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Kamesh Krishnamoorthy K, Malathi VG, Renukadevi P, Kumar SM, Raveendran M, Sudha M, Manivannan N, Karthikeyan G. Exogenous delivery of dsRNA for management of mungbean yellow mosaic virus on blackgram. PLANTA 2023; 258:94. [PMID: 37804329 DOI: 10.1007/s00425-023-04253-6] [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: 07/16/2023] [Accepted: 09/23/2023] [Indexed: 10/09/2023]
Abstract
MAIN CONCLUSION Exogenous application of dsRNA molecules targeting MYMV genes offers a promising approach to effectively mitigate yellow mosaic disease in blackgram, demonstrating potential for sustainable plant viral disease management. The exogenous application of double-stranded RNA (dsRNA) molecules to control plant viral diseases is gaining traction due to its advantages over conventional methods, such as target specificity, non-polluting nature, and absence of residue formation. Furthermore, this approach does not involve genome modification. In this study, dsRNA molecules targeting the coat protein gene (dsCP) and replication initiator protein gene (dsRep) of mungbean yellow mosaic virus (MYMV) were synthesised using an in vitro transcription method. To evaluate the effectiveness of dsRNA treatment, blackgram plants exhibiting MYMV symptoms at the first trifoliate stage were subjected to exogenous application of dsRNA. Second, third, and fourth trifoliate leaves, which emerged at 7, 15, and 21 days after dsRNA application, respectively, were monitored for MYMV symptoms. Remarkably, a significant reduction in yellow mosaic disease (YMD) symptoms was observed in the newly emerged trifoliate leaves of MYMV-infected blackgram plants after treatment with dsRNA targeting both gene regions. This reduction was evident as a decrease in the intensity of yellow mosaic coverage on the leaf lamina compared to control. dsCP effectively reduced the MYMV titre in the treated plants for up to 15 days. However, dsRep demonstrated greater efficiency in conferring resistance to MYMV at 15 days post-application. These findings were supported by quantitative real-time PCR analysis, where the observed Ct values for DNA extracted from dsRep-treated plants were significantly higher compared to the Ct values of DNA from dsCP-treated plants at 15 days post-application. Similarly, higher viral copy numbers were observed in dsCP-treated plants 15 days after dsRNA treatment, in contrast to plants treated with dsRep.
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Affiliation(s)
- K Kamesh Krishnamoorthy
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - V G Malathi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - P Renukadevi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - S Mohan Kumar
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - M Raveendran
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - M Sudha
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - N Manivannan
- National Pulses Research Centre, Tamil Nadu Agricultural University, Vamban, 622303, India
| | - G Karthikeyan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, 641003, India.
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2
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Qiu Y, Li P, Zhang Z, Wu M. Insights Into Exosomal Non-Coding RNAs Sorting Mechanism and Clinical Application. Front Oncol 2021; 11:664904. [PMID: 33987099 PMCID: PMC8111219 DOI: 10.3389/fonc.2021.664904] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
Exosomes are natural nanoscale bilayer phospholipid vesicles that can be secreted by almost all types of cells and are detected in almost all types of body fluids. Exosomes are effective mediators of cell–cell signaling communication because of their ability to carry and transfer a variety of bioactive molecules, including non-coding RNAs. Non-coding RNAs have also been found to exert strong effects on a variety of biological processes, including tumorigenesis. Many researchers have established that exosomes encapsulate bioactive non-coding RNAs that alter the biological phenotype of specific target cells in an autocrine or a paracrine manner. However, the mechanism by which the producer cells package non-coding RNAs into exosomes is not well understood. This review focuses on the current research on exosomal non-coding RNAs, including the biogenesis of exosomes, the possible mechanism of sorting non-coding RNAs, their biological functions, and their potential for clinical application in the future.
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Affiliation(s)
- Yi Qiu
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Peiyao Li
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, China National Health Commission Key Laboratory of Carcinogenesis, Xiangya Hospital, Central South University, Changsha, China
| | - Zuping Zhang
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Minghua Wu
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
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3
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Hovde BT, Hanschen ER, Steadman Tyler CR, Lo CC, Kunde Y, Davenport K, Daligault H, Msanne J, Canny S, Eyun SI, Riethoven JJM, Polle J, Starkenburg SR. Genomic characterization reveals significant divergence within Chlorella sorokiniana (Chlorellales, Trebouxiophyceae). ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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4
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Lou S, Sun T, Li H, Hu Z. Mechanisms of microRNA-mediated gene regulation in unicellular model alga Chlamydomonas reinhardtii. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:244. [PMID: 30202439 PMCID: PMC6129010 DOI: 10.1186/s13068-018-1249-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/31/2018] [Indexed: 05/30/2023]
Abstract
MicroRNAs are a class of endogenous non-coding RNAs that play a vital role in post-transcriptional gene regulation in eukaryotic cells. In plants and animals, miRNAs are implicated in diverse roles ranging from immunity against viral infections, developmental pathways, molecular pathology of cancer and regulation of protein expression. However, the role of miRNAs in the unicellular model green alga Chlamydomonas reinhardtii remains unclear. The mode of action of miRNA-induced gene silencing in C. reinhardtii is very similar to that of higher eukaryotes, in terms of the activation of the RNA-induced silencing complex and mRNA targeting. Certain studies indicate that destabilization of mRNAs and mRNA turnover could be the major possible functions of miRNAs in eukaryotic algae. Here, we summarize recent findings that have advanced our understanding of miRNA regulatory mechanisms in C. reinhardtii.
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Affiliation(s)
- Sulin Lou
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Key Laboratory of Optoeletronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoeletronic Engineering, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Ting Sun
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Key Laboratory of Optoeletronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoeletronic Engineering, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Hui Li
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Zhangli Hu
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
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5
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Identifying and characterizing functional 3' nucleotide addition in the miRNA pathway. Methods 2018; 152:23-30. [PMID: 30138674 DOI: 10.1016/j.ymeth.2018.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/02/2018] [Accepted: 08/14/2018] [Indexed: 02/07/2023] Open
Abstract
Over the past decade, modifications to microRNAs (miRNAs) via 3' end nucleotide addition have gone from a deep-sequencing curiosity to experimentally confirmed drivers of a range of regulatory activities. Here we overview the methods that have been deployed by researchers seeking to untangle these diverse functional roles and include characterizing not only the nucleotidyl transferases catalyzing the additions but also the nucleotides being added, and the timing of their addition during the miRNA pathway. These methods and their further development are key to clarifying the diverse and sometimes contradictory functional findings presently attributed to these nucleotide additions.
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6
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Niehl A, Soininen M, Poranen MM, Heinlein M. Synthetic biology approach for plant protection using dsRNA. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1679-1687. [PMID: 29479789 PMCID: PMC6097125 DOI: 10.1111/pbi.12904] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/26/2018] [Accepted: 02/13/2018] [Indexed: 05/05/2023]
Abstract
Pathogens induce severe damages on cultivated plants and represent a serious threat to global food security. Emerging strategies for crop protection involve the external treatment of plants with double-stranded (ds)RNA to trigger RNA interference. However, applying this technology in greenhouses and fields depends on dsRNA quality, stability and efficient large-scale production. Using components of the bacteriophage phi6, we engineered a stable and accurate in vivo dsRNA production system in Pseudomonas syringae bacteria. Unlike other in vitro or in vivo dsRNA production systems that rely on DNA transcription and postsynthetic alignment of single-stranded RNA molecules, the phi6 system is based on the replication of dsRNA by an RNA-dependent RNA polymerase, thus allowing production of high-quality, long dsRNA molecules. The phi6 replication complex was reprogrammed to multiply dsRNA sequences homologous to tobacco mosaic virus (TMV) by replacing the coding regions within two of the three phi6 genome segments with TMV sequences and introduction of these constructs into P. syringae together with the third phi6 segment, which encodes the components of the phi6 replication complex. The stable production of TMV dsRNA was achieved by combining all the three phi6 genome segments and by maintaining the natural dsRNA sizes and sequence elements required for efficient replication and packaging of the segments. The produced TMV-derived dsRNAs inhibited TMV propagation when applied to infected Nicotiana benthamiana plants. The established dsRNA production system enables the broad application of dsRNA molecules as an efficient, highly flexible, nontransgenic and environmentally friendly approach for protecting crops against viruses and other pathogens.
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Affiliation(s)
- Annette Niehl
- Université de StrasbourgCNRSIBMP UPR 2357StrasbourgFrance
- Present address:
Julius Kühn‐Institute (JKI)BraunschweigGermany
| | - Marjukka Soininen
- Molecular and Integrative Biosciences Research ProgrammeFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Minna M. Poranen
- Molecular and Integrative Biosciences Research ProgrammeFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
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7
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Yamasaki T, Cerutti H. Cooperative processing of primary miRNAs by DUS16 and DCL3 in the unicellular green alga Chlamydomonas reinhardtii. Commun Integr Biol 2017; 10:e1280208. [PMID: 28289490 PMCID: PMC5333524 DOI: 10.1080/19420889.2017.1280208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 11/05/2022] Open
Abstract
We have previously reported that the RNA-binding protein Dull slicer 16 (DUS16) plays a key role in the processing of primary miRNAs (pri-miRNAs) in the unicellular green alga Chlamydomonas reinhardtii. In the present report, we elaborate on the interaction of DUS16 with Dicer-like 3 (DCL3) during pri-miRNA processing. Comprehensive analyses of small RNA libraries derived from mutant and wild-type algal strains allowed the de novo prediction of 35 pri-miRNA genes, including 9 previously unknown ones. The pri-miRNAs dependent on DUS16 for processing largely overlapped with those dependent on DCL3. Our findings suggest that DUS16 and DCL3 work cooperatively, presumably as components of a microprocessor complex, in the processing of the majority of pri-miRNAs in C. reinhardtii.
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Affiliation(s)
- Tomohito Yamasaki
- Division of Environmental Photobiology, National Institute for Basic Biology , Okazaki, Aichi, Japan
| | - Heriberto Cerutti
- School of Biological Science and Center for Plant Science Innovation, University of Nebraska-Lincoln , Lincoln, NE, USA
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8
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Weinheimer I, Boonrod K, Moser M, Wassenegger M, Krczal G, Butcher SJ, Valkonen JPT. Binding and processing of small dsRNA molecules by the class 1 RNase III protein encoded by sweet potato chlorotic stunt virus. J Gen Virol 2013; 95:486-495. [PMID: 24187016 DOI: 10.1099/vir.0.058693-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Sweet potato chlorotic stunt virus (SPCSV; genus Crinivirus, family Closteroviridae) causes heavy yield losses in sweet potato plants co-infected with other viruses. The dsRNA-specific class 1 RNase III-like endoribonuclease (RNase3) encoded by SPCSV suppresses post-transcriptional gene silencing and eliminates antiviral defence in sweet potato plants in an endoribonuclease activity-dependent manner. RNase3 can cleave long dsRNA molecules, synthetic small interfering RNAs (siRNAs), and plant- and virus-derived siRNAs extracted from sweet potato plants. In this study, conditions for efficient expression and purification of enzymically active recombinant RNase3 were established. Similar to bacterial class 1 RNase III enzymes, RNase3-Ala (a dsRNA cleavage-deficient mutant) bound to and processed double-stranded siRNA (ds-siRNA) as a dimer. The results support the classification of SPCSV RNase3 as a class 1 RNase III enzyme. There is little information about the specificity of RNase III enzymes on small dsRNAs. In vitro assays indicated that ds-siRNAs and microRNAs (miRNAs) with a regular A-form conformation were cleaved by RNase3, but asymmetrical bulges, extensive mismatches and 2'-O-methylation of ds-siRNA and miRNA interfered with processing. Whereas Mg(2+) was the cation that best supported the catalytic activity of RNase3, binding of 21 nt small dsRNA molecules was most efficient in the presence of Mn(2+). Processing of long dsRNA by RNase3 was efficient at pH 7.5 and 8.5, whereas ds-siRNA was processed more efficiently at pH 8.5. The results revealed factors that influence binding and processing of small dsRNA substrates by class 1 RNase III in vitro or make them unsuitable for processing by the enzyme.
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Affiliation(s)
- Isabel Weinheimer
- AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt a.d.W., Germany.,Department of Agricultural Sciences, PO Box 27, 00014 University of Helsinki, Helsinki, Finland
| | - Kajohn Boonrod
- AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt a.d.W., Germany
| | - Mirko Moser
- AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt a.d.W., Germany
| | - Michael Wassenegger
- Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg, Germany.,AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt a.d.W., Germany
| | - Gabi Krczal
- AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt a.d.W., Germany
| | - Sarah J Butcher
- Institute of Biotechnology, PO Box 65, 00014 University of Helsinki, Helsinki, Finland
| | - Jari P T Valkonen
- Department of Agricultural Sciences, PO Box 27, 00014 University of Helsinki, Helsinki, Finland
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9
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Zhang J, Zhang S, Li S, Han S, Wu T, Li X, Qi L. A genome-wide survey of microRNA truncation and 3' nucleotide addition events in larch (Larix leptolepis). PLANTA 2013; 237:1047-56. [PMID: 23232766 DOI: 10.1007/s00425-012-1823-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 11/26/2012] [Indexed: 05/15/2023]
Abstract
MicroRNAs (miRNAs) play essential roles in numerous developmental and metabolic processes in animals and plants. Although the framework of miRNA biogenesis and function is established, the mechanism of miRNA degradation or modification remains to be investigated in plants. Mature miRNAs may be truncated or added nucleotides to generate variants. A detailed analysis of small RNA deep sequencing data sets resulted in the cloning of a large number of variants derived from larch miRNAs. Many 5'- and/or 3'-end truncated versions of miRNAs suggested that larch miRNAs might be degraded through either 5'-3' or 3'-5'. The relative abundance of variants truncated from 3'-end was higher than that of 5'-end for most miRNAs. The addition of adenine, uridine, and cytidine to the 3'-end of miRNAs was globally present, and the subtle variability in isomiR abundance might be regulated and biologically meaningful. It is the first report for cytidine addition in plant, and our examination of published small RNA deep sequencing data sets of Arabidopsis, rice, and moss suggests that cytidine addition to miRNA 3'-end exists broadly in plants. In addition, the nucleotide addition might be associated with 3'-5' miRNA degradation. Our results provide valuable information for a genome-wide survey of miRNA truncation and modification in larch or plants.
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Affiliation(s)
- Junhong Zhang
- Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.
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10
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Libri V, Miesen P, van Rij RP, Buck AH. Regulation of microRNA biogenesis and turnover by animals and their viruses. Cell Mol Life Sci 2013; 70:3525-44. [PMID: 23354060 PMCID: PMC3771402 DOI: 10.1007/s00018-012-1257-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 12/27/2012] [Accepted: 12/27/2012] [Indexed: 12/24/2022]
Abstract
MicroRNAs (miRNAs) are a ubiquitous component of gene regulatory networks that modulate the precise amounts of proteins expressed in a cell. Despite their small size, miRNA genes contain various recognition elements that enable specificity in when, where and to what extent they are expressed. The importance of precise control of miRNA expression is underscored by functional studies in model organisms and by the association between miRNA mis-expression and disease. In the last decade, identification of the pathways by which miRNAs are produced, matured and turned-over has revealed many aspects of their biogenesis that are subject to regulation. Studies in viral systems have revealed a range of mechanisms by which viruses target these pathways through viral proteins or non-coding RNAs in order to regulate cellular gene expression. In parallel, a field of study has evolved around the activation and suppression of antiviral RNA interference (RNAi) by viruses. Virus encoded suppressors of RNAi can impact miRNA biogenesis in cases where miRNA and small interfering RNA pathways converge. Here we review the literature on the mechanisms by which miRNA biogenesis and turnover are regulated in animals and the diverse strategies that viruses use to subvert or inhibit these processes.
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Affiliation(s)
- Valentina Libri
- Centre for Immunity, Infection and Evolution, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, EH9 3JT, UK
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11
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Meng Y, Shao C, Wang H, Ma X, Chen M. Construction of gene regulatory networks mediated by vegetative and reproductive stage-specific small RNAs in rice (Oryza sativa). THE NEW PHYTOLOGIST 2013; 197:441-453. [PMID: 23121287 DOI: 10.1111/nph.12018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 09/24/2012] [Indexed: 05/16/2023]
Abstract
Although huge amounts of high-throughput sequencing (HTS) data are available, limited systematic analyses have been performed by integrating these valuable resources. Based on small RNA (sRNA), RNA and degradome HTS data, the sRNAs specifically expressed at vegetative and reproductive stages were identified separately in rice. Two distinct groups of sRNA HTS data, which were prepared during the vegetative and the reproductive stages, were utilized to extract stage-specific sRNAs. Degradome sequencing data were employed for sRNA target validation. RNA sequencing data were used to construct expression-based, sRNA-mediated networks. As a result, 26 microRNAs and 413 sRNAs were specifically expressed at the vegetative stage, and 79 microRNAs and 539 sRNAs were specifically expressed at the reproductive stage. In addition to the microRNAs, numerous stage-specific sRNAs enriched in ARGONAUTE1 showed great potential to perform cleavage-based repression on the targets. Several stage-specific sRNAs were indicated to result from the wobble effect of Dicer-like 1-mediated processing of microRNA precursors. The expression patterns of the sRNA targets, and the stage-specific cleavage signals strongly indicated the reliability of the constructed networks. A set of rice stage-specific sRNAs along with the regulatory cascades, which have great potential in regulating specific developmental stages, were provided for further investigation.
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Affiliation(s)
- Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Chaogang Shao
- College of Life Sciences, Huzhou Teachers College, Huzhou, 313000, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Xiaoxia Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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12
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Atayde VD, Shi H, Franklin JB, Carriero N, Notton T, Lye LF, Owens K, Beverley SM, Tschudi C, Ullu E. The structure and repertoire of small interfering RNAs in Leishmania (Viannia) braziliensis reveal diversification in the trypanosomatid RNAi pathway. Mol Microbiol 2012; 87:580-93. [PMID: 23217017 DOI: 10.1111/mmi.12117] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2012] [Indexed: 12/01/2022]
Abstract
Among trypanosomatid protozoa the mechanism of RNA interference (RNAi) has been investigated in Trypanosoma brucei and to a lesser extent in Leishmania braziliensis. Although these two parasitic organisms belong to the same family, they are evolutionarily distantly related raising questions about the conservation of the RNAi pathway. Here we carried out an in-depth analysis of small interfering RNAs (siRNAs) associated with L. braziliensis Argonaute1 (LbrAGO1). In contrast to T. brucei, Leishmania siRNAs are sensitive to 3' end oxidation, indicating the absence of blocking groups, and the Leishmania genome does not code for a HEN1 RNA 2'-O-methyltransferase, which modifies small RNA 3' ends. Consistent with this observation, ~20% of siRNA 3' ends carry non-templated uridines. Thus siRNA biogenesis, and most likely their metabolism, is different in these organisms. Similarly to T. brucei, putative mobile elements and repeats constitute the major Leishmania siRNA-producing loci and AGO1 ablation leads to accumulation of long transcripts derived from putative mobile elements. However, contrary to T. brucei, no siRNAs were detected from other genomic regions with the potential to form double-stranded RNA, namely sites of convergent transcription and inverted repeats. Thus, our results indicate that organism-specific diversification has occurred in the RNAi pathway during evolution of the trypanosomatid lineage.
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Affiliation(s)
- Vanessa D Atayde
- Departments of Internal Medicine, Yale University, New Haven, CT 06536, USA
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