticulture, Chiba University, Chiba, Japan
| | - Eri Adachi
- Graduate School of Science and Technology, Chiba University, Inage-ku, Chiba, Japan
| | - Hiroaki Kodama
- Graduate School of Advanced Integration Science, Chiba University, Inage-ku, Chiba, Japan
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41
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Yoshikawa M. Biogenesis of trans-acting siRNAs, endogenous secondary siRNAs in plants. Genes Genet Syst 2014; 88:77-84. [PMID: 23832299 DOI: 10.1266/ggs.88.77] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Trans-acting small interfering RNAs (tasiRNAs) are plant-specific endogenous siRNAs that control non-identical mRNAs via cleavage. The production of tasiRNAs is triggered by cleavage of capped and polyadenylated primary TAS transcripts (pri-TASs) by specific miRNAs. Following miRNA-directed cleavage, either 5' or 3' cleavage fragments are converted into double-stranded RNAs (dsRNAs) by RNA-DEPENDENT RNA POLYMERASE 6. The dsRNAs are processed to tasiRNAs by DICER-LIKE 4 in a phasing manner. There are two forms of pri-TASs; One has a single miRNA target site that is targeted by 22-nucleotide microRNAs, and the other has two miR390 target sites. Secondary siRNAs that are important for the amplification of RNA silencing are defined as siRNAs whose production is initiated by the cleavage of primary small RNA-containing RNA-induced silencing complexes. Thus, tasiRNA production is a model system of secondary siRNA production in plants. This review focuses on the production of tasiRNAs that are endogenous secondary siRNAs.
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Affiliation(s)
- Manabu Yoshikawa
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan.
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42
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Bologna NG, Voinnet O. The diversity, biogenesis, and activities of endogenous silencing small RNAs in Arabidopsis. ANNUAL REVIEW OF PLANT BIOLOGY 2014; 65:473-503. [PMID: 24579988 DOI: 10.1146/annurev-arplant-050213-035728] [Citation(s) in RCA: 379] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In eukaryotic RNA silencing, RNase-III classes of enzymes in the Dicer family process double-stranded RNA of cellular or exogenous origin into small-RNA (sRNA) molecules. sRNAs are then loaded into effector proteins known as ARGONAUTEs (AGOs), which, as part of RNA-induced silencing complexes, target complementary RNA or DNA for silencing. Plants have evolved a large variety of pathways over the Dicer-AGO consortium, which most likely underpins part of their phenotypic plasticity. Dicer-like proteins produce all known classes of plant silencing sRNAs, which are invariably stabilized via 2'-O-methylation mediated by HUA ENHANCER 1 (HEN1), potentially amplified by the action of several RNA-dependent RNA polymerases, and function through a variety of AGO proteins. Here, we review the known characteristics and biochemical properties of the core silencing factors found in the model plant Arabidopsis thaliana. We also describe how interactions between these core factors and more specialized proteins allow the production of a plethora of silencing sRNAs involved in a large array of biological functions. We emphasize in particular the biogenesis and activities of silencing sRNAs of endogenous origin.
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Affiliation(s)
- Nicolas G Bologna
- Department of Biology, Swiss Federal Institute of Technology (ETH-Z), 8093 Zurich, Switzerland;
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43
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Pumplin N, Voinnet O. RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence. Nat Rev Microbiol 2013; 11:745-60. [PMID: 24129510 DOI: 10.1038/nrmicro3120] [Citation(s) in RCA: 395] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
RNA silencing is a central regulator of gene expression in most eukaryotes and acts both at the transcriptional level through DNA methylation and at the post-transcriptional level through direct mRNA interference mediated by small RNAs. In plants and invertebrates, the same pathways also function directly in host defence against viruses by targeting viral RNA for degradation. Successful viruses have consequently evolved diverse mechanisms to avoid silencing, most notably through the expression of viral suppressors of RNA silencing. RNA silencing suppressors have also been recently identified in plant pathogenic bacteria and oomycetes, suggesting that disruption of host silencing is a general virulence strategy across several kingdoms of plant pathogens. There is also increasing evidence that plants have evolved specific defences against RNA-silencing suppression by pathogens, providing yet another illustration of the never-ending molecular arms race between plant pathogens and their hosts.
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Affiliation(s)
- Nathan Pumplin
- Swiss Federal Institute of Technology Zurich (ETH-Zurich), Department of Biology, Zurich, Switzerland
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44
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Jabnoune M, Secco D, Lecampion C, Robaglia C, Shu Q, Poirier Y. A rice cis-natural antisense RNA acts as a translational enhancer for its cognate mRNA and contributes to phosphate homeostasis and plant fitness. THE PLANT CELL 2013; 25:4166-82. [PMID: 24096344 PMCID: PMC3877805 DOI: 10.1105/tpc.113.116251] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/03/2013] [Accepted: 09/18/2013] [Indexed: 05/16/2023]
Abstract
cis-natural antisense transcripts (cis-NATs) are widespread in plants and are often associated with downregulation of their associated sense genes. We found that a cis-NAT positively regulates the level of a protein critical for phosphate homeostasis in rice (Oryza sativa). PHOSPHATE1;2 (PHO1;2), a gene involved in phosphate loading into the xylem in rice, and its associated cis-NATPHO1;2 are both controlled by promoters active in the vascular cylinder of roots and leaves. While the PHO1;2 promoter is unresponsive to the plant phosphate status, the cis-NATPHO1;2 promoter is strongly upregulated under phosphate deficiency. Expression of both cis-NATPHO1;2 and the PHO1;2 protein increased in phosphate-deficient plants, while the PHO1;2 mRNA level remained stable. Downregulation of cis-NATPHO1;2 expression by RNA interference resulted in a decrease in PHO1;2 protein, impaired the transfer of phosphate from root to shoot, and decreased seed yield. Constitutive overexpression of NATPHO1;2 in trans led to a strong increase of PHO1;2, even under phosphate-sufficient conditions. Under all conditions, no changes occurred in the level of expression, sequence, or nuclear export of PHO1;2 mRNA. However, expression of cis-NATPHO1;2 was associated with a shift of both PHO1;2 and cis-NATPHO1;2 toward the polysomes. These findings reveal an unexpected role for cis-NATPHO1;2 in promoting PHO1;2 translation and affecting phosphate homeostasis and plant fitness.
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Affiliation(s)
- Mehdi Jabnoune
- Department of Plant Molecular Biology, University of Lausanne, Lausanne CH-1015, Switzerland
| | - David Secco
- Department of Plant Molecular Biology, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Cécile Lecampion
- Laboratory of Plant Genetics and Biophysics, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265, Commissariat à l’Energie Atomique, Institute of Environmental Biology and Biotechnology, Aix Marseille University, Faculty of Sciences, Luminy, Marseille F-13009, France
| | - Christophe Robaglia
- Laboratory of Plant Genetics and Biophysics, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265, Commissariat à l’Energie Atomique, Institute of Environmental Biology and Biotechnology, Aix Marseille University, Faculty of Sciences, Luminy, Marseille F-13009, France
| | - Qingyao Shu
- Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Yves Poirier
- Department of Plant Molecular Biology, University of Lausanne, Lausanne CH-1015, Switzerland
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45
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Braszewska-Zalewska AJ, Wolny EA, Smialek L, Hasterok R. Tissue-specific epigenetic modifications in root apical meristem cells of Hordeum vulgare. PLoS One 2013; 8:e69204. [PMID: 23935955 PMCID: PMC3729647 DOI: 10.1371/journal.pone.0069204] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 06/05/2013] [Indexed: 11/18/2022] Open
Abstract
Epigenetic modifications of chromatin structure are essential for many biological processes, including growth and reproduction. Patterns of DNA and histone modifications have recently been widely studied in many plant species, although there is virtually no data on the spatial and temporal distribution of epigenetic markers during plant development. Accordingly, we have used immunostaining techniques to investigate epigenetic modifications in the root apical meristem of Hordeum vulgare. Histone H4 acetylation (H4K5ac), histone H3 dimethylation (H3K4me2, H3K9me2) and DNA methylation (5mC) patterns were established for various root meristem tissues. Distinct levels of those modifications were visualised in the root cap, epidermis, cortex and vascular tissues. The lateral root cap cells seem to display the highest level of H3K9me2 and 5mC. In the epidermis, the highest level of 5mC and H3K9me2 was detected in the nuclei from the boundary of the proximal meristem and the elongation zone, while the vascular tissues were characterized by the highest level of H4K5ac. Some of the modified histones were also detectable in the cytoplasm in a highly tissue-specific manner. Immunolocalisation of epigenetic modifications of chromatin carried out in this way, on longitudinal or transverse sections, provides a unique topographic context within the organ, and will provide some answers to the significant biological question of tissue differentiation processes during root development in a monocotyledon plant species.
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Affiliation(s)
- Agnieszka J. Braszewska-Zalewska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Elzbieta A. Wolny
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Lukasz Smialek
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
- * E-mail:
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46
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Sikorskaite S, Rajamäki ML, Baniulis D, Stanys V, Valkonen JPT. Protocol: Optimised methodology for isolation of nuclei from leaves of species in the Solanaceae and Rosaceae families. PLANT METHODS 2013; 9:31. [PMID: 23886449 PMCID: PMC3728069 DOI: 10.1186/1746-4811-9-31] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 07/24/2013] [Indexed: 05/22/2023]
Abstract
In this study, a protocol is described for rapid preparation of an enriched, reasonably pure fraction of nuclear proteins from the leaves of tobacco (Nicotiana tabacum), potato (Solanum tuberosum) and apple (Malus domestica). The protocol gives reproducible results and can be carried out quickly in 2 hours. Tissue extracts clarified with filtration were treated with non-ionic detergent (Triton X-100) to lyse membranes of contaminating organelles. Nuclei were collected from a 60% Percoll layer of density gradient following low-speed centrifugation. Western blot analysis using antibodies to marker proteins of organelles indicated that the nuclear protein fractions were highly enriched and free or nearly free of proteins from the endoplasmic reticulum and chloroplasts.
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Affiliation(s)
- Sidona Sikorskaite
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas st 30, Babtai, LT-54333, Kaunas, Lithuania
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FIN-00014 Helsinki, Finland
| | - Minna-Liisa Rajamäki
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FIN-00014 Helsinki, Finland
| | - Danas Baniulis
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas st 30, Babtai, LT-54333, Kaunas, Lithuania
| | - Vidmantas Stanys
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas st 30, Babtai, LT-54333, Kaunas, Lithuania
| | - Jari PT Valkonen
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FIN-00014 Helsinki, Finland
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47
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Pontes O, Vitins A, Ream TS, Hong E, Pikaard CS, Costa-Nunes P. Intersection of small RNA pathways in Arabidopsis thaliana sub-nuclear domains. PLoS One 2013; 8:e65652. [PMID: 23776518 PMCID: PMC3680462 DOI: 10.1371/journal.pone.0065652] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 04/25/2013] [Indexed: 12/22/2022] Open
Abstract
In Arabidopsis thaliana, functionally diverse small RNA (smRNA) pathways bring about decreased RNA accumulation of target genes via several different mechanisms. Cytological experiments have suggested that the processing of microRNAs (miRNAs) and heterochromatic small interfering RNAs (hc-siRNAs) occurs within a specific nuclear domain that can present Cajal Body (CB) characteristics. It is unclear whether single or multiple smRNA-related domains are found within the same CB and how specialization of the smRNA pathways is determined within this specific sub-compartment. To ascertain whether nuclear smRNA centers are spatially related, we localized key proteins required for siRNA or miRNA biogenesis by immunofluorescence analysis. The intranuclear distribution of the proteins revealed that hc-siRNA, miRNA and trans-acting siRNA (ta-siRNA) pathway proteins accumulate and colocalize within a sub-nuclear structure in the nucleolar periphery. Furthermore, colocalization of miRNA- and siRNA-pathway members with CB markers, and reduced wild-type localization patterns in CB mutants indicates that proper nuclear localization of these proteins requires CB integrity. We hypothesize that these nuclear domains could be important for RNA silencing and may partially explain the functional redundancies and interactions among components of the same protein family. The CB may be the place in the nucleus where Dicer-generated smRNA precursors are processed and assigned to a specific pathway, and where storage, recycling or assembly of RNA interference components takes place.
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Affiliation(s)
- Olga Pontes
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America.
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Vermeersch L, De Winne N, Nolf J, Bleys A, Kovařík A, Depicker A. Transitive RNA silencing signals induce cytosine methylation of a transgenic but not an endogenous target. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:867-879. [PMID: 23480471 DOI: 10.1111/tpj.12172] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 02/25/2013] [Accepted: 03/04/2013] [Indexed: 05/27/2023]
Abstract
Post-transcriptional gene silencing of a primary target gene in plants can coincide with the production of secondary small interfering RNAs (siRNAs) of coding sequences adjacent to the target region and with de novo RNA-directed DNA methylation (RdDM) thereof. Here, we analyzed the susceptibility of transgenic and endogenous targets to RdDM induced by primary and secondary silencing signals. In three different configurations, primary silencing signals were able to direct in trans methylation of chimeric transgenes and the CATALASE2 (CAT2) endogene; however, extensive spreading of methylation occurred only in the transgene, resulting in the methylation of the flanking CAT2 sequence, whereas methylation of the CAT2 endogene was restricted to the target region and the enclosed introns. The secondary silencing signals arising from this transgenic primary target simultaneously silenced a secondary transgene target and the CAT2 endogene, but were only capable of directing RdDM to the transgene. Our data indicate that RdDM is correlated with the in situ generation of secondary siRNAs, occurring in P35S-driven transgenes but not in most endogenes. We conclude that although both endogenes and transgenes are equally sensitive to transitive silencing, differences exist in their susceptibility to undergo secondary RdDM.
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Affiliation(s)
- Leen Vermeersch
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
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RNA-induced silencing complex (RISC) Proteins PACT, TRBP, and Dicer are SRA binding nuclear receptor coregulators. Proc Natl Acad Sci U S A 2013; 110:6536-41. [PMID: 23550157 DOI: 10.1073/pnas.1301620110] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The cytoplasmic RNA-induced silencing complex (RISC) contains dsRNA binding proteins, including protein kinase RNA activator (PACT), transactivation response RNA binding protein (TRBP), and Dicer, that process pre-microRNAs into mature microRNAs (miRNAs) that target specific mRNA species for regulation. There is increasing evidence for important functional interactions between the miRNA and nuclear receptor (NR) signaling networks, with recent data showing that estrogen, acting through the estrogen receptor, can modulate initial aspects of nuclear miRNA processing. Here, we show that the cytoplasmic RISC proteins PACT, TRBP, and Dicer are steroid receptor RNA activator (SRA) binding NR coregulators that target steroid-responsive promoters and regulate NR activity and downstream gene expression. Furthermore, each of the RISC proteins, together with Argonaute 2, associates with SRA and specific pre-microRNAs in both the nucleus and cytoplasm, providing evidence for links between NR-mediated transcription and some of the factors involved in miRNA processing.
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Nazim Uddin M, Kim JY. Intercellular and systemic spread of RNA and RNAi in plants. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:279-93. [PMID: 23536229 DOI: 10.1002/wrna.1160] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Plants possess dynamic networks of intercellular communication that are crucial for plant development and physiology. In plants, intercellular communication involves a combination of ligand-receptor-based apoplasmic signaling, and plasmodesmata and phloem-mediated symplasmic signaling. The intercellular trafficking of macromolecules, including RNAs and proteins, has emerged as a novel mechanism of intercellular communication in plants. Various forms of regulatory RNAs move over distinct cellular boundaries through plasmodesmata and phloem. This plant-specific, non-cell-autonomous RNA trafficking network is also involved in development, nutrient homeostasis, gene silencing, pathogen defense, and many other physiological processes. However, the mechanism underlying macromolecular trafficking in plants remains poorly understood. Current progress made in RNA trafficking research and its biological relevance to plant development will be summarized. Diverse plant regulatory mechanisms of cell-to-cell and systemic long-distance transport of RNAs, including mRNAs, viral RNAs, and small RNAs, will also be discussed.
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Affiliation(s)
- Mohammad Nazim Uddin
- Division of Applied Life Science (BK21-WCU Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, South Korea
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