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Williams BP, Bechen LL, Pohlmann DA, Gehring M. Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time. THE PLANT CELL 2022; 34:1189-1206. [PMID: 34954804 PMCID: PMC8972289 DOI: 10.1093/plcell/koab319] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/21/2021] [Indexed: 05/29/2023]
Abstract
Cytosine methylation is a reversible epigenetic modification of DNA. In plants, removal of cytosine methylation is accomplished by the four members of the DEMETER (DME) family of 5-methylcytosine DNA glycosylases, named DME, DEMETER-LIKE2 (DML2), DML3, and REPRESSOR OF SILENCING1 (ROS1) in Arabidopsis thaliana. Demethylation by DME is critical for seed development, preventing experiments to determine the function of the entire gene family in somatic tissues by mutant analysis. Here, we bypassed the reproductive defects of dme mutants to create somatic quadruple homozygous mutants of the entire DME family. dme; ros1; dml2; and dml3 (drdd) leaves exhibit hypermethylated regions compared with wild-type leaves and rdd triple mutants, indicating functional redundancy among all four demethylases. Targets of demethylation include regions co-targeted by RNA-directed DNA methylation and, surprisingly, CG gene body methylation, indicating dynamic methylation at these less-understood sites. Additionally, many tissue-specific methylation differences are absent in drdd, suggesting a role for active demethylation in generating divergent epigenetic states across wild-type tissues. Furthermore, drdd plants display an early flowering phenotype, which involves 5'-hypermethylation and transcriptional down-regulation of FLOWERING LOCUS C. Active DNA demethylation is therefore required for proper methylation across somatic tissues and defines the epigenetic landscape of intergenic and coding regions.
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Affiliation(s)
- Ben P Williams
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Lindsey L Bechen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Deborah A Pohlmann
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mary Gehring
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Dong X, Liu C, Wang Y, Dong Q, Gai Y, Ji X. MicroRNA Profiling During Mulberry ( Morus atropurpurea Roxb) Fruit Development and Regulatory Pathway of miR477 for Anthocyanin Accumulation. FRONTIERS IN PLANT SCIENCE 2021; 12:687364. [PMID: 34567022 PMCID: PMC8455890 DOI: 10.3389/fpls.2021.687364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
To understand the mechanism of small non-coding RNAs (miRNA)-mediated development and ripening of mulberry fruits, three small RNA libraries from mulberry fruits at different development stages were constructed, and 159 conserved miRNAs as well as 86 novel miRNAs were successfully identified. Among the miRNAs identified, there were 90 miRNAs which showed differential expression patterns at different stages of fruit development and ripening. The target genes of these differential expressed (DE) miRNAs were involved in growth and development, transcription and regulation of transcription, metabolic processes, and etc. Interestingly, it was found that the expression level of mul-miR477 was increased with fruit ripening, and it can target the antisense lncRNA (Mul-ABCB19AS) of the ATP binding cassette (ABC) transporter B 19 gene (Mul-ABCB19). Our results showed that mul-miR477 can repress the expression of Mul-ABCB19AS and increase the expression of Mul-ABCB19, and it acted as a positive regulator participating anthocyanin accumulation through the regulatory network of mul-miR477-Mul-ABCB19AS-Mul-ABCB19.
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Affiliation(s)
- Xiaonan Dong
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Chaorui Liu
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Yuqi Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Qing Dong
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Yingping Gai
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Xianling Ji
- College of Forestry, Shandong Agricultural University, Tai’an, China
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Bhogireddy S, Mangrauthia SK, Kumar R, Pandey AK, Singh S, Jain A, Budak H, Varshney RK, Kudapa H. Regulatory non-coding RNAs: a new frontier in regulation of plant biology. Funct Integr Genomics 2021; 21:313-330. [PMID: 34013486 PMCID: PMC8298231 DOI: 10.1007/s10142-021-00787-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 11/27/2022]
Abstract
Beyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act as riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate plant growth, development, and stress responses. Regulatory ncRNAs, ranging from small to long ncRNAs (lncRNAs), exert their control over a vast array of biological processes. Based on the mode of biogenesis and their function, ncRNAs evolved into different forms that include microRNAs (miRNAs), small interfering RNAs (siRNAs), miRNA variants (isomiRs), lncRNAs, circular RNAs (circRNAs), and derived ncRNAs. This article explains the different classes of ncRNAs and their role in plant development and stress responses. Furthermore, the applications of regulatory ncRNAs in crop improvement, targeting agriculturally important traits, have been discussed.
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Affiliation(s)
- Sailaja Bhogireddy
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| | | | - Rakesh Kumar
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Life Sciences, Central University of Karnataka, Karnataka, India
| | - Arun K Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Sadhana Singh
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ankit Jain
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, Western Australia, Australia
| | - Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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Barley Seeds miRNome Stability during Long-Term Storage and Aging. Int J Mol Sci 2021; 22:ijms22094315. [PMID: 33919202 PMCID: PMC8122619 DOI: 10.3390/ijms22094315] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/27/2021] [Accepted: 04/18/2021] [Indexed: 12/18/2022] Open
Abstract
Seed aging is a complex biological process that has been attracting scientists’ attention for many years. High-throughput small RNA sequencing was applied to examine microRNAs contribution in barley seeds senescence. Unique samples of seeds that, despite having the same genetic makeup, differed in viability after over 45 years of storage in a dry state were investigated. In total, 61 known and 81 novel miRNA were identified in dry seeds. The highest level of expression was found in four conserved miRNA families, i.e., miR159, miR156, miR166, and miR168. However, the most astonishing result was the lack of significant differences in the level of almost all miRNAs in seed samples with significantly different viability. This result reveals that miRNAs in dry seeds are extremely stable. This is also the first identified RNA fraction that is not deteriorating along with the loss of seed viability. Moreover, the novel miRNA hvu-new41, with higher expression in seeds with the lowest viability as detected by RT-qPCR, has the potential to become an indicator of the decreasing viability of seeds during storage in a dry state.
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Sankaranarayanan R, Palani SN, Tamilmaran N, Punitha Selvakumar AS, Chandra Sekar P, Tennyson J. Novel approaches on identification of conserved miRNAs for broad-spectrum Potyvirus control measures. Mol Biol Rep 2021; 48:2377-2388. [PMID: 33743120 DOI: 10.1007/s11033-021-06271-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/05/2021] [Indexed: 10/21/2022]
Abstract
Potyviridae comprises more than 200 ssRNA viruses, many of which have a broad host range and geographical distributions. Potyvirids (members of Potyviridae) infect several economically important plants such as saffron, cardamom, cucumber, pepper, potato, tomato, yam, etc. Cumulatively, potyvirids cause a substantial economic loss. The major bottleneck in developing an efficient antiviral strategy is that viruses quickly evade host immunity owing to their higher mutation and recombination rates. Due to this reason, the emergence of newer and improved broad-spectrum approaches to combat viral infections is essential. The use of microRNA's (miRNA) to circumvent viral infection against animal viruses has been successfully employed. Fewer studies reported the development of efficient miRNA-based antivirus resistant strategies against plant viruses and none focused on multiple virus resistance. We focused on potyviruses since studies are limited and identification of conserved miRNAs among various host plants would be an initiative to design broad-spectrum antivirus strategies. In this study, we predicted evolutionarily conserved miRNAs by BLAST searching of reported miRNAs from 15 plants against the GSS and EST sequences of banana. A total of nine miRNAs were predicted and screened in nine diverse potyvirids' hosts (Banana, Tomato, Green gram, Jasmine, Chilli, Coriander, Onion, Rose and Colocasia) belonging to eight different orders (Zingiberales, Solanales, Fabales, Lamiales, Apiales, Asperagales, Rosales and Alismatales). Results suggested that miR168 and miR162 are conserved among all the selected plants. This comprehensive study laid the foundations to design broad-spectrum antivirus resistance using miRNAs. To conclude miR168 and miR162 are conserved among many plants and play a crucial role in evading virus infection which could be used as a potential candidate for developing antiviral strategies against potyvirid infections.
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Fard EM, Moradi S, Salekdeh NN, Bakhshi B, Ghaffari MR, Zeinalabedini M, Salekdeh GH. Plant isomiRs: origins, biogenesis, and biological functions. Genomics 2020; 112:3382-3395. [DOI: 10.1016/j.ygeno.2020.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/22/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022]
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Park SY, Choi JH, Oh DH, Johnson JC, Dassanayake M, Jeong DH, Oh MH. Genome-wide analysis of brassinosteroid responsive small RNAs in Arabidopsis thaliana. Genes Genomics 2020; 42:957-969. [PMID: 32648234 DOI: 10.1007/s13258-020-00964-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/29/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND Brassinosteroids (BRs) are a class of phytohormones with important roles in regulating physiological and developmental processes. Small RNAs, including small interfering RNAs and microRNAs (miRNAs), are non-protein coding RNAs that regulate gene expression at the transcriptional and post-transcriptional levels. However, the roles of small RNAs in BR response have not been studied well. OBJECTIVE In this study, we aimed to identify BR-responsive small RNA clusters and miRNAs in Arabidopsis. In addition, the effect of BR-responsive small RNAs on their transcripts and target genes were examined. METHODS Small RNA libraries were constructed from control and epibrassinolide-treated seedlings expressing wild-type BRI1-Flag protein under its native promoter in the bri1-5 mutant. After sequencing the small RNA libraries, differentially expressed small RNA clusters were identified by examining the expression levels of small RNAs in 100-nt bins of the Arabidopsis genome. To identify the BR-responsive miRNAs, the expression levels of all the annotated mature miRNAs, registered in miRBase, were analyzed. Previously published RNA-seq data were utilized to monitor the BR-responsive expression patterns of differentially expressed small RNA clusters and miRNA target genes. RESULTS In results, 38 BR-responsive small RNA clusters, including 30 down-regulated and eight up-regulated clusters, were identified. These differentially expressed small RNA clusters were from miRNA loci, transposons, protein-coding genes, pseudogenes and others. Of these, a transgene, BRI1, accumulates small RNAs, which are not found in the wild type. Small RNAs in this transgene are up-regulated by BRs while BRI1 mRNA is down-regulated by BRs. By analyzing the expression patterns of mature miRNAs, we have identified BR-repressed miR398a-5p and BR-induced miR156g. Although miR398a-5p is down-regulated by BRs, its predicted targets were not responsive to BRs. However, SPL3, a target of BR-inducible miR156g, is down-regulated by BRs. CONCLUSION BR-responsive small RNAs and miRNAs identified in this study will provide an insight into the role of small RNAs in BR responses in plants. Especially, we suggest that miR156g/SPL3 module might play a role in BR-mediated growth and development in Arabidopsis.
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Affiliation(s)
- So Young Park
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Jae-Han Choi
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 34134, Korea
| | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - John C Johnson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Dong-Hoon Jeong
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, 24252, Republic of Korea.
| | - Man-Ho Oh
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 34134, Korea.
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Balyan S, Joseph SV, Jain R, Mutum RD, Raghuvanshi S. Investigation into the miRNA/5' isomiRNAs function and drought-mediated miRNA processing in rice. Funct Integr Genomics 2020; 20:509-522. [DOI: 10.1007/s10142-020-00731-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 10/04/2019] [Accepted: 01/02/2020] [Indexed: 11/28/2022]
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10
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Yang K, Wen X, Mudunuri S, Varma GPS, Sablok G. Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants. Sci Rep 2019; 9:1406. [PMID: 30723229 PMCID: PMC6363768 DOI: 10.1038/s41598-019-38932-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/14/2019] [Indexed: 11/11/2022] Open
Abstract
Plants have an amazing ability to cope with wide variety of stresses by regulating the expression of genes and thus by altering the physiological status. In the past few years, canonical microRNA variants (isomiRs) have been shown to play pivotal roles by acting as regulators of the transcriptional machinery. In the present research, we present Diff isomiRs, a web-based exploratory repository of differential isomiRs across 16 sequenced plant species representing a total of 433 datasets across 21 different stresses and 158 experimental states. Diff isomiRs provides the high-throughput detection of differential isomiRs using mapping-based and model-based differential analysis revealing a total of 16,157 and 2,028 differential isomiRs, respectively. Easy-to-use and web-based exploration of differential isomiRs provides several features such as browsing of the differential isomiRs according to stress or species, as well as association of the differential isomiRs to targets and plant endogenous target mimics (PeTMs). Diff isomiRs also provides the relationship between the canonical miRNAs, isomiRs and the miRNA-target interactions. This is the first web-based large-scale repository for browsing differential isomiRs and will facilitate better understanding of the regulatory role of the isomiRs with respect to the canonical microRNAs. Diff isomiRs can be accessed at: www.mcr.org.in/diffisomirs.
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Affiliation(s)
- Kun Yang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, P. R. China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, P. R. China.
| | - Suresh Mudunuri
- Centre for Bioinformatics Research, SRKR Engineering College, Chinna Amiram, Bhimavaram, West Godavari District, Andhra Pradesh, 534204, India
| | - G P Saradhi Varma
- Centre for Bioinformatics Research, SRKR Engineering College, Chinna Amiram, Bhimavaram, West Godavari District, Andhra Pradesh, 534204, India
| | - Gaurav Sablok
- Finnish Museum of Natural History, Helsinki, Finland. .,Organismal and Evolutionary Biology (OEB) Research Programme, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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Yan F, Li H, Zhao P. Genome-Wide Identification and Transcriptional Expression of the PAL Gene Family in Common Walnut ( Juglans Regia L.). Genes (Basel) 2019; 10:E46. [PMID: 30650597 PMCID: PMC6357058 DOI: 10.3390/genes10010046] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/10/2019] [Accepted: 01/10/2019] [Indexed: 12/19/2022] Open
Abstract
Juglans regia L. is an economically important crop cultivated worldwide for its high quality and quantity of wood and nuts. Phenylalanine ammonia-lyase (PAL) is the first enzyme in the phenylpropanoid pathway that plays a critical role in plant growth, development, and adaptation, but there have been few reports of the PAL gene family in common walnut. Here, we report a genome-wide study of J. regiaPAL genes and analyze their phylogeny, duplication, microRNA, and transcriptional expression. A total of 12 PAL genes were identified in the common walnut and clustered into two subfamilies based on phylogenetic analysis. These common walnut PALs are distributed on eight different pseudo-chromosomes. Seven of the 12 PALs (JrPAL2-3, JrPAL4-2, JrPAL2-1, JrPAL4-1, JrPAL8, JrPAL9, and JrPAL6) were specific found in J. regia, and JrPAL3, JrPAL5, JrPAL1-2, JrPAL7, and JrPAL2-2 were found to be closely associated with the woody plant Populus trichocarpa. Additionally, the expression patterns of JrPAL3, JrPAL7, JrPAL9, and JrPAL2-1 showed that they had high expression in female and male flowers. The miRNA ath-miR830-5p regulates two genes, JrPAL5 and JrPAL1, such that they have low expression in the male and female flowers of the common walnut. Our research provides useful information for further research into the function of PAL genes in common walnut and Juglans.
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Affiliation(s)
- Feng Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.
| | - Huaizhu Li
- School of Chemistry and Chemical Engineering, Xianyang Normal University, Xianyang 712000, China.
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.
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Kuo YW, Lin JS, Li YC, Jhu MY, King YC, Jeng ST. MicroR408 regulates defense response upon wounding in sweet potato. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:469-483. [PMID: 30403812 PMCID: PMC6322576 DOI: 10.1093/jxb/ery381] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/02/2018] [Indexed: 05/08/2023]
Abstract
MiRNAs play diverse roles in plant development and defense responses by binding to their mRNA targets based on sequence complementarity. Here, we investigated a wound-related miR408 and its target genes in sweet potato (Ipomoea batatas) by small RNA deep sequencing and transcriptome analysis. The expression patterns of miR408 and the miR408 precursor were significantly repressed by wounding and jasmonate (JA). In contrast, expression of the putative target genes IbKCS (3-ketoacyl-CoA synthase 4), IbPCL (plantacyanin), and IbGAUT (galacturonosyltransferase 7-like) of miR408 was increased following wounding, whereas only IbKCS was increased after JA treatment. Target cleavage site mapping and Agrobacterium-mediated transient assay demonstrated that IbKCS, IbPCL, and IbGAUT were the targets of miR408. The expression of miR408 target genes was repressed in transgenic sweet potatoes overexpressing miR408. These data indicated a relationship between miR408 and its target genes. Notably, miR408-overexpressing plants showed a semi-dwarf phenotype and attenuated resistance to insect feeding, while transgenic plants overexpressing IbKCS exhibited more insect resistance than plants overexpressing only the empty vector. Collectively, sweet potato reduces the abundance of miR408 upon wounding to elevate the expression of IbKCS, IbPCL, and IbGAUT. The expression of IbKCS enhances the defense system against herbivore wounding.
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Affiliation(s)
- Yun-Wei Kuo
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Chi Li
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Min-Yao Jhu
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Chi King
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Shih-Tong Jeng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
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Kakrana A, Mathioni SM, Huang K, Hammond R, Vandivier L, Patel P, Arikit S, Shevchenko O, Harkess AE, Kingham B, Gregory BD, Leebens-Mack JH, Meyers BC. Plant 24-nt reproductive phasiRNAs from intramolecular duplex mRNAs in diverse monocots. Genome Res 2018; 28:1333-1344. [PMID: 30002159 PMCID: PMC6120631 DOI: 10.1101/gr.228163.117] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 07/11/2018] [Indexed: 11/25/2022]
Abstract
In grasses, two pathways that generate diverse and numerous 21-nt (premeiotic) and 24-nt (meiotic) phased siRNAs are highly enriched in anthers, the male reproductive organs. These "phasiRNAs" are analogous to mammalian piRNAs, yet their functions and evolutionary origins remain largely unknown. The 24-nt meiotic phasiRNAs have only been described in grasses, wherein their biogenesis is dependent on a specialized Dicer (DCL5). To assess how evolution gave rise to this pathway, we examined reproductive phasiRNA pathways in nongrass monocots: garden asparagus, daylily, and lily. The common ancestors of these species diverged approximately 115-117 million years ago (MYA). We found that premeiotic 21-nt and meiotic 24-nt phasiRNAs were abundant in all three species and displayed spatial localization and temporal dynamics similar to grasses. The miR2275-triggered pathway was also present, yielding 24-nt reproductive phasiRNAs, and thus originated more than 117 MYA. In asparagus, unlike in grasses, these siRNAs are largely derived from inverted repeats (IRs); analyses in lily identified thousands of precursor loci, and many were also predicted to form foldback substrates for Dicer processing. Additionally, reproductive phasiRNAs were present in female reproductive organs and thus may function in both male and female germinal development. These data describe several distinct mechanisms of production for 24-nt meiotic phasiRNAs and provide new insights into the evolution of reproductive phasiRNA pathways in monocots.
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Affiliation(s)
- Atul Kakrana
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19714, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
| | - Sandra M Mathioni
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Kun Huang
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
| | - Reza Hammond
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19714, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
| | - Lee Vandivier
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Parth Patel
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19714, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
| | - Siwaret Arikit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen and Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand
| | - Olga Shevchenko
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
| | - Alex E Harkess
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Bruce Kingham
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | | | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, USA
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14
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Gai YP, Zhao HN, Zhao YN, Zhu BS, Yuan SS, Li S, Guo FY, Ji XL. MiRNA-seq-based profiles of miRNAs in mulberry phloem sap provide insight into the pathogenic mechanisms of mulberry yellow dwarf disease. Sci Rep 2018; 8:812. [PMID: 29339758 PMCID: PMC5770470 DOI: 10.1038/s41598-018-19210-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/20/2017] [Indexed: 11/09/2022] Open
Abstract
A wide range of miRNAs have been identified as phloem-mobile molecules that play important roles in coordinating plant development and physiology. Phytoplasmas are associated with hundreds of plant diseases, and the pathogenesis involved in the interactions between phytoplasmas and plants is still poorly understood. To analyse the molecular mechanisms of phytoplasma pathogenicity, the miRNAs profiles in mulberry phloem saps were examined in response to phytoplasma infection. A total of 86 conserved miRNAs and 19 novel miRNAs were identified, and 30 conserved miRNAs and 13 novel miRNAs were differentially expressed upon infection with phytoplasmas. The target genes of the differentially expressed miRNAs are involved in diverse signalling pathways showing the complex interactions between mulberry and phytoplasma. Interestingly, we found that mul-miR482a-5p was up-regulated in the infected phloem saps, and grafting experiments showed that it can be transported from scions to rootstock. Based on the results, the complexity and roles of the miRNAs in phloem sap and the potential molecular mechanisms of their changes were discussed. It is likely that the phytoplasma-responsive miRNAs in the phloem sap modulate multiple pathways and work cooperatively in response to phytoplasma infection, and their expression changes may be responsible for some symptoms in the infected plants.
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Affiliation(s)
- Ying-Ping Gai
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Huai-Ning Zhao
- College of Forestry, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Ya-Nan Zhao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Bing-Sen Zhu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Shuo-Shuo Yuan
- College of Forestry, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Shuo Li
- College of Forestry, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Fang-Yue Guo
- College of Forestry, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Xian-Ling Ji
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China. .,College of Forestry, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China.
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15
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Yu D, Ma X, Zuo Z, Shao W, Wang H, Meng Y. Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs. RICE (NEW YORK, N.Y.) 2017; 10:38. [PMID: 28786034 PMCID: PMC5545994 DOI: 10.1186/s12284-017-0177-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/03/2017] [Indexed: 05/31/2023]
Abstract
The next-generation sequencing (NGS) technology has revolutionized our previous understanding of the plant genomes, relying on its innate advantages, such as high throughput and deep sequencing depth. In addition to the protein-coding gene loci, massive transcription signals have been detected within intergenic or intragenic regions. Most of these signals belong to non-coding ones, considering their weak protein-coding potential. Generally, these transcripts could be divided into long non-coding RNAs and small non-coding RNAs (sRNAs) based on their sequence length. In addition to the well-known microRNAs (miRNAs), many plant endogenous sRNAs were collectively referred to as small interfering RNAs. However, an increasing number of unclassified sRNA species are being discovered by NGS. The high heterogeneity of these novel sRNAs greatly hampered the mechanistic studies, especially on the clear description of their biogenesis and action pathways. Fortunately, public databases, bioinformatics softwares and NGS datasets are increasingly available for plant sRNA research. Here, by summarizing these valuable resources, we proposed a general workflow to decipher the RDR (RNA-dependent RNA polymerase)- and DCL (Dicer-like)-dependent biogenesis pathways, and the Argonaute-mediated action modes (such as target cleavages and chromatin modifications) for specific sRNA species in plants. Taken together, we hope that by summarizing a list of the public resources, this work will facilitate the plant biologists to perform classification and functional characterization of the interesting sRNA species.
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Affiliation(s)
- Dongliang Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Xiaoxia Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Ziwei Zuo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Weishan Shao
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China.
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China.
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16
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Balyan S, Kumar M, Mutum RD, Raghuvanshi U, Agarwal P, Mathur S, Raghuvanshi S. Identification of miRNA-mediated drought responsive multi-tiered regulatory network in drought tolerant rice, Nagina 22. Sci Rep 2017; 7:15446. [PMID: 29133823 PMCID: PMC5684420 DOI: 10.1038/s41598-017-15450-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 10/23/2017] [Indexed: 11/21/2022] Open
Abstract
Comparative characterization of microRNA-mediated stress regulatory networks in contrasting rice cultivars is critical to decipher plant stress response. Consequently, a multi-level comparative analysis, using sRNA sequencing, degradome analysis, enzymatic and metabolite assays and metal ion analysis, in drought tolerant and sensitive rice cultivars was conducted. The study identified a group of miRNAs "Cultivar-specific drought responsive" (CSDR)-miRNAs (osa-miR159f, osa-miR1871, osa-miR398b, osa-miR408-3p, osa-miR2878-5p, osa-miR528-5p and osa-miR397a) that were up-regulated in the flag-leaves of tolerant cultivar, Nagina 22 (N22) and Vandana, but down-regulated in the sensitive cultivar, Pusa Basmati 1 (PB1) and IR64, during drought. Interestingly, CSDR-miRNAs target several copper-protein coding transcripts like plantacyanins, laccases and Copper/Zinc superoxide dismutases (Cu/Zn SODs) and are themselves found to be similarly induced under simulated copper-starvation in both N22 and PB1. Transcription factor OsSPL9, implicated in Cu-homeostasis also interacted with osa-miR408-3p and osa-miR528-5p promoters. Further, N22 flag leaves showed lower SOD activity, accumulated ROS and had a higher stomata closure. Interestingly, compared to PB1, internal Cu levels significantly decreased in the N22 flag-leaves, during drought. Thus, the study identifies the unique drought mediated dynamism and interplay of Cu and ROS homeostasis, in the flag leaves of drought tolerant rice, wherein CSDR-miRNAs play a pivotal role.
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Affiliation(s)
- Sonia Balyan
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Mukesh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Roseeta Devi Mutum
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Utkarsh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Priyanka Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Saloni Mathur
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
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17
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Oliver C, Pradillo M, Jover-Gil S, Cuñado N, Ponce MR, Santos JL. Loss of function of Arabidopsis microRNA-machinery genes impairs fertility, and has effects on homologous recombination and meiotic chromatin dynamics. Sci Rep 2017; 7:9280. [PMID: 28839139 PMCID: PMC5571030 DOI: 10.1038/s41598-017-07702-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/30/2017] [Indexed: 02/03/2023] Open
Abstract
MicroRNAs (miRNAs) are ~22-nt single-stranded noncoding RNAs with regulatory roles in a wide range of cellular functions by repressing eukaryotic gene expression at a post-transcriptional level. Here, we analyzed the effects on meiosis and fertility of hypomorphic or null alleles of the HYL1, HEN1, DCL1, HST and AGO1 genes, which encode miRNA-machinery components in Arabidopsis. Reduced pollen and megaspore mother cell number and fertility were shown by the mutants analyzed. These mutants also exhibited a relaxed chromatin conformation in male meiocytes at the first meiotic division, and increased chiasma frequency, which is likely to be due to increased levels of mRNAs from key genes involved in homologous recombination. The hen1-13 mutant was found to be hypersensitive to gamma irradiation, which mainly causes double-strand breaks susceptible to be repaired by homologous recombination. Our findings uncover a role for miRNA-machinery components in Arabidopsis meiosis, as well as in the repression of key genes required for homologous recombination. These genes seem to be indirect miRNA targets.
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Affiliation(s)
- Cecilia Oliver
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, 28040, Madrid, Spain.,Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 34396, Montpellier, cedex 05, France
| | - Mónica Pradillo
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Sara Jover-Gil
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - Nieves Cuñado
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain.
| | - Juan Luis Santos
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, 28040, Madrid, Spain.
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18
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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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19
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Cho YB, Jones SI, Vodkin LO. Mutations in Argonaute5 Illuminate Epistatic Interactions of the K1 and I Loci Leading to Saddle Seed Color Patterns in Glycine max. THE PLANT CELL 2017; 29:708-725. [PMID: 28351993 PMCID: PMC5435447 DOI: 10.1105/tpc.17.00162] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 05/18/2023]
Abstract
The soybean (Glycine max) seed coat has distinctive, genetically programmed patterns of pigmentation, and the recessive k1 mutation can epistatically overcome the dominant I and ii alleles, which inhibit seed color by producing small interfering RNAs (siRNAs) targeting chalcone synthase (CHS) mRNAs. Small RNA sequencing of dissected regions of immature seed coats demonstrated that CHS siRNA levels cause the patterns produced by the ii and ik alleles of the I locus, which restrict pigment to the hilum or saddle region of the seed coat, respectively. To identify the K1 locus, we compared RNA-seq data from dissected regions of two Clark isolines having similar saddle phenotypes mediated by CHS siRNAs but different genotypes (homozygous ik K1 versus homozygous ii k1). By examining differentially expressed genes, mapping information, and genome resequencing, we identified a 129-bp deletion in Glyma.11G190900 encoding Argonaute5 (AGO5), a member of the Argonaute family. Amplicon sequencing of several independent saddle pattern mutants from different genetic backgrounds revealed independent lesions affecting AGO5, thus establishing Glyma.11G190900 as the K1 locus. Nonfunctional AGO5 from k1 alleles leads to altered distributions of CHS siRNAs, thus explaining how the k1 mutation reverses the phenotype of the seed coat regions from yellow to pigmented, even in the presence of the normally dominant I or ii alleles.
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Affiliation(s)
- Young B Cho
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
| | - Sarah I Jones
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
| | - Lila O Vodkin
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
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20
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Liu WW, Meng J, Cui J, Luan YS. Characterization and Function of MicroRNA ∗s in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:2200. [PMID: 29312425 PMCID: PMC5744440 DOI: 10.3389/fpls.2017.02200] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/14/2017] [Indexed: 05/20/2023]
Abstract
MicroRNAs, a group of non-coding RNA molecules, play essential roles in a wide range of cellular processes in different molecules, cells, and organisms. In plants, microRNAs are a class of 20- to 24-nucleotides endogenous small RNAs that repress gene expression. The microRNA guide strand (miRNA) and its complementary strand (miRNA∗) both originate from the miRNA/miRNA∗ duplex. Generally, the guide strands act as post-transcriptional regulators that suppress gene expression by cleaving their target mRNA transcripts, whereas the complementary strands were thought to be degraded as 'passenger strands.' However, the complementary strand has been confirmed to possess significant biological functionality in recent reports. In this review, we summarized the binding characteristics of the miRNA∗ strands with ARGONAUTE proteins, their tissue-specific accumulations and their biological functions, illustrating the essential roles of miRNA∗s in biological processes and therefore providing directions for further exploration.
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Affiliation(s)
- Wei-wei Liu
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, China
- *Correspondence: Jun Meng, Yu-shi Luan,
| | - Jun Cui
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, China
| | - Yu-shi Luan
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, China
- *Correspondence: Jun Meng, Yu-shi Luan,
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21
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22
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Sharma D, Tiwari M, Pandey A, Bhatia C, Sharma A, Trivedi PK. MicroRNA858 Is a Potential Regulator of Phenylpropanoid Pathway and Plant Development. PLANT PHYSIOLOGY 2016; 171:944-59. [PMID: 27208307 PMCID: PMC4902582 DOI: 10.1104/pp.15.01831] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/26/2016] [Indexed: 05/08/2023]
Abstract
MicroRNAs (miRNAs) are endogenous, noncoding small RNAs that function as critical regulators of gene expression. In plants, miRNAs have shown their potential as regulators of growth, development, signal transduction, and stress tolerance. Although the miRNA-mediated regulation of several processes is known, the involvement of miRNAs in regulating secondary plant product biosynthesis is poorly understood. In this study, we functionally characterized Arabidopsis (Arabidopsis thaliana) miR858a, which putatively targets R2R3-MYB transcription factors involved in flavonoid biosynthesis. Overexpression of miR858a in Arabidopsis led to the down-regulation of several MYB transcription factors regulating flavonoid biosynthesis. In contrast to the robust growth and early flowering of miR858OX plants, reduction of plant growth and delayed flowering were observed in Arabidopsis transgenic lines expressing an artificial miRNA target mimic (MIM858). Genome-wide expression analysis using transgenic lines suggested that miR858a targets a number of regulatory factors that modulate the expression of downstream genes involved in plant development and hormonal and stress responses. Furthermore, higher expression of MYBs in MIM858 lines leads to redirection of the metabolic flux towards the synthesis of flavonoids at the cost of lignin synthesis. Altogether, our study has established the potential role of light-regulated miR858a in flavonoid biosynthesis and plant growth and development.
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Affiliation(s)
- Deepika Sharma
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| | - Manish Tiwari
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| | - Ashutosh Pandey
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| | - Chitra Bhatia
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| | - Ashish Sharma
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| | - Prabodh Kumar Trivedi
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
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23
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Morea EGO, da Silva EM, e Silva GFF, Valente GT, Barrera Rojas CH, Vincentz M, Nogueira FTS. Functional and evolutionary analyses of the miR156 and miR529 families in land plants. BMC PLANT BIOLOGY 2016; 16:40. [PMID: 26841873 PMCID: PMC4739381 DOI: 10.1186/s12870-016-0716-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 01/18/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are important regulatory elements of gene expression. Similarly to coding genes, miRNA genes follow a birth and death pattern of evolution likely reflecting functional relevance and divergence. For instance, miRNA529 is evolutionarily related to miRNA156 (a highly conserved miRNA in land plants), but it is lost in Arabidopsis thaliana. Interestingly, both miRNAs target sequences overlap in some members of the SQUAMOSA promoter-binding protein like (SPL) family, raising important questions regarding the diversification of the miR156/miR529-associated regulatory network in land plants. RESULTS In this study, through phylogenic reconstruction of miR156/529 target sequences from several taxonomic groups, we have found that specific eudicot SPLs, despite miRNA529 loss, retained the corresponding target site. Detailed molecular evolutionary analyses of miR156/miR529-target sequence showed that loss of miR529 in core eudicots, such as Arabidopsis, is correlated with a more relaxed selection of the miRNA529 specific target element, while miRNA156-specific target sequence is under stronger selection, indicating that these two target sites might be under distinct evolutionary constraints. Importantly, over-expression in Arabidopsis of MIR529 precursor from a monocot, but not from a basal eudicot, demonstrates specific miR529 regulation of AtSPL9 and AtSPL15 genes, which contain conserved responsive elements for both miR156 and miR529. CONCLUSIONS Our results suggest loss of functionality of MIR529 genes in the evolutionary history of eudicots and show that the miR529-responsive element present in some eudicot SPLs is still functional. Our data support the notion that particular miRNA156 family members might have compensated for the loss of miR529 regulation in eudicot species, which concomitantly may have favored diversification of eudicot SPLs.
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Affiliation(s)
- Edna Gicela Ortiz Morea
- Laboratório de Genetica Molecular do Desenvolvimento Vegetal, Departamento de Ciencias Biológicas, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de Sao Paulo, Avenida Padua Dias, 11, 13418-900, Piracicaba, Sao Paulo, Brazil.
- Departamento de Genética, Instituto de Biociencias, Universidade Estadual Paulista (UNESP), Botucatu, Sao Paulo, Brazil.
| | - Eder Marques da Silva
- Laboratório de Genetica Molecular do Desenvolvimento Vegetal, Departamento de Ciencias Biológicas, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de Sao Paulo, Avenida Padua Dias, 11, 13418-900, Piracicaba, Sao Paulo, Brazil.
| | - Geraldo Felipe Ferreira e Silva
- Laboratório de Genetica Molecular do Desenvolvimento Vegetal, Departamento de Ciencias Biológicas, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de Sao Paulo, Avenida Padua Dias, 11, 13418-900, Piracicaba, Sao Paulo, Brazil.
| | - Guilherme Targino Valente
- Departmento de Bioprocessos e Biotecnologia, Universidade Estadual Paulista (UNESP), Botucatu, Sao Paulo, Brazil.
| | - Carlos Hernan Barrera Rojas
- Laboratório de Genetica Molecular do Desenvolvimento Vegetal, Departamento de Ciencias Biológicas, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de Sao Paulo, Avenida Padua Dias, 11, 13418-900, Piracicaba, Sao Paulo, Brazil.
- Departamento de Genética, Instituto de Biociencias, Universidade Estadual Paulista (UNESP), Botucatu, Sao Paulo, Brazil.
| | - Michel Vincentz
- Centro de Biologia Molecular e Engenharia Genetica (CBMEG), Universidade Estadual de Campinas, Campinas, Sao Paulo, Brazil.
| | - Fabio Tebaldi Siveira Nogueira
- Laboratório de Genetica Molecular do Desenvolvimento Vegetal, Departamento de Ciencias Biológicas, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de Sao Paulo, Avenida Padua Dias, 11, 13418-900, Piracicaba, Sao Paulo, Brazil.
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24
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Flores-Sandoval E, Dierschke T, Fisher TJ, Bowman JL. Efficient and Inducible Use of Artificial MicroRNAs in Marchantia polymorpha. PLANT & CELL PHYSIOLOGY 2016; 57:281-90. [PMID: 25971256 DOI: 10.1093/pcp/pcv068] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 05/07/2015] [Indexed: 05/07/2023]
Abstract
We describe the efficient use of artificial microRNAs (amiRs) in Marchantia polymorpha using both endogenous and heterologous primary microRNA (pri-miR) hairpin backbones. Targeting of two transcription factor genes, MpARF1 and MpRR-B, mediating different hormonal responses, demonstrated that amiRs can create specific and reproducible physiological and morphological defects, facilitating interpretation of gene function. A third amiR was designed to target a gene encoding a component of the Polycomb recessive complex 2, MpE(z), and constitutive expression of this amiR results in sporeling lethality. Adaptation of an estrogen-inducible system allowed analysis of the phenotypic effects of induction of this amiR during other stages of the life cycle. We discuss the advantages and challenges of the use of amiRs as a tool for reverse genetic analysis in M. polymorpha.
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Affiliation(s)
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Tom J Fisher
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia Department of Plant Biology, UC Davis, Davis, CA 95616, USA
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25
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Rodriguez RE, Ercoli MF, Debernardi JM, Breakfield NW, Mecchia MA, Sabatini M, Cools T, De Veylder L, Benfey PN, Palatnik JF. MicroRNA miR396 Regulates the Switch between Stem Cells and Transit-Amplifying Cells in Arabidopsis Roots. THE PLANT CELL 2015; 27:3354-66. [PMID: 26645252 PMCID: PMC4707450 DOI: 10.1105/tpc.15.00452] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 09/30/2015] [Accepted: 11/11/2015] [Indexed: 05/18/2023]
Abstract
To ensure an adequate organ mass, the daughters of stem cells progress through a transit-amplifying phase displaying rapid cell division cycles before differentiating. Here, we show that Arabidopsis thaliana microRNA miR396 regulates the transition of root stem cells into transit-amplifying cells by interacting with GROWTH-REGULATING FACTORs (GRFs). The GRFs are expressed in transit-amplifying cells but are excluded from the stem cells through inhibition by miR396. Inactivation of the GRFs increases the meristem size and induces periclinal formative divisions in transit-amplifying cells. The GRFs repress PLETHORA (PLT) genes, regulating their spatial expression gradient. Conversely, PLT activates MIR396 in the stem cells to repress the GRFs. We identified a pathway regulated by GRF transcription factors that represses stem cell-promoting genes in actively proliferating cells, which is essential for the progression of the cell cycle and the orientation of the cell division plane. If unchecked, the expression of the GRFs in the stem cell niche suppresses formative cell divisions and distorts the organization of the quiescent center. We propose that the interactions identified here between miR396 and GRF and PLT transcription factors are necessary to establish the boundary between the stem cell niche and the transit-amplifying region.
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Affiliation(s)
- Ramiro E Rodriguez
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
| | - María Florencia Ercoli
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
| | - Juan Manuel Debernardi
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
| | - Natalie W Breakfield
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, North Carolina 27708
| | - Martin A Mecchia
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
| | - Martin Sabatini
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
| | - Toon Cools
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Philip N Benfey
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, North Carolina 27708
| | - Javier F Palatnik
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
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Budak H, Bulut R, Kantar M, Alptekin B. MicroRNA nomenclature and the need for a revised naming prescription. Brief Funct Genomics 2015; 15:65-71. [PMID: 26148500 DOI: 10.1093/bfgp/elv026] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A central environment and interface for microRNA (miRNA) registry and repository and a general standardized framework for their systematic annotation was established over a decade ago. However, the numbers of experimentally and computationally identified miRNAs are swiftly accumulating, and new aspects of miRNA-mediated gene regulation are being revealed. Currently, it is of great significance that the annotation framework should be redefined to include newly discovered miRNA species such as the variants of mature miRNAs (isomiRNAs), and organellar miRNAs: cipomiRNAs and mitomiRNAs. It is also of great importance that key terminology referring to the novelty, evolutionary history or biogenesis of miRNAs, as well as the confidence of their identification are standardized in the literature and disseminated in a central miRNA registry. Here, we review the status of miRNA nomenclature, curation and critical points of need for a revision of miRNA nomenclature and terminology.
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Hu H, Rashotte AM, Singh NK, Weaver DB, Goertzen LR, Singh SR, Locy RD. The Complexity of Posttranscriptional Small RNA Regulatory Networks Revealed by In Silico Analysis of Gossypium arboreum L. Leaf, Flower and Boll Small Regulatory RNAs. PLoS One 2015; 10:e0127468. [PMID: 26070200 PMCID: PMC4466472 DOI: 10.1371/journal.pone.0127468] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 04/15/2015] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) and secondary small interfering RNAs (principally phased siRNAs or trans-acting siRNAs) are two distinct subfamilies of small RNAs (sRNAs) that are emerging as key regulators of posttranscriptional gene expression in plants. Both miRNAs and secondary-siRNAs (sec-siRNAs) are processed from longer RNA precursors by DICER-LIKE proteins (DCLs). Gossypium arboreum L., also known as tree cotton or Asian cotton, is a diploid, possibly ancestral relative of tetraploid Gossypium hirsutum L., the predominant type of commercially grown cotton worldwide known as upland cotton. To understand the biological significance of these gene regulators in G. arboreum, a bioinformatics analysis was performed on G. arboreum small RNAs produced from G. arboreum leaf, flower, and boll tissues. Consequently, 263 miRNAs derived from 353 precursors, including 155 conserved miRNAs (cs-miRNAs) and 108 novel lineage-specific miRNAs (ls-miRNAs). Along with miRNAs, 2,033 miRNA variants (isomiRNAs) were identified as well. Those isomiRNAs with variation at the 3'-miRNA end were expressed at the highest levels, compared to other types of variants. In addition, 755 pha-siRNAs derived 319 pha-siRNA gene transcripts (PGTs) were identified, and the potential pha-siRNA initiators were predicted. Also, 2,251 non-phased siRNAs were found as well, of which 1,088 appeared to be produced by so-called cis- or trans-cleavage of the PGTs observed at positions differing from pha-siRNAs. Of those sRNAs, 148 miRNAs/isomiRNAs and 274 phased/non-phased siRNAs were differentially expressed in one or more pairs of tissues examined. Target analysis revealed that target genes for both miRNAs and pha-siRNAs are involved a broad range of metabolic and enzymatic activities. We demonstrate that secondary siRNA production could result from initial cleavage of precursors by both miRNAs or isomiRNAs, and that subsequently produced phased and unphased siRNAs could result that also serve as triggers of a second round of both cis- and trans-cleavage of additional siRNAs, leading to the formation of complex sRNA regulatory networks mediating posttranscriptional gene silencing. Results from this study extended our knowledge on G. arboreum sRNAs and their biological importance, which would facilitate future studies on regulatory mechanism of tissue development in cotton and other plant species.
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Affiliation(s)
- Hongtao Hu
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, United States of America; Center for Nano Biotechnology Research, Alabama State University, Montgomery, AL 33104, United States of America
| | - Aaron M Rashotte
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Narendra K Singh
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - David B Weaver
- Department of Crop, Soil & Environmental Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Leslie R Goertzen
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Shree R Singh
- Center for Nano Biotechnology Research, Alabama State University, Montgomery, AL 33104, United States of America
| | - Robert D Locy
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, United States of America
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Budak H, Kantar M, Bulut R, Akpinar BA. Stress responsive miRNAs and isomiRs in cereals. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 235:1-13. [PMID: 25900561 DOI: 10.1016/j.plantsci.2015.02.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 05/18/2023]
Abstract
Abiotic and biotic stress conditions are vital determinants in the production of cereals, the major caloric source in human nutrition. Small RNAs, miRNAs and isomiRs are central to post-transcriptional regulation of gene expression in a variety of cellular processes including development and stress responses. Several miRNAs have been identified using new technologies and have roles in stress responses in plants, including cereals. The overall knowledge about the cereal miRNA repertoire, as well as an understanding of complex miRNA mediated mechanisms of target regulation in response to stress conditions, is far from complete. Ongoing efforts that add to our understanding of complex miRNA machinery have implications in plant response to stress conditions. Additionally, sequence variants of miRNAs (isomiRNAs or isomiRs), regulation of their expression through dissection of upstream regulatory elements, the role of Processing-bodies (P-bodies) in miRNA exerted gene regulation and yet unveiled organellar plant miRNAs are newly emerging topics, which will contribute to the elucidation of the miRNA machinery and its role in cereal tolerance against abiotic and biotic stresses.
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Affiliation(s)
- Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey.
| | - Melda Kantar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Reyyan Bulut
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Bala Ani Akpinar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
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Belli Kullan J, Lopes Paim Pinto D, Bertolini E, Fasoli M, Zenoni S, Tornielli GB, Pezzotti M, Meyers BC, Farina L, Pè ME, Mica E. miRVine: a microRNA expression atlas of grapevine based on small RNA sequencing. BMC Genomics 2015; 16:393. [PMID: 25981679 PMCID: PMC4434875 DOI: 10.1186/s12864-015-1610-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/01/2015] [Indexed: 11/10/2022] Open
Abstract
Background miRNAs are the most abundant class of small non-coding RNAs, and they are involved in post-transcriptional regulations, playing a crucial role in the refinement of genetic programming during plant development. Here we present a comprehensive picture of miRNA regulation in Vitis vinifera L. plant during its complete life cycle. Furthering our knowledge about the post-transcriptional regulation of plant development is fundamental to understand the biology of such an important crop. Results We analyzed 70 small RNA libraries, prepared from berries, inflorescences, tendrils, buds, carpels, stamens and other samples at different developmental stages. One-hundred and ten known and 175 novel miRNAs have been identified and a wide grapevine expression atlas has been described. The distribution of miRNA abundance reveals that 22 novel miRNAs are specific to stamen, and two of them are, interestingly, involved in ethylene biosynthesis, while only few miRNAs are highly specific to other organs. Thirty-eight miRNAs are present in all our samples, suggesting a role in key regulatory circuit. On the basis of miRNAs abundance and distribution across samples and on the estimated correlation, we suggest that miRNA expression define organ identity. We performed target prediction analysis and focused on miRNA expression analysis in berries and inflorescence during their development, providing an initial functional description of the identified miRNAs. Conclusions Our findings represent a very extensive miRNA expression atlas in grapevine, allowing the definition of how the spatio-temporal distribution of miRNAs defines organ identity. We describe miRNAs abundance in specific tissues not previously described in grapevine and contribute to future targeted functional analyses. Finally, we present a deep characterization of miRNA involvement in berry and inflorescence development, suggesting a role for miRNA-driven hormonal regulation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1610-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jayakumar Belli Kullan
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Daniela Lopes Paim Pinto
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Marianna Fasoli
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Sara Zenoni
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | | | - Mario Pezzotti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Blake C Meyers
- Department of Plant and Soil Sciences, University of Delaware, 15 Innovation Way, 19711, Newark, DE, USA.
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, University of Rome "La Sapienza", Via Ariosto 25, 00185, Rome, Italy.
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Erica Mica
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. .,Genomics Research Centre, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Via S. Protaso 302, 29017, Fiorenzuola d'Arda (PC), Italy.
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Trumbo JL, Zhang B, Stewart CN. Manipulating microRNAs for improved biomass and biofuels from plant feedstocks. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:337-54. [PMID: 25707745 DOI: 10.1111/pbi.12319] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 11/25/2014] [Accepted: 11/29/2014] [Indexed: 05/22/2023]
Abstract
Petroleum-based fuels are nonrenewable and unsustainable. Renewable sources of energy, such as lignocellulosic biofuels and plant metabolite-based drop-in fuels, can offset fossil fuel use and reverse environmental degradation through carbon sequestration. Despite these benefits, the lignocellulosic biofuels industry still faces many challenges, including the availability of economically viable crop plants. Cell wall recalcitrance is a major economic barrier for lignocellulosic biofuels production from biomass crops. Sustainability and biomass yield are two additional, yet interrelated, foci for biomass crop improvement. Many scientists are searching for solutions to these problems within biomass crop genomes. MicroRNAs (miRNAs) are involved in almost all biological and metabolic process in plants including plant development, cell wall biosynthesis and plant stress responses. Because of the broad functions of their targets (e.g. auxin response factors), the alteration of plant miRNA expression often results in pleiotropic effects. A specific miRNA usually regulates a biologically relevant bioenergy trait. For example, relatively low miR156 overexpression leads to a transgenic feedstock with enhanced biomass and decreased recalcitrance. miRNAs have been overexpressed in dedicated bioenergy feedstocks such as poplar and switchgrass yielding promising results for lignin reduction, increased plant biomass, the timing of flowering and response to harsh environments. In this review, we present the status of miRNA-related research in several major biofuel crops and relevant model plants. We critically assess published research and suggest next steps for miRNA manipulation in feedstocks for increased biomass and sustainability for biofuels and bioproducts.
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Affiliation(s)
- Jennifer Lynn Trumbo
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, USA; Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
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Smith LM, Burbano HA, Wang X, Fitz J, Wang G, Ural-Blimke Y, Weigel D. Rapid divergence and high diversity of miRNAs and miRNA targets in the Camelineae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:597-610. [PMID: 25557441 DOI: 10.1111/tpj.12754] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 12/10/2014] [Accepted: 12/15/2014] [Indexed: 06/04/2023]
Abstract
MicroRNAs (miRNAs) are short RNAs involved in gene regulation through translational inhibition and transcript cleavage. After processing from imperfect fold-back structures, miRNAs are incorporated into RNA-induced silencing complexes (RISCs) before targeting transcripts with varying degrees of complementarity. Some miRNAs are evolutionarily deep-rooted, and sequence complementarity with their targets is maintained through purifying selection. Both Arabidopsis and Capsella belong to the tribe Camelineae in the Brassicaceae, with Capsella rubella serving as an outgroup to the genus Arabidopsis. The genome sequence of C. rubella has recently been released, which allows characterization of its miRNA complement in comparison with Arabidopsis thaliana and Arabidopsis lyrata. Through next-generation sequencing, we identify high-confidence miRNA candidates specific to the C. rubella lineage. Only a few lineage-specific miRNAs have been studied for evolutionary constraints, and there have been no systematic studies of miRNA target diversity within or divergence between closely related plant species. Therefore we contrast sequence variation in miRNAs and their targets within A. thaliana, and between A. thaliana, A. lyrata and C. rubella. We document a surprising amount of small-scale variation in miRNA-target pairs, where many miRNAs are predicted to have species-specific targets in addition to ones that are shared between species. Our results emphasize that the transitive nature of many miRNA-target pairs can be observed even on a relatively short evolutionary time-scale, with non-random occurrences of differences in miRNAs and their complements in the miRNA precursors, the miRNA* sequences.
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Affiliation(s)
- Lisa M Smith
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK; Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany
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32
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Thatcher SR, Burd S, Wright C, Lers A, Green PJ. Differential expression of miRNAs and their target genes in senescing leaves and siliques: insights from deep sequencing of small RNAs and cleaved target RNAs. PLANT, CELL & ENVIRONMENT 2015; 38:188-200. [PMID: 24965556 PMCID: PMC4304344 DOI: 10.1111/pce.12393] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 06/06/2014] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) are a class of small RNAs, which typically function by guiding cleavage of target mRNAs. They are known to play roles in a variety of plant processes including development, responses to environmental stresses and senescence. To identify senescence regulation of miRNAs in Arabidopsis thaliana, eight small RNA libraries were constructed and sequenced at four different stages of development and senescence from both leaves and siliques, resulting in more than 200 million genome-matched sequences. Parallel analysis of RNA ends libraries, which enable the large-scale examination of miRNA-guided cleavage products, were constructed and sequenced, resulting in over 750 million genome-matched sequences. These large datasets led to the identification a new senescence-inducible small RNA locus, as well as new regulation of known miRNAs and their target genes during senescence, many of which have established roles in nutrient responsiveness and cell structural integrity. In keeping with remobilization of nutrients thought to occur during senescence, many miRNAs and targets had opposite expression pattern changes between leaf and silique tissues during the progression of senescence. Taken together, these findings highlight the integral role that miRNAs may play in the remobilization of resources and alteration of cellular structure that is known to occur in senescence.
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Affiliation(s)
- Shawn R Thatcher
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
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33
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Barciszewska-Pacak M, Milanowska K, Knop K, Bielewicz D, Nuc P, Plewka P, Pacak AM, Vazquez F, Karlowski W, Jarmolowski A, Szweykowska-Kulinska Z. Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses. FRONTIERS IN PLANT SCIENCE 2015; 6:410. [PMID: 26089831 PMCID: PMC4454879 DOI: 10.3389/fpls.2015.00410] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/21/2015] [Indexed: 05/19/2023]
Abstract
Arabidopsis microRNA expression regulation was studied in a wide array of abiotic stresses such as drought, heat, salinity, copper excess/deficiency, cadmium excess, and sulfur deficiency. A home-built RT-qPCR mirEX platform for the amplification of 289 Arabidopsis microRNA transcripts was used to study their response to abiotic stresses. Small RNA sequencing, Northern hybridization, and TaqMan® microRNA assays were performed to study the abundance of mature microRNAs. A broad response on the level of primary miRNAs (pri-miRNAs) was observed. However, stress response at the level of mature microRNAs was rather confined. The data presented show that in most instances, the level of a particular mature miRNA could not be predicted based on the level of its pri-miRNA. This points to an essential role of posttranscriptional regulation of microRNA expression. New Arabidopsis microRNAs responsive to abiotic stresses were discovered. Four microRNAs: miR319a/b, miR319b.2, and miR400 have been found to be responsive to several abiotic stresses and thus can be regarded as general stress-responsive microRNA species.
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Affiliation(s)
- Maria Barciszewska-Pacak
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
- *Correspondence: Maria Barciszewska-Pacak and Zofia Szweykowska-Kulinska, Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland ;
| | - Kaja Milanowska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Katarzyna Knop
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Dawid Bielewicz
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Przemyslaw Nuc
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Patrycja Plewka
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Andrzej M. Pacak
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Franck Vazquez
- Zurich-Basel Plant Science Center, Swiss Plant Science Web, Botanical Institute, University of BaselBasel, Switzerland
| | - Wojciech Karlowski
- Department of Computational Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
- *Correspondence: Maria Barciszewska-Pacak and Zofia Szweykowska-Kulinska, Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland ;
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Sablok G, Srivastva AK, Suprasanna P, Baev V, Ralph PJ. isomiRs: Increasing Evidences of isomiRs Complexity in Plant Stress Functional Biology. FRONTIERS IN PLANT SCIENCE 2015; 6:949. [PMID: 26617614 PMCID: PMC4639611 DOI: 10.3389/fpls.2015.00949] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/17/2015] [Indexed: 05/11/2023]
Affiliation(s)
- Gaurav Sablok
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology SydneySydney, NSW, Australia
- *Correspondence: Gaurav Sablok
| | - Ashish K. Srivastva
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research CentreMumbai, India
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research CentreMumbai, India
| | - Vesselin Baev
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
| | - Peter J. Ralph
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology SydneySydney, NSW, Australia
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Lin Y, Lai Z, Tian Q, Lin L, Lai R, Yang M, Zhang D, Chen Y, Zhang Z. Endogenous target mimics down-regulate miR160 mediation of ARF10, -16, and -17 cleavage during somatic embryogenesis in Dimocarpus longan Lour. FRONTIERS IN PLANT SCIENCE 2015. [PMID: 26594219 DOI: 10.1007/s11032-015-0420-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
MicroRNA160 plays a critical role in plant development by negatively regulating the auxin response factors ARF10, -16, and -17. However, the ways in which miR160 expression is regulated at the transcriptional level, and how miR160 interacts with its targets during plant embryo development, remain unknown. Here, we studied the regulatory relationships among endogenous target mimics (eTMs), and miR160 and its targets, and their involvement in hormone signaling and somatic embryogenesis (SE) in Dimocarpus longan. We identified miR160 family members and isolated the miR160 precursor, primary transcript, and promoter. The promoter contained cis-acting elements responsive to stimuli such as light, abscisic acid, salicylic acid (SA) and heat stress. The pri-miR160 was down-regulated in response to SA but up-regulated by gibberellic acid, ethylene, and methyl jasmonate treatment, suggesting that pri-miR160 was associated with hormone transduction. Dlo-miR160a, -a(∗) and -d(∗) reached expression peaks in torpedo-shaped embryos, globular embryos and cotyledonary embryos, respectively, but were barely detectable in friable-embryogenic callus. This suggests that they have expression-related and functional diversity, especially during the middle and later developmental stages of SE. Four potential eTMs for miR160 were identified. Two of them, glucan endo-1,3-beta- glucosidase-like protein 2-like and calpain-type cysteine protease DEK1, were confirmed to control the corresponding dlo-miR160a(∗) expression level. This suggests that they may function to abolish the binding between dlo-miR160a(∗) and its targets. These two eTMs also participated in 2,4-D and ABA signal transduction. DlARF10, -16, and -17 targeting by dlo-miR160a was confirmed; their expression levels were higher in friable-embryogenic callus and incomplete compact pro-embryogenic cultures and responded to 2,4-D, suggesting they may play a major role in the early stages of longan SE dependent on 2,4-D. The eTMs, miR160, and ARF10, -16, and -17 exhibited tissue specificity in 'Sijimi' longan vegetative and reproductive organs, but were not significant negatively correlated. These results provide insights into the possible role of the eTM-miR160-ARF10-16-17 pathway in longan somatic embryo development.
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Affiliation(s)
- Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Qilin Tian
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Lixia Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Ruilian Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Manman Yang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Dongmin Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
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Liu J, Cheng X, Liu D, Xu W, Wise R, Shen QH. The miR9863 family regulates distinct Mla alleles in barley to attenuate NLR receptor-triggered disease resistance and cell-death signaling. PLoS Genet 2014; 10:e1004755. [PMID: 25502438 PMCID: PMC4263374 DOI: 10.1371/journal.pgen.1004755] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 09/15/2014] [Indexed: 01/19/2023] Open
Abstract
Barley (Hordeum vulgare L.) Mla alleles encode coiled-coil (CC), nucleotide binding, leucine-rich repeat (NB-LRR) receptors that trigger isolate-specific immune responses against the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh). How Mla or NB-LRR genes in grass species are regulated at post-transcriptional level is not clear. The microRNA family, miR9863, comprises four members that differentially regulate distinct Mla alleles in barley. We show that miR9863 members guide the cleavage of Mla1 transcripts in barley, and block or reduce the accumulation of MLA1 protein in the heterologous Nicotiana benthamiana expression system. Regulation specificity is determined by variation in a unique single-nucleotide-polymorphism (SNP) in mature miR9863 family members and two SNPs in the Mla miR9863-binding site that separates these alleles into three groups. Further, we demonstrate that 22-nt miR9863s trigger the biogenesis of 21-nt phased siRNAs (phasiRNAs) and together these sRNAs form a feed-forward regulation network for repressing the expression of group I Mla alleles. Overexpression of miR9863 members specifically attenuates MLA1, but not MLA10-triggered disease resistance and cell-death signaling. We propose a key role of the miR9863 family in dampening immune response signaling triggered by a group of MLA immune receptors in barley. Plants rely on cell-surface and intracellular immune receptors to sense pathogen invasion and to mediate defense responses. However, uncontrolled activation of immune responses is harmful to plant growth and development. Small RNAs have recently been shown to fine-tune the expression of intracellular immune receptors and contribute to the regulation of defense signaling in dicot plants, while similar processes have not been well documented in monocot grain crops, such as barley and wheat. Here, we show that, in barley, some members of the miR9863 family target a subset of Mla alleles that confer race-specific disease resistance to the powdery mildew fungus. These miRNAs act on Mla transcripts by cleavage and translational repression. Production of a type of trans-acting small RNAs, designated as phasiRNAs, enhances the effects of miRNA regulation on Mla targets. We propose that Mla-mediated immune signaling is fine-tuned by the miRNAs at later stage of MLA activation to avoid overloading of immune responses in barley cells.
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Affiliation(s)
- Jie Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Centre for Molecular Agrobiology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiliu Cheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Centre for Molecular Agrobiology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Da Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Centre for Molecular Agrobiology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weihui Xu
- Department of Plant Pathology & Microbiology, Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, Iowa, United States of America
| | - Roger Wise
- Department of Plant Pathology & Microbiology, Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, Iowa, United States of America
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Iowa State University, Ames, Iowa, United States of America
| | - Qian-Hua Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Centre for Molecular Agrobiology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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37
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Shao C, Dong AW, Ma X, Meng Y. Is Argonaute 1 the only effective slicer of small RNA-mediated regulation of gene expression in plants? JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6293-9. [PMID: 25240066 DOI: 10.1093/jxb/eru382] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To maintain normal growth and development in a plant, gene expression must be under strict surveillance. One of the post-transcriptional regulatory pathways involves small RNA (sRNA)-guided, Argonaute (AGO) protein complex-mediated target cleavages. MicroRNAs (miRNAs) are the well-known sRNA species participating in the cleavage-based regulation of gene expression. In plants, most miRNAs are incorporated into AGO1-associated silencing complexes. Thus, the AGO1 protein is considered to be the most important slicer for sRNA-mediated target cleavages. Previous phylogenetic analysis revealed that AGO1, AGO5, and AGO10 belonged to the same clade in Arabidopsis (Arabidopsis thaliana). In addition, experimental evidence pointed to the possibility that AGO2, AGO7, and AGO10 were implicated in specific miRNA-mediated regulatory pathways. To investigate the potential slicer activities of AGO2, AGO5, AGO7, and AGO10, a comprehensive search was performed for the sRNAs enriched in the four AGO proteins in Arabidopsis. A total of 3 499, 1 618, 4 632, and 63 sRNAs are enriched in AGO2, AGO5, AGO7, and AGO10, respectively. Interestingly, several miRNAs were found to be enriched in AGO2 or AGO5. Transcriptome-wide target identification based on degradome sequencing data uncovered that a number of sRNAs enriched in the four AGOs could perform target cleavages like AGO1-associated miRNAs in plants. Based on the above results, the opinion was put forward that not only AGO1, but also AGO2, AGO5, AGO7, and AGO10 might be essential for the sRNA-mediated regulation of gene expression in plants.
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Affiliation(s)
- Chaogang Shao
- College of Life Sciences, Huzhou University, Huzhou 313000, PR China
| | - Ai-Wen Dong
- Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, Jishou University, Zhangjiajie 427000, PR China
| | - Xiaoxia Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Xuelin Street 16#, Xiasha, Hangzhou 310036, PR China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Xuelin Street 16#, Xiasha, Hangzhou 310036, PR China
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38
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Li J, Reichel M, Li Y, Millar AA. The functional scope of plant microRNA-mediated silencing. TRENDS IN PLANT SCIENCE 2014; 19:750-6. [PMID: 25242049 DOI: 10.1016/j.tplants.2014.08.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 08/05/2014] [Accepted: 08/23/2014] [Indexed: 05/26/2023]
Abstract
Deep sequencing has identified a complex set of plant miRNAs that potentially regulates many target genes of high complementarity. Furthermore, the discovery that many plant miRNAs work through a translational repression mechanism, along with the identification of noncanonical targets, has encouraged bioinformatic searches with less stringent parameters, identifying an even wider range of potential targets. Together, these findings suggest that any given plant miRNA family may regulate a highly diverse set of mRNAs. Here we present evolutionary, genetic, and mechanistic evidence that opposes this idea but instead suggests that families of sequence-related miRNAs regulate very few functionally related targets. We propose that complexities beyond complementarity impact plant miRNA target recognition, possibly explaining the current disparity between bioinformatic prediction and functional evidence.
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Affiliation(s)
- Junyan Li
- Plant Science Division, Research School of Biology, Australian National University, 0200 ACT, Australia
| | - Marlene Reichel
- Plant Science Division, Research School of Biology, Australian National University, 0200 ACT, Australia
| | - Yanjiao Li
- Plant Science Division, Research School of Biology, Australian National University, 0200 ACT, Australia
| | - Anthony A Millar
- Plant Science Division, Research School of Biology, Australian National University, 0200 ACT, Australia.
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39
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Schmidt SA, Foley PL, Jeong DH, Rymarquis LA, Doyle F, Tenenbaum SA, Belasco JG, Green PJ. Identification of SMG6 cleavage sites and a preferred RNA cleavage motif by global analysis of endogenous NMD targets in human cells. Nucleic Acids Res 2014; 43:309-23. [PMID: 25429978 PMCID: PMC4288159 DOI: 10.1093/nar/gku1258] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In metazoans, cleavage by the endoribonuclease SMG6 is often the first degradative event in non-sense-mediated mRNA decay (NMD). However, the exact sites of SMG6 cleavage have yet to be determined for any endogenous targets, and most evidence as to the identity of SMG6 substrates is indirect. Here, we use Parallel Analysis of RNA Ends to specifically identify the 5′ termini of decay intermediates whose production is dependent on SMG6 and the universal NMD factor UPF1. In this manner, the SMG6 cleavage sites in hundreds of endogenous NMD targets in human cells have been mapped at high resolution. In addition, a preferred sequence motif spanning most SMG6 cleavage sites has been discovered and validated by mutational analysis. For many SMG6 substrates, depletion of SMG6 resulted in the accumulation of decapped transcripts, an effect indicative of competition between SMG6-dependent and SMG6-independent NMD pathways. These findings provide key insights into the mechanisms by which mRNAs targeted by NMD are degraded.
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Affiliation(s)
- Skye A Schmidt
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Patricia L Foley
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Dong-Hoon Jeong
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Linda A Rymarquis
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Francis Doyle
- Department of Life Science, Hallym University, Chuncheon, Gangwon, Republic of Korea
| | - Scott A Tenenbaum
- Department of Life Science, Hallym University, Chuncheon, Gangwon, Republic of Korea
| | - Joel G Belasco
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Pamela J Green
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
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40
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Schommer C, Debernardi JM, Bresso EG, Rodriguez RE, Palatnik JF. Repression of cell proliferation by miR319-regulated TCP4. MOLECULAR PLANT 2014; 7:1533-44. [PMID: 25053833 DOI: 10.1093/mp/ssu084] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Leaf development has been extensively studied on a genetic level. However, little is known about the interplay between the developmental regulators and the cell cycle machinery--a link that ultimately affects leaf form and size. miR319 is a conserved microRNA that regulates TCP transcription factors involved in multiple developmental pathways, including leaf development and senescence, organ curvature, and hormone biosynthesis and signaling. Here, we analyze the participation of TCP4 in the control of cell proliferation. A small increase in TCP4 activity has an immediate impact on leaf cell number, by significantly reducing cell proliferation. Plants with high TCP4 levels have a strong reduction in the expression of genes known to be active in G2-M phase of the cell cycle. Part of these effects is mediated by induction of miR396, which represses Growth-Regulating Factor (GRF) transcription factors. Detailed analysis revealed TCP4 to be a direct regulator of MIR396b. However, we found that TCP4 can control cell proliferation through additional pathways, and we identified a direct connection between TCP4 and ICK1/KRP1, a gene involved in the progression of the cell cycle. Our results show that TCP4 can activate different pathways that repress cell proliferation.
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Affiliation(s)
- Carla Schommer
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
| | - Juan M Debernardi
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
| | - Edgardo G Bresso
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
| | - Ramiro E Rodriguez
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
| | - Javier F Palatnik
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
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Kakrana A, Hammond R, Patel P, Nakano M, Meyers BC. sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software. Nucleic Acids Res 2014; 42:e139. [PMID: 25120269 PMCID: PMC4191380 DOI: 10.1093/nar/gku693] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Parallel analysis of RNA ends (PARE) is a technique utilizing high-throughput sequencing to profile uncapped, mRNA cleavage or decay products on a genome-wide basis. Tools currently available to validate miRNA targets using PARE data employ only annotated genes, whereas important targets may be found in unannotated genomic regions. To handle such cases and to scale to the growing availability of PARE data and genomes, we developed a new tool, 'sPARTA' (small RNA-PARE target analyzer) that utilizes a built-in, plant-focused target prediction module (aka 'miRferno'). sPARTA not only exhibits an unprecedented gain in speed but also it shows greater predictive power by validating more targets, compared to a popular alternative. In addition, the novel 'seed-free' mode, optimized to find targets irrespective of complementarity in the seed-region, identifies novel intergenic targets. To fully capitalize on the novelty and strengths of sPARTA, we developed a web resource, 'comPARE', for plant miRNA target analysis; this facilitates the systematic identification and analysis of miRNA-target interactions across multiple species, integrated with visualization tools. This collation of high-throughput small RNA and PARE datasets from different genomes further facilitates re-evaluation of existing miRNA annotations, resulting in a 'cleaner' set of microRNAs.
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Affiliation(s)
- Atul Kakrana
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19714, USA Delaware Biotechnology Institute, University of Delaware, Newark, DE 19714, USA
| | - Reza Hammond
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19714, USA Delaware Biotechnology Institute, University of Delaware, Newark, DE 19714, USA
| | - Parth Patel
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19714, USA Delaware Biotechnology Institute, University of Delaware, Newark, DE 19714, USA
| | - Mayumi Nakano
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Blake C Meyers
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19714, USA Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
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Bao M, Bian H, Zha Y, Li F, Sun Y, Bai B, Chen Z, Wang J, Zhu M, Han N. miR396a-Mediated basic helix-loop-helix transcription factor bHLH74 repression acts as a regulator for root growth in Arabidopsis seedlings. PLANT & CELL PHYSIOLOGY 2014; 55:1343-53. [PMID: 24793750 DOI: 10.1093/pcp/pcu058] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
miR396 targets seven GROWTH-REGULATING FACTOR (GRF) genes and the BASIC HELIX-LOOP-HELIX (bHLH) TRANSCRIPTION FACTOR 74 gene (bHLH74) in Arabidopsis. Previous research revealed that the miR396 target module regulates cell proliferation and plays a critical role in leaf development. However, no additional biological functions of miR396 have been investigated in detail. In this study, T-DNA insertion mutants and transgenic plants with altered levels of miR396 or its target genes were used to characterize the regulatory role of miR396 in root development. We found that AtMIR396a was the predominant source for miR396 accumulation in the roots of seedlings, and that the mir396a-1 mutant had longer roots than wild-type seedlings. Overexpression of AtMIR396a decreased the transcript levels of target genes such as GRF genes and bHLH74, and resulted in a shorter root phenotype. Furthermore, the bhlh74-1 mutant had shorter roots, whereas overexpression of an miR396-resistant form of bHLH74 (mbHLH74) had an enhanced root growth phenotype. Moreover, MIR396a regulated root growth by affecting the elongation zone. Taken together, these data indicate that miR396a-mediated bHLH74 repression helps regulate root growth in Arabidopsis seedlings.
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Affiliation(s)
- Maolin Bao
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Hongwu Bian
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yulong Zha
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Fengyun Li
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yuzhe Sun
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Bin Bai
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Zhehao Chen
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, ChinaCollege of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, Zhejiang, China
| | - Junhui Wang
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Muyuan Zhu
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Ning Han
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
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43
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Lei J, Sun Y. miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data. ACTA ACUST UNITED AC 2014; 30:2837-9. [PMID: 24930140 DOI: 10.1093/bioinformatics/btu380] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
SUMMARY Plant microRNA prediction tools that use small RNA-sequencing data are emerging quickly. These existing tools have at least one of the following problems: (i) high false-positive rate; (ii) long running time; (iii) work only for genomes in their databases; (iv) hard to install or use. We developed miR-PREFeR (miRNA PREdiction From small RNA-Seq data), which uses expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species. We tested miR-PREFeR on several plant species. The results show that miR-PREFeR is sensitive, accurate, fast and has low-memory footprint. AVAILABILITY AND IMPLEMENTATION https://github.com/hangelwen/miR-PREFeR
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Affiliation(s)
- Jikai Lei
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Yanni Sun
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
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44
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Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs. Nat Commun 2014; 5:3722. [PMID: 24759728 DOI: 10.1038/ncomms4722] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 03/26/2014] [Indexed: 01/13/2023] Open
Abstract
Small RNAs are pivotal regulators of gene expression that guide transcriptional and post-transcriptional silencing mechanisms in eukaryotes, including plants. Here we report a comprehensive atlas of sRNA and miRNA from 3 species of algae and 31 representative species across vascular plants, including non-model plants. We sequence and quantify sRNAs from 99 different tissues or treatments across species, resulting in a data set of over 132 million distinct sequences. Using miRBase mature sequences as a reference, we identify the miRNA sequences present in these libraries. We apply diverse profiling methods to examine critical sRNA and miRNA features, such as size distribution, tissue-specific regulation and sequence conservation between species, as well as to predict putative new miRNA sequences. We also develop database resources, computational analysis tools and a dedicated website, http://smallrna.udel.edu/. This study provides new insights on plant sRNAs and miRNAs, and a foundation for future studies.
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45
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Coruh C, Shahid S, Axtell MJ. Seeing the forest for the trees: annotating small RNA producing genes in plants. CURRENT OPINION IN PLANT BIOLOGY 2014; 18:87-95. [PMID: 24632306 PMCID: PMC4001702 DOI: 10.1016/j.pbi.2014.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/28/2014] [Accepted: 02/14/2014] [Indexed: 05/09/2023]
Abstract
A key goal in genomics is the complete annotation of the expressed regions of the genome. In plants, substantial portions of the genome make regulatory small RNAs produced by Dicer-Like (DCL) proteins and utilized by Argonaute (AGO) proteins. These include miRNAs and various types of endogenous siRNAs. Small RNA-seq, enabled by cheap and fast DNA sequencing, has produced an enormous volume of data on plant miRNA and siRNA expression in recent years. In this review, we discuss recent progress in using small RNA-seq data to produce stable and reliable annotations of miRNA and siRNA genes in plants. In addition, we highlight key goals for the future of small RNA gene annotation in plants.
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Affiliation(s)
- Ceyda Coruh
- Department of Biology, Penn State University, University Park, PA 16802, USA; Plant Biology Intercollegiate Ph.D. Program, Penn State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA
| | - Saima Shahid
- Department of Biology, Penn State University, University Park, PA 16802, USA; Plant Biology Intercollegiate Ph.D. Program, Penn State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA
| | - Michael J Axtell
- Department of Biology, Penn State University, University Park, PA 16802, USA; Plant Biology Intercollegiate Ph.D. Program, Penn State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA.
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