1
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Ma L, Zhang X, Deng Z, Zhang P, Wang T, Li R, Li J, Cheng K, Wang J, Ma N, Qu G, Zhu B, Fu D, Luo Y, Li F, Zhu H. Dicer-like2b suppresses the wiry leaf phenotype in tomato induced by tobacco mosaic virus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1737-1747. [PMID: 37694805 DOI: 10.1111/tpj.16462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/28/2023] [Accepted: 09/01/2023] [Indexed: 09/12/2023]
Abstract
Dicer-like (DCL) proteins are principal components of RNA silencing, a major defense mechanism against plant virus infections. However, their functions in suppressing virus-induced disease phenotypes remain largely unknown. Here, we identified a role for tomato (Solanum lycopersicum) DCL2b in regulating the wiry leaf phenotype during defense against tobacco mosaic virus (TMV). Knocking out SlyDCL2b promoted TMV accumulation in the leaf primordium, resulting in a wiry phenotype in distal leaves. Biochemical and bioinformatics analyses showed that 22-nt virus-derived small interfering RNAs (vsiRNAs) accumulated less abundantly in slydcl2b mutants than in wild-type plants, suggesting that SlyDCL2b-dependent 22-nt vsiRNAs are required to exclude virus from leaf primordia. Moreover, the wiry leaf phenotype was accompanied by upregulation of Auxin Response Factors (ARFs), resulting from a reduction in trans-acting siRNAs targeting ARFs (tasiARFs) in TMV-infected slydcl2b mutants. Loss of tasiARF production in the slydcl2b mutant was in turn caused by inhibition of miRNA390b function. Importantly, silencing SlyARF3 and SlyARF4 largely restored the wiry phenotype in TMV-infected slydcl2b mutants. Our work exemplifies the complex relationship between RNA viruses and the endogenous RNA silencing machinery, whereby SlyDCL2b protects the normal development of newly emerging organs by excluding virus from these regions and thus maintaining developmental silencing.
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Affiliation(s)
- Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xi Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhiqi Deng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Peiyu Zhang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Tian Wang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Ran Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Jubin Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nan Ma
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Guiqin Qu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Benzhong Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Daqi Fu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yunbo Luo
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Feng Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
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2
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Paciorek T, Chiapelli BJ, Wang JY, Paciorek M, Yang H, Sant A, Val DL, Boddu J, Liu K, Gu C, Brzostowski LF, Wang H, Allen EM, Dietrich CR, Gillespie KM, Edwards J, Goldshmidt A, Neelam A, Slewinski TL. Targeted suppression of gibberellin biosynthetic genes ZmGA20ox3 and ZmGA20ox5 produces a short stature maize ideotype. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1140-1153. [PMID: 35244326 PMCID: PMC9129074 DOI: 10.1111/pbi.13797] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/11/2022] [Accepted: 02/15/2022] [Indexed: 06/12/2023]
Abstract
Maize is one of the world's most widely cultivated crops. As future demands for maize will continue to rise, fields will face ever more frequent and extreme weather patterns that directly affect crop productivity. Development of environmentally resilient crops with improved standability in the field, like wheat and rice, was enabled by shifting the architecture of plants to a short stature ideotype. However, such architectural change has not been implemented in maize due to the unique interactions between gibberellin (GA) and floral morphology which limited the use of the same type of mutations as in rice and wheat. Here, we report the development of a short stature maize ideotype in commercial hybrid germplasm, which was generated by targeted suppression of the biosynthetic pathway for GA. To accomplish this, we utilized a dominant, miRNA-based construct expressed in a hemizygous state to selectively reduce expression of the ZmGA20ox3 and ZmGA20ox5 genes that control GA biosynthesis primarily in vegetative tissues. Suppression of both genes resulted in the reduction of GA levels leading to inhibition of cell elongation in internodal tissues, which reduced plant height. Expression of the miRNA did not alter GA levels in reproductive tissues, and thus, the reproductive potential of the plants remained unchanged. As a result, we developed a dominant, short-stature maize ideotype that is conducive for the commercial production of hybrid maize. We expect that the new maize ideotype would enable more efficient and more sustainable maize farming for a growing world population.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kang Liu
- Bayer Crop ScienceChesterfieldMOUSA
| | - Chiyu Gu
- Bayer Crop ScienceChesterfieldMOUSA
| | | | | | | | | | | | | | - Alexander Goldshmidt
- Bayer Crop ScienceChesterfieldMOUSA
- Present address:
Department of Field Crops ScienceInstitute of Plant ScienceAgricultural Research OrganizationThe Volcani CenterP.O. Box 15159Rishon Lezion7528809Israel
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3
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Luo L, Yang X, Guo M, Lan T, Yu Y, Mo B, Chen X, Gao L, Liu L. TRANS-ACTING SIRNA3-derived short interfering RNAs confer cleavage of mRNAs in rice. PLANT PHYSIOLOGY 2022; 188:347-362. [PMID: 34599593 PMCID: PMC8774828 DOI: 10.1093/plphys/kiab452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/29/2021] [Indexed: 05/11/2023]
Abstract
Plant TRANS-ACTING SIRNA3 (TAS3)-derived short interfering RNAs (siRNAs) include tasiR-AUXIN RESPONSE FACTORs (ARFs), which are functionally conserved in targeting ARF genes, and a set of non-tasiR-ARF siRNAs, which have rarely been studied. In this study, TAS3 siRNAs were systematically characterized in rice (Oryza sativa). Small RNA sequencing results showed that an overwhelming majority of TAS3 siRNAs belong to the non-tasiR-ARF group, while tasiR-ARFs occupy a diminutive fraction. Phylogenetic analysis of TAS3 genes across dicot and monocot plants revealed that the siRNA-generating regions were highly conserved in grass species, especially in the Oryzoideae. Target genes were identified for not only tasiR-ARFs but also non-tasiR-ARF siRNAs by analyzing rice Parallel Analysis of RNA Ends datasets, and some of these siRNA-target interactions were experimentally confirmed using tas3 mutants generated by genome editing. Consistent with the de-repression of target genes, phenotypic alterations were observed for mutants in three TAS3 loci in comparison to wild-type rice. The regulatory role of ribosomes in the TAS3 siRNA-target interactions was further revealed by the fact that TAS3 siRNA-mediated target cleavage, in particular tasiR-ARFs targeting ARF2/3/14/15, occurred extensively in rice polysome samples. Altogether, our study sheds light into TAS3 genes in plants and expands our knowledge about rice TAS3 siRNA-target interactions.
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Affiliation(s)
- Linlin Luo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Mingxi Guo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Yu Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
- Author for communication:
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4
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Darlington M, Reinders JD, Sethi A, Lu AL, Ramaseshadri P, Fischer JR, Boeckman CJ, Petrick JS, Roper JM, Narva KE, Vélez AM. RNAi for Western Corn Rootworm Management: Lessons Learned, Challenges, and Future Directions. INSECTS 2022; 13:57. [PMID: 35055900 PMCID: PMC8779393 DOI: 10.3390/insects13010057] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/17/2021] [Accepted: 12/28/2021] [Indexed: 02/06/2023]
Abstract
The western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte, is considered one of the most economically important pests of maize (Zea mays L.) in the United States (U.S.) Corn Belt with costs of management and yield losses exceeding USD ~1-2 billion annually. WCR management has proven challenging given the ability of this insect to evolve resistance to multiple management strategies including synthetic insecticides, cultural practices, and plant-incorporated protectants, generating a constant need to develop new management tools. One of the most recent developments is maize expressing double-stranded hairpin RNA structures targeting housekeeping genes, which triggers an RNA interference (RNAi) response and eventually leads to insect death. Following the first description of in planta RNAi in 2007, traits targeting multiple genes have been explored. In June 2017, the U.S. Environmental Protection Agency approved the first in planta RNAi product against insects for commercial use. This product expresses a dsRNA targeting the WCR snf7 gene in combination with Bt proteins (Cry3Bb1 and Cry34Ab1/Cry35Ab1) to improve trait durability and will be introduced for commercial use in 2022.
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Affiliation(s)
- Molly Darlington
- Department of Entomology, University of Nebraska, Lincoln, NE 68583, USA; (M.D.); (J.D.R.)
| | - Jordan D. Reinders
- Department of Entomology, University of Nebraska, Lincoln, NE 68583, USA; (M.D.); (J.D.R.)
| | - Amit Sethi
- Corteva Agriscience, Johnston, IA 50131, USA; (A.S.); (A.L.L.); (C.J.B.); (J.M.R.)
| | - Albert L. Lu
- Corteva Agriscience, Johnston, IA 50131, USA; (A.S.); (A.L.L.); (C.J.B.); (J.M.R.)
| | | | - Joshua R. Fischer
- Bayer Crop Science, Chesterfield, MO 63017, USA; (P.R.); (J.R.F.); (J.S.P.)
| | - Chad J. Boeckman
- Corteva Agriscience, Johnston, IA 50131, USA; (A.S.); (A.L.L.); (C.J.B.); (J.M.R.)
| | - Jay S. Petrick
- Bayer Crop Science, Chesterfield, MO 63017, USA; (P.R.); (J.R.F.); (J.S.P.)
| | - Jason M. Roper
- Corteva Agriscience, Johnston, IA 50131, USA; (A.S.); (A.L.L.); (C.J.B.); (J.M.R.)
| | | | - Ana M. Vélez
- Department of Entomology, University of Nebraska, Lincoln, NE 68583, USA; (M.D.); (J.D.R.)
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5
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Xie D, Yu Y, Dai Z, Sun J, Su J. Identification and characterization of miRNAs and target genes in developing flax seeds by multigroup analysis. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1903337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Dongwei Xie
- Department of Biotechnology, School of Life Science, Nantong University, Jiangsu, Nantong, PR China
| | - Yue Yu
- Laboratory of Germplasm Resources and Utilization of Economic Crops in South China, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Hunan, Changsha, PR China
| | - Zhigang Dai
- Laboratory of Germplasm Resources and Utilization of Economic Crops in South China, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Hunan, Changsha, PR China
| | - Jian Sun
- Department of Biotechnology, School of Life Science, Nantong University, Jiangsu, Nantong, PR China
| | - Jianguang Su
- Laboratory of Germplasm Resources and Utilization of Economic Crops in South China, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Hunan, Changsha, PR China
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6
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Ahmed W, Li R, Xia Y, Bai G, Siddique KHM, Zhang H, Zheng Y, Yang X, Guo P. Comparative Analysis of miRNA Expression Profiles Between Heat-Tolerant and Heat-Sensitive Genotypes of Flowering Chinese Cabbage Under Heat Stress Using High-Throughput Sequencing. Genes (Basel) 2020; 11:E264. [PMID: 32121287 PMCID: PMC7140848 DOI: 10.3390/genes11030264] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022] Open
Abstract
Heat stress disturbs cellular homeostasis, thus usually impairs yield of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). MicroRNAs (miRNAs) play a significant role in plant responses to different stresses by modulating gene expression at the post-transcriptional level. However, the roles that miRNAs and their target genes may play in heat tolerance of flowering Chinese cabbage remain poorly characterized. The current study sequenced six small RNA libraries generated from leaf tissues of flowering Chinese cabbage collected at 0, 6, and 12 h after 38 °C heat treatment, and identified 49 putative novel miRNAs and 43 known miRNAs that differentially expressed between heat-tolerant and heat-sensitive flowering Chinese cabbage. Among them, 14 novel and nine known miRNAs differentially expressed only in the heat-tolerant genotype under heat-stress, therefore, their target genes including disease resistance protein TAO1-like, RPS6, reticuline oxidase-like protein, etc. might play important roles in enhancing heat-tolerance. Gene Ontology (GO) analysis revealed that targets of these differentially expressed miRNAs may play key roles in responses to temperature stimulus, cell part, cellular process, cell, membrane, biological regulation, binding, and catalytic activities. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified their important functions in signal transduction, environmental adaptation, global and overview maps, as well as in stress adaptation and in MAPK signaling pathways such as cell death. These findings provide insight into the functions of the miRNAs in heat stress tolerance of flowering Chinese cabbage.
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Affiliation(s)
- Waqas Ahmed
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Guihua Bai
- United States Department of Agriculture - Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas 66506, United States of America
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, LB 5005, Perth WA 6001, Australia
| | - Hua Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510308, China
| | - Yansong Zheng
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510308, China
| | - Xinquan Yang
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
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7
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Rodrigues TB, Petrick JS. Safety Considerations for Humans and Other Vertebrates Regarding Agricultural Uses of Externally Applied RNA Molecules. FRONTIERS IN PLANT SCIENCE 2020; 11:407. [PMID: 32391029 PMCID: PMC7191066 DOI: 10.3389/fpls.2020.00407] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/20/2020] [Indexed: 05/13/2023]
Abstract
The potential of double-stranded RNAs (dsRNAs) for use as topical biopesticides in agriculture was recently discussed during an OECD (Organisation for Economic Co-operation and Development) Conference on RNA interference (RNAi)-based pesticides. Several topics were presented and these covered different aspects of RNAi technology, its application, and its potential effects on target and non-target organisms (including both mammals and non-mammals). This review presents information relating to RNAi mechanisms in vertebrates, the history of safe RNA consumption, the biological barriers that contribute to the safety of its consumption, and effects related to humans and other vertebrates as discussed during the conference. We also review literature related to vertebrates exposed to RNA molecules and further consider human health safety assessments of RNAi-based biopesticides. This includes possible routes of exposure other than the ingestion of potential residual material in food and water (such as dermal and inhalation exposures during application in the field), the implications of different types of formulations and RNA structures, and the possibility of non-specific effects such as the activation of the innate immune system or saturation of the RNAi machinery.
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Affiliation(s)
| | - Jay S. Petrick
- Bayer Crop Science, Chesterfield, MO, United States
- *Correspondence: Jay S. Petrick,
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8
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Cervera-Seco L, Marques MAC, Sanz-Carbonell A, Marquez-Molins J, Carbonell A, Darï S JA, Gomez G. Identification and Characterization of Stress-Responsive TAS3-Derived TasiRNAs in Melon. PLANT & CELL PHYSIOLOGY 2019; 60:2382-2393. [PMID: 31290971 DOI: 10.1093/pcp/pcz131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/27/2019] [Indexed: 05/27/2023]
Abstract
Small interfering RNAs (siRNA) are key regulators of gene expression that play essential roles in diverse biological processes. Trans-acting siRNAs (tasiRNAs) are a class of plant-endogenous siRNAs that lead the cleavage of nonidentical transcripts. TasiRNAs are usually involved in fine-tuning development. However, increasing evidence supports that tasiRNAs may be involved in stress response. Melon is a crop of great economic importance extensively cultivated in semiarid regions frequently exposed to changing environmental conditions that limit its productivity. However, knowledge of the precise role of siRNAs in general, and of tasiRNAs in particular, in regulating the response to adverse environmental conditions is limited. Here, we provide the first comprehensive analysis of computationally inferred melon-tasiRNAs responsive to two biotic (viroid-infection) and abiotic (cold treatment) stress conditions. We identify two TAS3-loci encoding to length (TAS3-L) and short (TAS3-S) transcripts. The TAS candidates predicted from small RNA-sequencing data were characterized according to their chromosome localization and expression pattern in response to stress. The functional activity of cmTAS genes was validated by transcript quantification and degradome assays of the tasiRNA precursors and their predicted targets. Finally, the functionality of a representative cmTAS3-derived tasiRNA (TAS3-S) was confirmed by transient assays showing the cleavage of ARF target transcripts.
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Affiliation(s)
- Luis Cervera-Seco
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cient�ficas (CSIC)-Universitat de Val�ncia (UV), Parc Cient�fic, Cat. Agust�n Escardino 9, Paterna, Spain
| | - Marï A Carmen Marques
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cient�ficas (CSIC)-Universitat de Val�ncia (UV), Parc Cient�fic, Cat. Agust�n Escardino 9, Paterna, Spain
| | - Alejandro Sanz-Carbonell
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cient�ficas (CSIC)-Universitat de Val�ncia (UV), Parc Cient�fic, Cat. Agust�n Escardino 9, Paterna, Spain
| | - Joan Marquez-Molins
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cient�ficas (CSIC)-Universitat de Val�ncia (UV), Parc Cient�fic, Cat. Agust�n Escardino 9, Paterna, Spain
| | - Alberto Carbonell
- Instituto de Biolog�a Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cient�ficas (CSIC) Universitat Polit�cnica de Val�ncia, CPI 8E, Av. de los Naranjos s/n, Valencia, Spain
| | - Josï-Antonio Darï S
- Instituto de Biolog�a Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cient�ficas (CSIC) Universitat Polit�cnica de Val�ncia, CPI 8E, Av. de los Naranjos s/n, Valencia, Spain
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cient�ficas (CSIC)-Universitat de Val�ncia (UV), Parc Cient�fic, Cat. Agust�n Escardino 9, Paterna, Spain
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9
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Azizi P, Osman M, Hanafi MM, Sahebi M, Rafii MY, Taheri S, Harikrishna JA, Tarinejad AR, Mat Sharani S, Yusuf MN. Molecular insights into the regulation of rice kernel elongation. Crit Rev Biotechnol 2019; 39:904-923. [PMID: 31303070 DOI: 10.1080/07388551.2019.1632257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A large number of rice agronomic traits are complex, multi factorial and polygenic. As the mechanisms and genes determining grain size and yield are largely unknown, the identification of regulatory genes related to grain development remains a preeminent approach in rice genetic studies and breeding programs. Genes regulating cell proliferation and expansion in spikelet hulls and participating in endosperm development are the main controllers of rice kernel elongation and grain size. We review here and discuss recent findings on genes controlling rice grain size and the mechanisms, epialleles, epigenomic variation, and assessment of controlling genes using genome-editing tools relating to kernel elongation.
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Affiliation(s)
- P Azizi
- a Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia , Serdang , Malaysia.,b Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia , Serdang , Malaysia
| | - M Osman
- c Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia , Serdang , Malaysia
| | - M M Hanafi
- a Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia , Serdang , Malaysia.,b Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia , Serdang , Malaysia.,d Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia , Serdang , Malaysia
| | - M Sahebi
- b Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia , Serdang , Malaysia
| | - M Y Rafii
- b Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia , Serdang , Malaysia.,c Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia , Serdang , Malaysia
| | - S Taheri
- e Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya , Kuala Lumpur , Malaysia
| | - J A Harikrishna
- e Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya , Kuala Lumpur , Malaysia
| | - A R Tarinejad
- f Department of Biotechnology, Faculty of Agriculture, Azarbaijan Shahid Madani University , Tabriz , Iran
| | - S Mat Sharani
- g Malaysia Genome Institute , Jalan Bangi , Malaysia
| | - M N Yusuf
- g Malaysia Genome Institute , Jalan Bangi , Malaysia
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10
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Nadiya F, Anjali N, Thomas J, Gangaprasad A, Sabu KK. Deep sequencing identified potential miRNAs involved in defence response, stress and plant growth characteristics of wild genotypes of cardamom. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:3-14. [PMID: 30098091 DOI: 10.1111/plb.12888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 08/06/2018] [Indexed: 06/08/2023]
Abstract
Cardamom has long been used as a food flavouring agent and in ayurvedic medicines for mouth ulcers, digestive problems and even depression. Extensive occurrence of pests and diseases adversely affect its cultivation and result in substantial reductions in total production and productivity. Numerous studies revealed the significant role of miRNAs in plant biotic stress responses. In the current study, miRNA profiling of cultivar and wild cardamom genotypes was performed using an Ion Proton sequencer. We identified 161 potential miRNAs representing 42 families, including monocot/tissue-specific and 14 novel miRNAs in both genotypes. Significant differences in miRNA family abundance between the libraries were observed in read frequencies. A total of 19 miRNAs (from known miRNAs) displayed a twofold difference in expression between wild and cultivar genotypes. We found 1168 unique potential targets for 40 known miRNA families in wild and 1025 potential targets for 42 known miRNA families in cultivar genotypes. The differential expression analysis revealed that most miRNAs identified were highly expressed in cultivars and, furthermore, lower expression of miR169 and higher expression of miR529 in wild cardamom proved evidence that wild genotypes have stronger drought stress tolerance and floral development than cultivars. Potential targets predicted for the newly identified miRNAs from the miRNA libraries of wild and cultivar cardamom genotypes involved in metabolic and developmental processes and in response to various stimuli. qRT-PCR confirmed miRNAs were differentially expressed between wild and cultivar genotypes. Furthermore, four target genes were validated experimentally to confirm miRNA-mRNA target pairing using RNA ligase-mediated 5' Rapid Amplification of cDNA Ends (5'RLM-RACE) PCR.
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Affiliation(s)
- F Nadiya
- Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Palode, Thiruvananthapuram, India
| | - N Anjali
- Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Palode, Thiruvananthapuram, India
| | - J Thomas
- Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Palode, Thiruvananthapuram, India
| | - A Gangaprasad
- Department of Botany, University of Kerala, Thiruvananthapuram, India
| | - K K Sabu
- Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Palode, Thiruvananthapuram, India
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11
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Liu Y, Ke L, Wu G, Xu Y, Wu X, Xia R, Deng X, Xu Q. miR3954 is a trigger of phasiRNAs that affects flowering time in citrus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:263-275. [PMID: 28749585 DOI: 10.1111/tpj.13650] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 07/20/2017] [Accepted: 07/25/2017] [Indexed: 05/27/2023]
Abstract
In plant, a few 22-nt miRNAs direct cleavages of their targets and trigger the biogenesis of phased small interfering RNAs (phasiRNAs) in plant. In this study, we characterized a miRNA triggering phasiRNAs generation, miR3954, and explored its downstream target genes and potential function. Our results demonstrated that miR3954 showed specific expression in the flowers of citrus species, and it targeted a NAC transcription factor (Cs7 g22460) and two non-coding RNA transcripts (lncRNAs, Cs1 g09600 and Cs1 g09635). The production of phasiRNAs was detected from transcripts targeted by miR3954, and was further verified in both sequencing data and transient expression experiments. PhasiRNAs derived from the two lncRNAs targeted not only miR3954-targeted NAC gene but also additional NAC homologous genes. No homologous genes of these two lncRNAs were found in plants other than citrus species, implying that this miR3954-lncRNAs-phasiRNAs-NAC pathway is likely citrus-specific. Transgenic analysis indicated that the miR3954-overexpressing lines showed decreased transcripts of lncRNA, elevated abundance of phasiRNAs and reduced expression of NAC genes. Interestingly, the overexpression of miR3954 leads to early flowering in citrus plants. In summary, our results illustrated a model of the regulatory network of miR3954-lncRNA-phasiRNAs-NAC, which may be functionally involved in flowering in citrus.
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Affiliation(s)
- Yuanlong Liu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lili Ke
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guizhi Wu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuantao Xu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaomeng Wu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, 510642, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
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12
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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13
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Singh A, Saraf S, Dasgupta I, Mukherjee SK. Identification and validation of a virus-inducible ta-siRNA-generating TAS4 locus in tomato. J Biosci 2016; 41:109-18. [PMID: 26949093 DOI: 10.1007/s12038-016-9590-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Trans-acting small interfering RNAs (ta-siRNAs) are a class of endogenous small RNA, associated with posttranscriptional gene silencing. Their biogenesis requires an initial microRNA (miRNA)-mediated cleavage of precursor RNA. Around 20 different ta-siRNA-producing loci (TASs), whose sequences are conserved, are reported in plants. In tomato, two TAS gene families have been identified, which are found to target auxin response factor gene and bacterial spot disease resistance protein Bs4 gene. Using high-throughput computational and experimental approach, we identified a new locus-producing ta-siRNA in tomato. We have also identified the putative miRNA regulating the production of ta-siRNA from this locus. The ta-siRNAs generated from TAS4 were up-regulated upon infection with a DNA virus. The potential targets of ta-siRNAs were predicted to be variety of proteins including MYB transcription factors and cell cycle regulators for some of the ta-siRNAs produced.
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Affiliation(s)
- Archana Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
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14
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Hackenberg M, Rueda A, Gustafson P, Langridge P, Shi BJ. Generation of different sizes and classes of small RNAs in barley is locus, chromosome and/or cultivar-dependent. BMC Genomics 2016; 17:735. [PMID: 27633252 PMCID: PMC5025612 DOI: 10.1186/s12864-016-3023-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 08/17/2016] [Indexed: 12/20/2022] Open
Abstract
Background Various small RNA (sRNA) sizes and varieties have been identified, but their relationship as well as relationship with their origins and allocations have not been well understood or investigated. Results By comparing sRNAs generated from two barley cultivars, Golden Promise (GP) and Pallas, we identified that the generation of different sizes and types of sRNAs in barley was locus-, chromosome- and/or cultivar-dependent. 20-nt sRNAs mainly comprising miRNAs and chloroplast-derived sRNAs were significantly over-expressed in Pallas vs. GP on chromosomes 3H and 6H. MiRNAs-enriched 21-nt sRNAs were significantly over-expressed in Pallas vs. GP only on chromosome 4H. On chromosome 5H this size of sRNAs was significantly under-expressed in Pallas, so were 22-nt sRNAs mainly comprising miRNAs and repeat-derived sRNAs. 24-nt sRNAs mostly derived from repeats were evenly distributed in all chromosomes and expressed similarly between GP and Pallas. Unlike other sizes of sRNAs, 24-nt sRNAs were little conserved in other plant species. Abundant sRNAs were mostly generated from 3’ terminal regions of chromosome 1H and 5’ terminal regions of chromosome 5H. Over-expressed miRNAs in GP vs. Pallas primarily function in stress responses and iron-binding. Conclusions Our study indicates that 23−24-nt sRNAs may be linked to repressive chromatin modifications and function in genome stability while 20−21-nt sRNAs may be important for the cultivar specificity. This study provides a novel insight into the mechanism of sRNA expression and function in barley. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3023-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Hackenberg
- Computational Genomics and Bioinformatics Group, Genetics Department, University of Granada, 18071, Granada, Spain
| | - Antonio Rueda
- Genomics and Bioinformatics Platform of Andalusia (GBPA), Edificio INSUR, Calle Albert Einstein, 41092, Seville, Spain
| | - Perry Gustafson
- USDA-ARS, 206 Curtis Hall, University of Missouri, Columbia, MO, 65211-7020, USA
| | - Peter Langridge
- Australian Centre for Plant Functional Genomics, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Bu-Jun Shi
- Australian Centre for Plant Functional Genomics, The University of Adelaide, Adelaide, South Australia 5005, Australia.
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15
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Ecological risk assessment for DvSnf7 RNA: A plant-incorporated protectant with targeted activity against western corn rootworm. Regul Toxicol Pharmacol 2016; 81:77-88. [PMID: 27494948 DOI: 10.1016/j.yrtph.2016.08.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 12/31/2022]
Abstract
MON 87411 maize, which expresses DvSnf7 RNA, was developed to provide an additional mode of action to confer protection against corn rootworm (Diabrotica spp.). A critical step in the registration of a genetically engineered crop with an insecticidal trait is performing an ecological risk assessment to evaluate the potential for adverse ecological effects. For MON 87411, an assessment plan was developed that met specific protection goals by characterizing the routes and levels of exposure, and testing representative functional taxa that would be directly or indirectly exposed in the environment. The potential for toxicity of DvSnf7 RNA was evaluated with a harmonized battery of non-target organisms (NTOs) that included invertebrate predators, parasitoids, pollinators, soil biota as well as aquatic and terrestrial vertebrate species. Laboratory tests evaluated ecologically relevant endpoints such as survival, growth, development, and reproduction and were of sufficient duration to assess the potential for adverse effects. No adverse effects were observed with any species tested at, or above, the maximum expected environmental concentration (MEEC). All margins of exposure for NTOs were >10-fold the MEEC. Therefore, it is reasonable to conclude that exposure to DvSnf7 RNA, both directly and indirectly, is safe for NTOs at the expected field exposure levels.
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16
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Li H, Hu B, Wang W, Zhang Z, Liang Y, Gao X, Li P, Liu Y, Zhang L, Chu C. Identification of microRNAs in rice root in response to nitrate and ammonium. J Genet Genomics 2016; 43:651-661. [PMID: 27372185 DOI: 10.1016/j.jgg.2015.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/15/2015] [Accepted: 12/18/2015] [Indexed: 01/03/2023]
Abstract
Nitrate and ammonium are two major nitrogen (N) sources for higher plants, but they differ in utilization and signaling. MicroRNAs (miRNAs) play an essential role in N signal transduction; however, knowledge remains limited about the regulatory role of miRNAs responsive to different N sources, especially in crop plants. To get global overview on miRNAs involved in N response in rice, we performed high-throughput small RNA-sequencing under different nitrate and ammonium treatments. The results demonstrated that only 16 and 11 miRNAs were significantly induced by nitrate and ammonium under short-term treatment, respectively. However, 60 differentially expressed miRNAs were found between nitrate and ammonium under long-term cultivation. These results suggested that miRNA response greatly differentiates between nitrate and ammonium treatments. Furthermore, 44 miRNAs were found to be differentially expressed between high- and low-N conditions. Our study reveals comprehensive expression profiling of miRNAs responsive to different N sources and different N treatments, which advances our understanding on the regulation of different N signaling and homeostasis mediated by miRNAs.
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Affiliation(s)
- Hua Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Hu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Wang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihua Zhang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Liang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaokai Gao
- School of Agriculture, Henan University of Science and Technology, Luoyang 471023, China
| | - Peng Li
- School of Agriculture, Henan University of Science and Technology, Luoyang 471023, China
| | - Yongqiang Liu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lianhe Zhang
- School of Agriculture, Henan University of Science and Technology, Luoyang 471023, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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17
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Khatabi B, Arikit S, Xia R, Winter S, Oumar D, Mongomake K, Meyers BC, Fondong VN. High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs. BMC Genomics 2016; 17:85. [PMID: 26822616 PMCID: PMC4730657 DOI: 10.1186/s12864-016-2391-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 01/13/2016] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Small RNAs (sRNAs) are endogenous sRNAs that play regulatory roles in plant growth, development, and biotic and abiotic stress responses. In plants, one subset of sRNAs, microRNAs (miRNAs) exhibit tissue-differential expression and regulate gene expression mainly through direct cleavage of mRNA or indirectly via production of secondary phased siRNAs (phasiRNAs) that silence cognate target transcripts in trans. RESULTS Here, we have identified cassava (Manihot esculenta Crantz) miRNAs using high resolution sequencing of sRNA libraries from leaf, stem, callus, male and female flower tissues. To analyze the data, we built a cassava genome database and, via sequence analysis and secondary structure prediction, 38 miRNAs not previously reported in cassava were identified. These new cassava miRNAs included two miRNAs not previously been reported in any plant species. The miRNAs exhibited tissue-differential accumulation as confirmed by quantitative RT-PCR and Northern blot analysis, largely reflecting levels observed in sequencing data. Some of the miRNAs identified were predicted to trigger production of secondary phased siRNAs (phasiRNAs) from 80 PHAS loci. CONCLUSIONS Cassava is a woody perennial shrub, grown principally for its starch-rich storage roots, which are rich in calories. In this study, new miRNAs were identified and their expression was validated using qRT-PCR of RNA from five different tissues. The data obtained expand the list of annotated miRNAs and provide additional new resources for cassava improvement research.
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Affiliation(s)
- Behnam Khatabi
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA.
| | - Siwaret Arikit
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA.
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen and Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand.
| | - Rui Xia
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA.
| | - Stephan Winter
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
| | - Doungous Oumar
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA.
- Ekona Research Centre, Southwest, Cameroon.
| | - Kone Mongomake
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA.
- Université Nangui Abrogoua, Abidjan, Côte d'Ivoire.
| | - Blake C Meyers
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Vincent N Fondong
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA.
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18
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Pappas MDCR, Pappas GJ, Grattapaglia D. Genome-wide discovery and validation of Eucalyptus small RNAs reveals variable patterns of conservation and diversity across species of Myrtaceae. BMC Genomics 2015; 16:1113. [PMID: 26714854 PMCID: PMC4696225 DOI: 10.1186/s12864-015-2322-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 12/15/2015] [Indexed: 11/17/2022] Open
Abstract
Background Micro RNAs are a class of small non coding RNAs of 20–24 nucleotides transcribed as single stranded precursors from MIR gene loci. Initially described as post-transcriptional regulators involved in development, two decades ago, miRNAs have been proven to regulate a wide range of processes in plants such as germination, morphology and responses to biotic and abiotic stress. Despite wide conservation in plants, a number of miRNAs are lineage specific. We describe the first genome wide survey of Eucalyptus miRNAs based on high throughput sequencing. Results In addition to discovering small RNA sequences, MIR loci were mapped onto the reference genome and interspecific variability investigated. Sequencing was carried out for the two most world widely planted species, E. grandis and E. globulus. To maximize discovery, E. grandis samples were from BRASUZ1, the same tree whose genome provided the reference sequence. Interspecific analysis reinforces the variability in small RNA repertoire even between closely related species. Characterization of Eucalyptus small RNA sequences showed 95 orthologous to conserved miRNAs and 193 novel miRNAs. In silico target prediction confirmed 163 novel miRNAs and degradome sequencing experimentally confirmed several hundred targets. Experimental evidence based on the exclusive expression of a set of small RNAs across 16 species within Myrtaceae further highlighted variable patterns of conservation and diversity of these regulatory elements. Conclusions The description of miRNAs in Eucalyptus contributes to scientific knowledge of this vast genre, which is the most widely planted hardwood crop in the tropical and subtropical world, adding another important element to the annotation of Eucalyptus grandis reference genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2322-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Dario Grattapaglia
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil. .,Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil.
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19
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Carbonell A, Fahlgren N, Mitchell S, Cox KL, Reilly KC, Mockler TC, Carrington JC. Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:1061-1075. [PMID: 25809382 PMCID: PMC4464980 DOI: 10.1111/tpj.12835] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/11/2015] [Accepted: 03/19/2015] [Indexed: 05/17/2023]
Abstract
Artificial microRNAs (amiRNAs) are used for selective gene silencing in plants. However, current methods to produce amiRNA constructs for silencing transcripts in monocot species are not suitable for simple, cost-effective and large-scale synthesis. Here, a series of expression vectors based on Oryza sativa MIR390 (OsMIR390) precursor was developed for high-throughput cloning and high expression of amiRNAs in monocots. Four different amiRNA sequences designed to target specifically endogenous genes and expressed from OsMIR390-based vectors were validated in transgenic Brachypodium distachyon plants. Surprisingly, amiRNAs accumulated to higher levels and were processed more accurately when expressed from chimeric OsMIR390-based precursors that include distal stem-loop sequences from Arabidopsis thaliana MIR390a (AtMIR390a). In all cases, transgenic plants displayed the predicted phenotypes induced by target gene repression, and accumulated high levels of amiRNAs and low levels of the corresponding target transcripts. Genome-wide transcriptome profiling combined with 5'-RLM-RACE analysis in transgenic plants confirmed that amiRNAs were highly specific.
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Affiliation(s)
| | - Noah Fahlgren
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Skyler Mitchell
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Kevin L Cox
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Kevin C Reilly
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
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20
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Predicted trans-acting siRNAs in the human brain. Int J Mol Sci 2015; 16:3377-90. [PMID: 25654231 PMCID: PMC4346901 DOI: 10.3390/ijms16023377] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/10/2014] [Accepted: 12/25/2014] [Indexed: 01/27/2023] Open
Abstract
Endogenous small non-coding RNAs play pivotal roles in regulating gene expression in eukaryotes. Many studies have investigated the function and molecular mechanism of microRNAs in the development and disease of various organisms via mRNA repression of protein-coding genes. Recent findings indicate microRNAs might trigger the generation of trans-acting small interfering RNAs (ta-siRNAs). The interaction among different types of small RNA molecules reveals an even more complicated and elaborate pattern of RNA regulation during gene expression than previously thought. We developed a method for mining ta-siRNA sequences and evaluated the performance of our novel method using data from Arabidopsis thaliana. Additionally, using small RNA and degradome data for the human brain, we identified 155 small RNAs that satisfied ta-siRNA characteristics. The DRAXIN and ATCAY genes, which are preferentially expressed in the human brain, were predicted to be the targets of 12 potential ta-siRNAs.
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21
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Zhang B, Wang Q. MicroRNA-based biotechnology for plant improvement. J Cell Physiol 2015; 230:1-15. [PMID: 24909308 DOI: 10.1002/jcp.24685] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 05/21/2014] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are an extensive class of newly discovered endogenous small RNAs, which negatively regulate gene expression at the post-transcription levels. As the application of next-generation deep sequencing and advanced bioinformatics, the miRNA-related study has been expended to non-model plant species and the number of identified miRNAs has dramatically increased in the past years. miRNAs play a critical role in almost all biological and metabolic processes, and provide a unique strategy for plant improvement. Here, we first briefly review the discovery, history, and biogenesis of miRNAs, then focus more on the application of miRNAs on plant breeding and the future directions. Increased plant biomass through controlling plant development and phase change has been one achievement for miRNA-based biotechnology; plant tolerance to abiotic and biotic stress was also significantly enhanced by regulating the expression of an individual miRNA. Both endogenous and artificial miRNAs may serve as important tools for plant improvement.
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Affiliation(s)
- Baohong Zhang
- Department of Biology, East Carolina University, Greenville, North Carolina; Henan Institute of Sciences and Technology, Xinxiang, Henan, China
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22
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Xian Z, Huang W, Yang Y, Tang N, Zhang C, Ren M, Li Z. miR168 influences phase transition, leaf epinasty, and fruit development via SlAGO1s in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6655-66. [PMID: 25378580 DOI: 10.1093/jxb/eru387] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In Arabidopsis thaliana, Argonaute1 (AGO1) interacts with miR168 to modulate the small RNA regulatory pathway. However, the underlying mechanism of regulation and relationship between AGO1 and miR168 is poorly understood in the cash crop Solanum lycopersicum (tomato). We previously found that SlAGO1A and SlAGO1B were cleaved by miR168 in tomato. In this study, we show that SlAGO1A and SlAGO1B accumulate in miR168-sponge transgenic plants, and that expression of miR168-resistant SlAGO1A (4m-SlAGO1A) and SlAGO1B (4m-SlAGO1B) in tomato results in a series of defects affecting growth rate, floral timing, leaves, and fruit. Accumulation of miR156 was found when 4m-SlAGO1A was at an early developmental stage compared to the wild type and original SlAGO1A transgenic plants, and miR172 was highly expressed in adult 4m-SlAGO1A compared to the controls. In addition, the expression of multiple small RNAs was altered in 4m-SlAGO1A. Taken together, our data provide novel insights into the interaction between SlAGO1s and miR168 in determining growth rate, phase change, leaf epinasty, fruit initiation and expansion, and other developmental processes in tomato.
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Affiliation(s)
- Zhiqiang Xian
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing 400044, People's Republic of China
| | - Wei Huang
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing 400044, People's Republic of China
| | - Yingwu Yang
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing 400044, People's Republic of China
| | - Ning Tang
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing 400044, People's Republic of China
| | - Chao Zhang
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing 400044, People's Republic of China
| | - Maozhi Ren
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing 400044, People's Republic of China
| | - Zhengguo Li
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing 400044, People's Republic of China
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23
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Petrick JS, Moore WM, Heydens WF, Koch MS, Sherman JH, Lemke SL. A 28-day oral toxicity evaluation of small interfering RNAs and a long double-stranded RNA targeting vacuolar ATPase in mice. Regul Toxicol Pharmacol 2014; 71:8-23. [PMID: 25445299 DOI: 10.1016/j.yrtph.2014.10.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 10/24/2022]
Abstract
New biotechnology-derived crop traits have been developed utilizing the natural process of RNA interference (RNAi). However, plant-produced double stranded RNAs (dsRNAs) are not known to present a hazard to mammals because numerous biological barriers limit uptake and potential for activity. To evaluate this experimentally, dsRNA sequences matching the mouse vATPase gene (an established target for control of corn rootworms) were evaluated in a 28-day toxicity study with mice. Test groups were orally gavaged with escalating doses of either a pool of four 21-mer vATPase small interfering RNAs (siRNAs) or a 218-base pair vATPase dsRNA. There were no treatment-related effects on body weight, food consumption, clinical observations, clinical chemistry, hematology, gross pathology, or histopathology endpoints. The highest dose levels tested were considered to be the no observed adverse effect levels (NOAELs) for the 21-mer siRNAs (48 mg/kg/day) and the 218 bp dsRNA (64 mg/kg/day). As an additional exploratory endpoint, vATPase gene expression, was evaluated in selected gastrointestinal tract and systemic tissues. The results of this assay did not indicate treatment-related suppression of vATPase. The results of this study indicate that orally ingested dsRNAs, even those targeting a gene in the test species, do not produce adverse health effects in mammals.
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Affiliation(s)
- Jay S Petrick
- Monsanto Company, 800 North Lindbergh Boulevard, Creve Coeur, MO 63167, USA.
| | - William M Moore
- Monsanto Company, 800 North Lindbergh Boulevard, Creve Coeur, MO 63167, USA
| | - William F Heydens
- Monsanto Company, 800 North Lindbergh Boulevard, Creve Coeur, MO 63167, USA
| | - Michael S Koch
- Monsanto Company, 800 North Lindbergh Boulevard, Creve Coeur, MO 63167, USA
| | - James H Sherman
- Monsanto Company, 800 North Lindbergh Boulevard, Creve Coeur, MO 63167, USA
| | - Shawna L Lemke
- Monsanto Company, 800 North Lindbergh Boulevard, Creve Coeur, MO 63167, USA
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Lack of detectable oral bioavailability of plant microRNAs after feeding in mice. Nat Biotechnol 2014; 31:965-7. [PMID: 24213763 DOI: 10.1038/nbt.2737] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process. Sci Rep 2014; 4:5559. [PMID: 24993353 PMCID: PMC4081896 DOI: 10.1038/srep05559] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/16/2014] [Indexed: 11/08/2022] Open
Abstract
Genomic methylation is variable under biotic and abiotic stresses in plants. In particular, viral infection is thought to significantly increase genomic methylation with particularly high activity around transposable elements. Here we present the genomic methylation profiles of grains of archaeological barley (Hordeum vulgare) from several strata from a site in southern Egypt, from the Napatan to the Islamic periods (800 BCE - 1812 CE). One sample tested positive for viral infection and exhibits an unusually high degree of genomic methylation compared to the rest. A decreasing trend in global methylation levels according to deposition date shows in-situ de-methylation of 5-methylcytosine, which can be described as a diagenetic process. This is most likely a deamination mediated de-methylation process and is expected to lead to 5 mC > T base modifications in addition to the C > U modifications due to cytosine deamination, so represents a time-dependent process of DNA diagenesis in ancient DNA.
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Sun F, Guo G, Du J, Guo W, Peng H, Ni Z, Sun Q, Yao Y. Whole-genome discovery of miRNAs and their targets in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2014; 14:142. [PMID: 24885911 PMCID: PMC4048363 DOI: 10.1186/1471-2229-14-142] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 05/19/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are small, non-coding RNAs playing essential roles in plant growth, development, and stress responses. Sequencing of small RNAs is a starting point for understanding their number, diversity, expression and possible roles in plants. RESULTS In this study, we conducted a genome-wide survey of wheat miRNAs from 11 tissues, characterizing a total of 323 novel miRNAs belonging to 276 families in wheat. A miRNA conservation analysis identified 191 wheat-specific miRNAs, 2 monocot-specific miRNAs, and 30 wheat-specific variants from 9 highly conserved miRNA families. To understand possible roles of wheat miRNAs, we determined 524 potential targets for 124 miRNA families through degradome sequencing, and cleavage of a subset of them was validated via 5' RACE. Based on the genome-wide identification and characterization of miRNAs and their associated target genes, we further identified 64 miRNAs preferentially expressing in developing or germinating grains, which could play important roles in grain development. CONCLUSION We discovered 323 wheat novel miRNAs and 524 target genes for 124 miRNA families in a genome-wide level, and our data will serve as a foundation for future research into the functional roles of miRNAs in wheat.
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Affiliation(s)
- Fenglong Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Guanghui Guo
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Jinkun Du
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Weiwei Guo
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
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Xiao B, Yang X, Ye CY, Liu Y, Yan C, Wang Y, Lu X, Li Y, Fan L. A diverse set of miRNAs responsive to begomovirus-associated betasatellite in Nicotiana benthamiana. BMC PLANT BIOLOGY 2014; 14:60. [PMID: 24618068 PMCID: PMC4008317 DOI: 10.1186/1471-2229-14-60] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 03/04/2014] [Indexed: 05/22/2023]
Abstract
BACKGROUND Roles of microRNAs (miRNAs) and short interfering RNAs (siRNAs) in biotic stress responses, e.g., viral infection, have been demonstrated in plants by many studies. Tomato yellow leaf curl China virus (TYLCCNV) is a monopartite begomovirus that can systemically infect Solanaceae plants, and induces leaf curling, yellowing and enation symptoms when co-inoculated with a betasatellite (TYLCCNB). The released genome sequence of Nicotiana benthamiana provides an opportunity to identify miRNAs and siRNAs responsive to begomovirus-associated betasatellite in N. benthamiana. RESULTS miRNAs were identified in three small RNA libraries generated using RNA isolated from N. benthamiana plants systemically infected with TYLCCNV (Y10A) alone, co-infected with Y10A and its betasatellite TYLCCNB (Y10β) or a TYLCCNB mutant (Y10mβ) that contains a mutated βC1, the sole betasatellite-encoded protein. A total of 196 conserved miRNAs from 38 families and 197 novel miRNAs from 160 families were identified. Northern blot analysis confirmed that expression of species-specific miRNAs was much lower than that of conserved miRNAs. Several conserved and novel miRNAs were found to be responsive to co-infection of Y10A and Y10β but not to co-infection of Y10A and Y10mβ, suggesting that these miRNAs might play a role unique to interaction between Y10β and N. benthamiana. Additionally, we identified miRNAs that can trigger the production of phased secondary siRNAs (phasiRNAs). CONCLUSIONS Identification of miRNAs with differential expression profiles in N. benthamiana co-infected with Y10A and Y10β and co-infected with Y10A and Y10mβ indicates that these miRNAs are betasatellite-responsive. Our result also suggested a potential role of miRNA-mediated production of phasiRNAs in interaction between begomovirus and N. benthamiana.
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Affiliation(s)
- Bingguang Xiao
- Yunnan Academy of Tobacco Agricultural Sciences and China Tobacco Breeding Research Center at Yunnan, Yuxi 653100, China
| | - Xiuling Yang
- Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chu-Yu Ye
- Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yang Liu
- Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chenhai Yan
- Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu Wang
- Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiuping Lu
- Yunnan Academy of Tobacco Agricultural Sciences and China Tobacco Breeding Research Center at Yunnan, Yuxi 653100, China
| | - Yongping Li
- Yunnan Academy of Tobacco Agricultural Sciences and China Tobacco Breeding Research Center at Yunnan, Yuxi 653100, China
| | - Longjiang Fan
- Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
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Jiang J, Lv M, Liang Y, Ma Z, Cao J. Identification of novel and conserved miRNAs involved in pollen development in Brassica campestris ssp. chinensis by high-throughput sequencing and degradome analysis. BMC Genomics 2014; 15:146. [PMID: 24559317 PMCID: PMC3936892 DOI: 10.1186/1471-2164-15-146] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 02/07/2014] [Indexed: 11/21/2022] Open
Abstract
Background microRNAs (miRNAs) are endogenous, noncoding, small RNAs that have essential regulatory functions in plant growth, development, and stress response processes. However, limited information is available about their functions in sexual reproduction of flowering plants. Pollen development is an important process in the life cycle of a flowering plant and is a major factor that affects the yield and quality of crop seeds. Results This study aims to identify miRNAs involved in pollen development. Two independent small RNA libraries were constructed from the flower buds of the male sterile line (Bcajh97-01A) and male fertile line (Bcajh97-01B) of Brassica campestris ssp. chinensis. The libraries were subjected to high-throughput sequencing by using the Illumina Solexa system. Eight novel miRNAs on the other arm of known pre-miRNAs, 54 new conserved miRNAs, and 8 novel miRNA members were identified. Twenty-five pairs of novel miRNA/miRNA* were found. Among all the identified miRNAs, 18 differentially expressed miRNAs with over two-fold change between flower buds of male sterile line (Bcajh97-01A) and male fertile line (Bcajh97-01B) were identified. qRT-PCR analysis revealed that most of the differentially expressed miRNAs were preferentially expressed in flower buds of the male fertile line (Bcajh97-01B). Degradome analysis showed that a total of 15 genes were predicted to be the targets of seven miRNAs. Conclusions Our findings provide an overview of potential miRNAs involved in pollen development and interactions between miRNAs and their corresponding targets, which may provide important clues on the function of miRNAs in pollen development.
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Affiliation(s)
| | | | | | | | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.
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Liu Y, Wang Y, Zhu QH, Fan L. Identification of phasiRNAs in wild rice (Oryza rufipogon). PLANT SIGNALING & BEHAVIOR 2013; 8:25079. [PMID: 23733069 PMCID: PMC4005798 DOI: 10.4161/psb.25079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Plant miRNAs can trigger the production of phased, secondary siRNAs from either non-coding or protein-coding genes. In this study, at least 864 and 3,961 loci generating 21-nt and 24-nt phased siRNAs (phasiRNAs),respectively, were identified in three tissues from wild rice. Of these phasiRNA-producing loci, or PHAS genes, biogenesis of phasiRNAs in at least 160 of 21-nt and 254 of 24-nt loci could be triggered by interaction with miRNA(s). Developing seeds had more PHAS genes than leaves and roots. Genetic constrain on miRNA-triggered PHAS genes suggests that phasiRNAs might be one of the driving forces contributed to rice domestication.
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Affiliation(s)
- Yang Liu
- Department of Agronomy & James D. Watson Institute of Genome Sciences; Zhejiang University; Hangzhou, PR China
| | - Yu Wang
- Department of Agronomy & James D. Watson Institute of Genome Sciences; Zhejiang University; Hangzhou, PR China
| | | | - Longjiang Fan
- Department of Agronomy & James D. Watson Institute of Genome Sciences; Zhejiang University; Hangzhou, PR China
- Correspondence to: Longjiang Fan,
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Fei Q, Xia R, Meyers BC. Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks. THE PLANT CELL 2013; 25:2400-15. [PMID: 23881411 PMCID: PMC3753373 DOI: 10.1105/tpc.113.114652] [Citation(s) in RCA: 353] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 06/07/2013] [Accepted: 07/08/2013] [Indexed: 05/18/2023]
Abstract
Plant genomes are the source of large numbers of small RNAs, generated via a variety of genetically separable pathways. Several of these pathways converge in the production of phased, secondary, small interfering RNAs (phasiRNAs), originally designated as trans-acting small interfering RNAs or tasiRNAs. PhasiRNA biogenesis requires the involvement of microRNAs as well as the cellular machinery for the production of siRNAs. PhasiRNAs in Arabidopsis thaliana have been well described for their ability to function in trans to suppress target transcript levels. Plant genomic data from an expanding set of species have demonstrated that Arabidopsis is relatively sparing in its use of phasiRNAs, while other genomes contain hundreds or even thousands of phasiRNA-generating loci. In the dicots, targets of those phasiRNAs include several large or conserved families of genes, such as those encoding disease resistance proteins or transcription factors. Suppression of nucleotide-binding, leucine-rich repeat (NB-LRR) disease resistance genes by small RNAs is particularly unusual because of a high level of redundancy. In this review, we discuss plant phasiRNAs and the possible mechanistic significance of phasiRNA-based regulation of the NB-LRRs.
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Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature 2013; 498:385-9. [PMID: 23636332 DOI: 10.1038/nature12178] [Citation(s) in RCA: 250] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 04/12/2013] [Indexed: 12/31/2022]
Abstract
DNA methylation is an epigenetic modification that has critical roles in gene silencing, development and genome integrity. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and targeted by 24-nucleotide small interfering RNAs (siRNAs) through a pathway termed RNA-directed DNA methylation (RdDM). This pathway requires two plant-specific RNA polymerases: Pol-IV, which functions to initiate siRNA biogenesis, and Pol-V, which functions to generate scaffold transcripts that recruit downstream RdDM factors. To understand the mechanisms controlling Pol-IV targeting we investigated the function of SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1), a Pol-IV-interacting protein. Here we show that SHH1 acts upstream in the RdDM pathway to enable siRNA production from a large subset of the most active RdDM targets, and that SHH1 is required for Pol-IV occupancy at these same loci. We also show that the SHH1 SAWADEE domain is a novel chromatin-binding module that adopts a unique tandem Tudor-like fold and functions as a dual lysine reader, probing for both unmethylated K4 and methylated K9 modifications on the histone 3 (H3) tail. Finally, we show that key residues within both lysine-binding pockets of SHH1 are required in vivo to maintain siRNA and DNA methylation levels as well as Pol-IV occupancy at RdDM targets, demonstrating a central role for methylated H3K9 binding in SHH1 function and providing the first insights into the mechanism of Pol-IV targeting. Given the parallels between methylation systems in plants and mammals, a further understanding of this early targeting step may aid our ability to control the expression of endogenous and newly introduced genes, which has broad implications for agriculture and gene therapy.
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Petrick JS, Brower-Toland B, Jackson AL, Kier LD. Safety assessment of food and feed from biotechnology-derived crops employing RNA-mediated gene regulation to achieve desired traits: a scientific review. Regul Toxicol Pharmacol 2013; 66:167-76. [PMID: 23557984 DOI: 10.1016/j.yrtph.2013.03.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 03/19/2013] [Accepted: 03/22/2013] [Indexed: 01/09/2023]
Abstract
Gene expression can be modulated in plants to produce desired traits through agricultural biotechnology. Currently, biotechnology-derived crops are compared to their conventional counterparts, with safety assessments conducted on the genetic modification and the intended and unintended differences. This review proposes that this comparative safety assessment paradigm is appropriate for plants modified to express mediators of RNA-mediated gene regulation, including RNA interference (RNAi), a gene suppression mechanism that naturally occurs in plants and animals. The molecular mediators of RNAi, including long double-stranded RNAs (dsRNA), small interfering RNAs (siRNA), and microRNAs (miRNA), occur naturally in foods; therefore, there is an extensive history of safe consumption. Systemic exposure following consumption of plants containing dsRNAs that mediate RNAi is limited in higher organisms by extensive degradation of ingested nucleic acids and by biological barriers to uptake and efficacy of exogenous nucleic acids. A number of mammalian RNAi studies support the concept that a large margin of safety will exist for any small fraction of RNAs that might be absorbed following consumption of foods from biotechnology-derived plants that employ RNA-mediated gene regulation. Food and feed derived from these crops utilizing RNA-based mechanisms is therefore expected to be as safe as food and feed derived through conventional plant breeding.
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Affiliation(s)
- Jay S Petrick
- Monsanto Company, 800 N. Lindbergh Blvd, St. Louis, MO 63167, USA.
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Yi R, Zhu Z, Hu J, Qian Q, Dai J, Ding Y. Identification and expression analysis of microRNAs at the grain filling stage in rice(Oryza sativa L.)via deep sequencing. PLoS One 2013; 8:e57863. [PMID: 23469249 PMCID: PMC3585941 DOI: 10.1371/journal.pone.0057863] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 01/27/2013] [Indexed: 12/30/2022] Open
Abstract
MicroRNAs (miRNAs) have been shown to play crucial roles in the regulation of plant development. In this study, high-throughput RNA-sequencing technology was used to identify novel miRNAs, and to reveal miRNAs expression patterns at different developmental stages during rice (Oryza sativa L.) grain filling. A total of 434 known miRNAs (380, 402, 390 and 392 at 5, 7, 12 and 17 days after fertilization, respectively.) were obtained from rice grain. The expression profiles of these identified miRNAs were analyzed and the results showed that 161 known miRNAs were differentially expressed during grain development, a high proportion of which were up-regulated from 5 to 7 days after fertilization. In addition, sixty novel miRNAs were identified, and five of these were further validated experimentally. Additional analysis showed that the predicted targets of the differentially expressed miRNAs may participate in signal transduction, carbohydrate and nitrogen metabolism, the response to stimuli and epigenetic regulation. In this study, differences were revealed in the composition and expression profiles of miRNAs among individual developmental stages during the rice grain filling process, and miRNA editing events were also observed, analyzed and validated during this process. The results provide novel insight into the dynamic profiles of miRNAs in developing rice grain and contribute to the understanding of the regulatory roles of miRNAs in grain filling.
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Affiliation(s)
- Rong Yi
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Zhixuan Zhu
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Jihong Hu
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Qian Qian
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Jincheng Dai
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
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Sun YH, Shi R, Zhang XH, Chiang VL, Sederoff RR. MicroRNAs in trees. PLANT MOLECULAR BIOLOGY 2012; 80:37-53. [PMID: 22161564 DOI: 10.1007/s11103-011-9864-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 10/26/2011] [Indexed: 05/31/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide long molecules processed from a specific class of RNA polymerase II transcripts that mainly regulate the stability of mRNAs containing a complementary sequence by targeted degradation in plants. Many features of tree biology are regulated by miRNAs affecting development, metabolism, adaptation and evolution. MiRNAs may be modified and harnessed for controlled suppression of specific genes to learn about gene function, or for practical applications through genetic engineering. Modified (artificial) miRNAs act as dominant suppressors and are particularly useful in tree genetics because they bypass the generations of inbreeding needed for fixation of recessive mutations. The purpose of this review is to summarize the current status of information on miRNAs in trees and to guide future studies on the role of miRNAs in the biology of woody perennials and to illustrate their utility in directed genetic modification of trees.
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Affiliation(s)
- Ying-Hsuan Sun
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
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Li F, Zheng Q, Ryvkin P, Dragomir I, Desai Y, Aiyer S, Valladares O, Yang J, Bambina S, Sabin LR, Murray JI, Lamitina T, Raj A, Cherry S, Wang LS, Gregory BD. Global analysis of RNA secondary structure in two metazoans. Cell Rep 2012; 1:69-82. [PMID: 22832108 DOI: 10.1016/j.celrep.2011.10.002] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/26/2011] [Accepted: 10/21/2011] [Indexed: 01/09/2023] Open
Abstract
The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach to identify the paired (double-stranded RNA [dsRNA]) and unpaired (single-stranded RNA [ssRNA]) components of the Drosophila melanogaster and Caenorhabditis elegans transcriptomes, which allows us to identify conserved features of RNA secondary structure in metazoans. From this analysis, we find that ssRNAs and dsRNAs are significantly correlated with specific epigenetic modifications. Additionally, we find key structural patterns across protein-coding transcripts that indicate that RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in animals. Finally, we identify and characterize 546 mRNAs whose folding pattern is significantly correlated between these metazoans, suggesting that their structure has some function. Overall, our findings provide a global assessment of RNA folding in animals.
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Affiliation(s)
- Fan Li
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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Zhu QH, Curaba J, de Lima JC, Helliwell C. Functions of miRNAs in Rice. MICRORNAS IN PLANT DEVELOPMENT AND STRESS RESPONSES 2012. [DOI: 10.1007/978-3-642-27384-1_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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37
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Nunes CC, Sailsbery JK, Dean RA. Characterization and application of small RNAs and RNA silencing mechanisms in fungi. FUNGAL BIOL REV 2011. [DOI: 10.1016/j.fbr.2011.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Jiao Y, Song W, Zhang M, Lai J. Identification of novel maize miRNAs by measuring the precision of precursor processing. BMC PLANT BIOLOGY 2011; 11:141. [PMID: 22014170 PMCID: PMC3214924 DOI: 10.1186/1471-2229-11-141] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 10/20/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND miRNAs are known to play important regulatory roles throughout plant development. Until recently, nearly all the miRNAs in maize were identified by comparative analysis to miRNAs sequences of other plant species, such as rice and Arabidopsis. RESULTS To find new miRNA in this important crop, small RNAs from mixed tissues were sequenced, resulting in over 15 million unique sequences. Our sequencing effort validated 23 of the 28 known maize miRNA families, including 49 unique miRNAs. Using a newly established criterion, based on the precision of miRNA processing from precursors, we identified 66 novel miRNAs in maize. These miRNAs can be grouped into 58 families, 54 of which have not been identified in any other species. Five new miRNAs were validated by northern blot. Moreover, we found targets for 23 of the 66 new miRNAs. The targets of two of these newly identified miRNAs were confirmed by 5'RACE. CONCLUSION We have implemented a novel method of identifying miRNA by measuring the precision of miRNA processing from precursors. Using this method, 66 novel miRNAs and 50 potential miRNAs have been identified in maize.
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Affiliation(s)
- Yinping Jiao
- State Key Laboratory of Agrobiotechnology; National Maize Improvement Center; Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Weibin Song
- State Key Laboratory of Agrobiotechnology; National Maize Improvement Center; Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Mei Zhang
- State Key Laboratory of Agrobiotechnology; National Maize Improvement Center; Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology; National Maize Improvement Center; Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
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Lelandais-Brière C, Sorin C, Declerck M, Benslimane A, Crespi M, Hartmann C. Small RNA diversity in plants and its impact in development. Curr Genomics 2011; 11:14-23. [PMID: 20808519 PMCID: PMC2851111 DOI: 10.2174/138920210790217918] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 07/13/2009] [Accepted: 07/13/2009] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs are a class of non-coding RNAs involved in post-transcriptional control of gene expression, either via degradation or translational inhibition of target mRNAs. Both experimental and computational approaches have been used to identify miRNAs and their target genes. In plants, deep sequencing methods have recently allowed the analysis of small RNA diversity in different species and/or mutants. Most sequencing efforts have been concentrated on the identification of miRNAs and their mRNA targets have been predicted based on complementarity criteria. The recent demonstration that certain plant miRNAs could act partly via inhibition of protein translation certainly opens new fields of analysis for plant miRNA function on a broader group of targets. The roles of conserved miRNAs on target mRNA stability have been analysed in different species and defined common mechanisms in development and stress responses. In contrast, much less is known about expression patterns or functions of non-conserved miRNAs. In this review, we focus on the comparative analyses of plant small RNA diversity and the action of si/miRNAs in post-transcriptional regulation of some key genes involved in root development.
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Affiliation(s)
- Christine Lelandais-Brière
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique (C.N.R.S.), F-91198 Gif-sur-Yvette Cedex, France
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Calviño M, Bruggmann R, Messing J. Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems. BMC Genomics 2011; 12:356. [PMID: 21740560 PMCID: PMC3143107 DOI: 10.1186/1471-2164-12-356] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 07/08/2011] [Indexed: 01/03/2023] Open
Abstract
Background Sorghum belongs to the tribe of the Andropogoneae that includes potential biofuel crops like switchgrass, Miscanthus and successful biofuel crops like corn and sugarcane. However, from a genomics point of view sorghum has compared to these other species a simpler genome because it lacks the additional rounds of whole genome duplication events. Therefore, it has become possible to generate a high-quality genome sequence. Furthermore, cultivars exists that rival sugarcane in levels of stem sugar so that a genetic approach can be used to investigate which genes are differentially expressed to achieve high levels of stem sugar. Results Here, we characterized the small RNA component of the transcriptome from grain and sweet sorghum stems, and from F2 plants derived from their cross that segregated for sugar content and flowering time. We found that variation in miR172 and miR395 expression correlated with flowering time whereas variation in miR169 expression correlated with sugar content in stems. Interestingly, genotypic differences in the ratio of miR395 to miR395* were identified, with miR395* species expressed as abundantly as miR395 in sweet sorghum but not in grain sorghum. Finally, we provided experimental evidence for previously annotated miRNAs detecting the expression of 25 miRNA families from the 27 known and discovered 9 new miRNAs candidates in the sorghum genome. Conclusions Sequencing the small RNA component of sorghum stem tissue provides us with experimental evidence for previously predicted microRNAs in the sorghum genome and microRNAs with a potential role in stem sugar accumulation and flowering time.
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Affiliation(s)
- Martín Calviño
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020, USA
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41
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Li Y, Li C, Ding G, Jin Y. Evolution of MIR159/319 microRNA genes and their post-transcriptional regulatory link to siRNA pathways. BMC Evol Biol 2011; 11:122. [PMID: 21569383 PMCID: PMC3118147 DOI: 10.1186/1471-2148-11-122] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 05/12/2011] [Indexed: 12/20/2022] Open
Abstract
Background MicroRNAs (miRNAs) are prevalent and important endogenous gene regulators in eukaryotes. MiR159 and miR319 are highly conserved miRNAs essential for plant development and fertility. Despite high similarity in conservation pattern and mature miRNA sequences, miR159 and miR319 have distinct expression patterns, targets and functions. In addition, both MIR319 and MIR159 precursors produce multiple miRNAs in a phased loop-to-base manner. Thus, MIR159 and MIR319 appear to be related in origin and considerably diverged. However the phylogeny of MIR159 and MIR319 genes and why such unusual style of miRNA production has been conserved during evolution is not well understood. Results We reconstructed the phylogeny of MIR159/319 genes and analyzed their mature miRNA expression. The inferred phylogeny suggests that the MIR159/319 genes may have formed at least ten extant early-branching clades through gene duplication and loss. A series of duplications occurred in the common ancestor of seed plants leading to the original split of flowering plant MIR159 and MIR319. The results also indicate that the expression of MIR159/319 is regulated at post-transcriptional level to switch on the expression of alternative miRNAs during development in a highly spatio-temporal specific manner, and to selectively respond to the disruption of defensive siRNA pathways. Such intra-stem-loop regulation appears diverged across the early-branching clades of MIR159/319 genes. Conclusions Our results support that the MIR159 and MIR319 genes evolve from a common ancestor, which is likely to be a phased stem-loop small RNA. Through duplication and loss of genes this miRNA gene family formed clades specific to moss, lycopods, gymnosperms and angiosperms including the two major clades of flowering plants containing the founding members of MIR319 and MIR159 genes in A.thaliana. Our analyses also suggest that some MIR159/319 have evolved into unusual miRNA genes that are regulated at post-transcriptional level to express multiple mature products with variable proportions under different circumstances. Moreover, our analyses reveal conserved regulatory link of MIR159/319 genes to siRNA pathway through post-transcriptional regulation.
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Affiliation(s)
- Yang Li
- School of Life Sciences, Shanghai University, 200444, Shanghai, P,R,China
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42
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Li Y, Li C, Xia J, Jin Y. Domestication of transposable elements into MicroRNA genes in plants. PLoS One 2011; 6:e19212. [PMID: 21559273 PMCID: PMC3086885 DOI: 10.1371/journal.pone.0019212] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 03/29/2011] [Indexed: 12/20/2022] Open
Abstract
Transposable elements (TE) usually take up a substantial portion of eukaryotic genome. Activities of TEs can cause genome instability or gene mutations that are harmful or even disastrous to the host. TEs also contribute to gene and genome evolution at many aspects. Part of miRNA genes in mammals have been found to derive from transposons while convincing evidences are absent for plants. We found that a considerable number of previously annotated plant miRNAs are identical or homologous to transposons (TE-MIR), which include a small number of bona fide miRNA genes that conform to generally accepted plant miRNA annotation rules, and hairpin derived siRNAs likely to be pre-evolved miRNAs. Analysis of these TE-MIRs indicate that transitions from the medium to high copy TEs into miRNA genes may undergo steps such as inverted repeat formation, sequence speciation and adaptation to miRNA biogenesis. We also identified initial target genes of the TE-MIRs, which contain homologous sequences in their CDS as consequence of cognate TE insertions. About one-third of the initial target mRNAs are supported by publicly available degradome sequencing data for TE-MIR sRNA induced cleavages. Targets of the TE-MIRs are biased to non-TE related genes indicating their penchant to acquire cellular functions during evolution. Interestingly, most of these TE insertions span boundaries between coding and non-coding sequences indicating their incorporation into CDS through alteration of splicing or translation start or stop signals. Taken together, our findings suggest that TEs in gene rich regions can form foldbacks in non-coding part of transcripts that may eventually evolve into miRNA genes or be integrated into protein coding sequences to form potential targets in a “temperate” manner. Thus, transposons may supply as resources for the evolution of miRNA-target interactions in plants.
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Affiliation(s)
- Yang Li
- School of Life Sciences, Shanghai University, Shanghai, People's Republic of China
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Chaoqun Li
- Department of Gastroenterology, Shanghai Public Health Clinical Center Affiliated to Fudan University, Shanghai, People's Republic of China
| | - Jie Xia
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Youxin Jin
- School of Life Sciences, Shanghai University, Shanghai, People's Republic of China
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
- * E-mail:
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43
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McCormick KP, Willmann MR, Meyers BC. Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments. SILENCE 2011; 2:2. [PMID: 21356093 PMCID: PMC3055805 DOI: 10.1186/1758-907x-2-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 02/28/2011] [Indexed: 01/30/2023]
Abstract
Prior to the advent of new, deep sequencing methods, small RNA (sRNA) discovery was dependent on Sanger sequencing, which was time-consuming and limited knowledge to only the most abundant sRNA. The innovation of large-scale, next-generation sequencing has exponentially increased knowledge of the biology, diversity and abundance of sRNA populations. In this review, we discuss issues involved in the design of sRNA sequencing experiments, including choosing a sequencing platform, inherent biases that affect sRNA measurements and replication. We outline the steps involved in preprocessing sRNA sequencing data and review both the principles behind and the current options for normalization. Finally, we discuss differential expression analysis in the absence and presence of biological replicates. While our focus is on sRNA sequencing experiments, many of the principles discussed are applicable to the sequencing of other RNA populations.
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Affiliation(s)
- Kevin P McCormick
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Matthew R Willmann
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Blake C Meyers
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
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44
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Cuperus JT, Fahlgren N, Carrington JC. Evolution and functional diversification of MIRNA genes. THE PLANT CELL 2011; 23:431-42. [PMID: 21317375 PMCID: PMC3077775 DOI: 10.1105/tpc.110.082784] [Citation(s) in RCA: 495] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
MicroRNAs (miRNAs) are small regulatory RNAs found in diverse eukaryotic lineages. In plants, a minority of annotated MIRNA gene families are conserved between plant families, while the majority are family- or species-specific, suggesting that most known MIRNA genes arose relatively recently in evolutionary time. Given the high proportion of young MIRNA genes in plant species, new MIRNA families are likely spawned and then lost frequently. Unlike highly conserved, ancient miRNAs, young miRNAs are often weakly expressed, processed imprecisely, lack targets, and display patterns of neutral variation, suggesting that young MIRNA loci tend to evolve neutrally. Genome-wide analyses from several plant species have revealed that variation in miRNA foldback expression, structure, processing efficiency, and miRNA size have resulted in the unique functionality of MIRNA loci and resulting miRNAs. Additionally, some miRNAs have evolved specific properties and functions that regulate other transcriptional or posttranscriptional silencing pathways. The evolution of miRNA processing and functional diversity underscores the dynamic nature of miRNA-based regulation in complex regulatory networks.
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Affiliation(s)
- Josh T. Cuperus
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - Noah Fahlgren
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - James C. Carrington
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- Address correspondence to
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45
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Lin SI, Santi C, Jobet E, Lacut E, El Kholti N, Karlowski WM, Verdeil JL, Breitler JC, Périn C, Ko SS, Guiderdoni E, Chiou TJ, Echeverria M. Complex regulation of two target genes encoding SPX-MFS proteins by rice miR827 in response to phosphate starvation. PLANT & CELL PHYSIOLOGY 2010; 51:2119-31. [PMID: 21062869 DOI: 10.1093/pcp/pcq170] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Here we report on the characterization of rice osa-miR827 and its two target genes, OsSPX-MFS1 and OsSPX-MFS2, which encode SPX-MFS proteins predicted to be implicated in phosphate (Pi) sensing or transport. We first show by Northern blot analysis that osa-miR827 is strongly induced by Pi starvation in both shoots and roots. Hybridization of osa-miR827 in situ confirms its strong induction by Pi starvation, with signals concentrated in mesophyll, epidermis and ground tissues of roots. In parallel, we analyzed the responses of the two OsSPX-MFS1 and OsSPX-MFS2 gene targets to Pi starvation. OsSPX-MFS1 mRNA is mainly expressed in shoots under sufficient Pi supply while its expression is reduced on Pi starvation, revealing a direct relationship between induction of osa-miR827 and down-regulation of OsSPX-MFS1. In contrast, OsSPX-MFS2 responds in a diametrically opposed manner to Pi starvation. The accumulation of OsSPX-MFS2 mRNA is dramatically enhanced under Pi starvation, suggesting the involvement of complex regulation of osa-miR827 and its two target genes. We further produced transgenic rice lines overexpressing osa-miR827 and T-DNA knockout mutant lines in which the expression of osa-miR827 is abolished. Compared with wild-type controls, both target mRNAs exhibit similar changes, their expression being reduced and increased in overexpressing and knockout lines, respectively. This suggests that OsSPX-MFS1 and OsSPX-MFS2 are both negatively regulated by osa-miR827 abundance although they respond differently to external Pi conditions. We propose that this is a complex mechanism comprising fine tuning of spatial or temporal regulation of both targets by osa-miR827.
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MESH Headings
- Adaptation, Physiological
- DNA, Bacterial
- Gene Expression Regulation, Plant
- Genes, Plant
- MicroRNAs/physiology
- Oryza/cytology
- Oryza/genetics
- Oryza/metabolism
- Phosphates/deficiency
- Phosphates/metabolism
- Plant Roots/genetics
- Plant Shoots/genetics
- Plants, Genetically Modified/cytology
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- RNA Transport
- RNA, Messenger/genetics
- RNA, Plant/genetics
- Sequence Deletion
- Stress, Physiological
- Transcription, Genetic
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Affiliation(s)
- Shu-I Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
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46
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Application of food and feed safety assessment principles to evaluate transgenic approaches to gene modulation in crops. Food Chem Toxicol 2010; 48:1773-90. [DOI: 10.1016/j.fct.2010.04.017] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 04/03/2010] [Accepted: 04/12/2010] [Indexed: 11/15/2022]
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47
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Li YF, Zheng Y, Addo-Quaye C, Zhang L, Saini A, Jagadeeswaran G, Axtell MJ, Zhang W, Sunkar R. Transcriptome-wide identification of microRNA targets in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 62:742-59. [PMID: 20202174 DOI: 10.1111/j.1365-313x.2010.04187.x] [Citation(s) in RCA: 272] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
MicroRNA (miRNA)-guided target RNA expression is vital for a wide variety of biological processes in eukaryotes. Currently, miRBase (version 13) lists 142 and 353 miRNAs from Arabidopsis and rice (Oryza sativa), respectively. The integration of miRNAs in diverse biological networks relies upon the confirmation of their RNA targets. In contrast with the well-characterized miRNA targets that are cleaved in Arabidopsis, only a few such targets have been confirmed in rice. To identify small RNA targets in rice, we applied the 'degradome sequencing' approach, which globally identifies the remnants of small RNA-directed target cleavage by sequencing the 5' ends of uncapped RNAs. One hundred and sixty targets of 53 miRNA families (24 conserved and 29 rice-specific) and five targets of TAS3-small interfering RNAs (siRNAs) were identified. Surprisingly, an additional conserved target for miR398, which has not been reported so far, has been validated. Besides conserved homologous transcripts, 23 non-conserved genes for nine conserved miRNAs and 56 genes for 29 rice-specific miRNAs were also identified as targets. Besides miRNA targets, the rice degradome contained fragments derived from MIRNA precursors. A closer inspection of these fragments revealed a unique pattern distinct from siRNA-producing loci. This attribute can serve as one of the ancillary criteria for separating miRNAs from siRNAs in plants.
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Affiliation(s)
- Yong-Fang Li
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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48
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Wang Y, Shen D, Bo S, Chen H, Zheng J, Zhu QH, Cai D, Helliwell C, Fan L. Sequence variation and selection of small RNAs in domesticated rice. BMC Evol Biol 2010; 10:119. [PMID: 20429951 PMCID: PMC2887405 DOI: 10.1186/1471-2148-10-119] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 04/30/2010] [Indexed: 01/21/2023] Open
Abstract
Background Endogenous non-coding small RNAs (21-24 nt) play an important role in post-transcriptional gene regulation in plants. Domestication selection is the most important evolutionary force in shaping crop genomes. The extent of polymorphism at small RNA loci in domesticated rice and whether small RNA loci are targets of domestication selection have not yet been determined. Results A polymorphism survey of 94 small RNA loci (88 MIRNAs, four TAS3 loci and two miRNA-like long hairpins) was conducted in domesticated rice, generating 2 Mb of sequence data. Many mutations (substitution or insertion/deletion) were observed at small RNA loci in domesticated rice, e.g. 12 mutation sites were observed in the mature miRNA sequences of 11 MIRNAs (12.5% of the investigated MIRNAs). Several small RNA loci showed significant signals for positive selection and/or potential domestication selection. Conclusions Sequence variation at miRNAs and other small RNAs is higher than expected in domesticated rice. Like protein-coding genes, non-coding small RNA loci could be targets of domestication selection and play an important role in rice domestication and improvement.
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Affiliation(s)
- Yu Wang
- Department of Agronomy, Zhejiang University, Hangzhou, China
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49
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Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y. DNA methylation mediated by a microRNA pathway. Mol Cell 2010; 38:465-75. [PMID: 20381393 DOI: 10.1016/j.molcel.2010.03.008] [Citation(s) in RCA: 397] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2009] [Revised: 02/16/2010] [Accepted: 03/17/2010] [Indexed: 12/26/2022]
Abstract
In plants, the known microRNAs (miRNAs) are produced as approximately 21 nucleotide (nt) duplexes from their precursors by Dicer-like 1 (DCL1). They are incorporated into Argonaute 1 (AGO1) protein to regulate target gene expression primarily through mRNA cleavage. We report here the discovery of a class of miRNAs in the model monocot rice (Oryza sativa). These are 24 nt in length and require another member of the Dicer family, DCL3, for their biogenesis. The 24 nt long miRNAs (lmiRNAs) are loaded into AGO4 clade proteins according to hierarchical rules, depending on the upstream biogenesis machinery and the 5'-terminal nucleotide. We demonstrated that lmiRNAs direct DNA methylation at loci from which they are produced as well as in trans at their target genes and play roles in gene regulation. Considered together, our findings define a miRNA pathway that mediates DNA methylation.
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Affiliation(s)
- Liang Wu
- National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China; College of Life Sciences, Beijing Normal University, Beijing 100875, China
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50
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Fahlgren N, Jogdeo S, Kasschau KD, Sullivan CM, Chapman EJ, Laubinger S, Smith LM, Dasenko M, Givan SA, Weigel D, Carrington JC. MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. THE PLANT CELL 2010; 22:1074-89. [PMID: 20407027 PMCID: PMC2879733 DOI: 10.1105/tpc.110.073999] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 03/16/2010] [Accepted: 04/05/2010] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are short regulatory RNAs processed from partially self-complementary foldbacks within longer MIRNA primary transcripts. Several MIRNA families are conserved deeply through land plants, but many are present only in closely related species or are species specific. The finding of numerous evolutionarily young MIRNA, many with low expression and few if any targets, supports a rapid birth-death model for MIRNA evolution. A systematic analysis of MIRNA genes and families in the close relatives, Arabidopsis thaliana and Arabidopsis lyrata, was conducted using both whole-genome comparisons and high-throughput sequencing of small RNAs. Orthologs of 143 A. thaliana MIRNA genes were identified in A. lyrata, with nine having significant sequence or processing changes that likely alter function. In addition, at least 13% of MIRNA genes in each species are unique, despite their relatively recent speciation (approximately 10 million years ago). Alignment of MIRNA foldbacks to the Arabidopsis genomes revealed evidence for recent origins of 32 families by inverted or direct duplication of mostly protein-coding gene sequences, but less than half of these yield miRNA that are predicted to target transcripts from the originating gene family. miRNA nucleotide divergence between A. lyrata and A. thaliana orthologs was higher for young MIRNA genes, consistent with reduced purifying selection compared with deeply conserved MIRNA genes. Additionally, target sites of younger miRNA were lost more frequently than for deeply conserved families. In summary, our systematic analyses emphasize the dynamic nature of the MIRNA complement of plant genomes.
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Affiliation(s)
- Noah Fahlgren
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Sanjuro Jogdeo
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Kristin D. Kasschau
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Christopher M. Sullivan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Elisabeth J. Chapman
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Sascha Laubinger
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Lisa M. Smith
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Mark Dasenko
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - Scott A. Givan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - James C. Carrington
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- Address correspondence to
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