1
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Fan S, Tang Y, Zhu N, Meng Q, Zhou Y, Zhao Y, Xu J, Gu C, Dai S, Zhu B, Yuan X. Analyzing the defense response mechanism of Atractylodes macrocephala to Fusarium oxysporum through small RNA and degradome sequencing. FRONTIERS IN PLANT SCIENCE 2024; 15:1415209. [PMID: 39104842 PMCID: PMC11298489 DOI: 10.3389/fpls.2024.1415209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 07/08/2024] [Indexed: 08/07/2024]
Abstract
Introduction Fusarium oxysporum is a significant soil-borne fungal pathogen that affects over 100 plant species, including crucial crops like tomatoes, bananas, cotton, cucumbers, and watermelons, leading to wilting, yellowing, growth inhibition, and ultimately plant death. The root rot disease of A. macrocephala, caused by F. oxysporum, is one of the most serious diseases in continuous cropping, which seriously affects its sustainable development. Methods In this study, we explored the interaction between A. macrocephala and F. oxysporum through integrated small RNA (sRNA) and degradome sequencing to uncover the microRNA (miRNA)-mediated defense mechanisms. Results We identified colonization of F. oxysporum in A. macrocephala roots on day 6. Nine sRNA samples were sequenced to examine the dynamic changes in miRNA expression in A. macrocephala infected by F. oxysporum at 0, 6, and 12 days after inoculation. Furthermore, we using degradome sequencing and quantitative real-time PCR (qRT-PCR), validated four miRNA/target regulatory units involved in A. macrocephala-F. oxysporum interactions. Discussion This study provides new insights into the molecular mechanisms underlying A. macrocephala's early defense against F. oxysporum infection, suggesting directions for enhancing resistance against this pathogen.
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Affiliation(s)
- Sen Fan
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yunjia Tang
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, China
| | - Na Zhu
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qingling Meng
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yanguang Zhou
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yujin Zhao
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jingyan Xu
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Chenxian Gu
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Shijie Dai
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Bo Zhu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaofeng Yuan
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
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2
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Huang K, Meyers BC, Caplan JL. Fluorescent In Situ Detection of Small RNAs in Plants Using sRNA-FISH. Methods Mol Biol 2024; 2784:101-111. [PMID: 38502481 DOI: 10.1007/978-1-0716-3766-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Plant small RNAs are 21-24 nucleotide, noncoding RNAs that function as regulators in plant growth and development. Colorimetric detection of plant small RNAs was made possible with the introduction of locked nucleic acid probes. However, fluorescent detection of plant small RNAs has been challenging due to the high autofluorescence from plant tissue. Here we report a fluorescent in situ detection method for plant small RNAs. This method can be applied to most plant samples and tissue types and also can be adapted for single-molecule detection of small RNAs with super-resolution microscopy.
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Affiliation(s)
- Kun Huang
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA
- Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
- Molecular Imaging Core, Dana-Farber Cancer Institute, Boston, USA
| | - Blake C Meyers
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
- Division of Plant Science and Technology, University of Missouri - Columbia, Columbia, MO, USA.
| | - Jeffrey L Caplan
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.
- Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
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3
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Czymmek KJ, Duncan KE, Berg H. Realizing the Full Potential of Advanced Microscopy Approaches for Interrogating Plant-Microbe Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:245-255. [PMID: 36947723 DOI: 10.1094/mpmi-10-22-0208-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Microscopy has served as a fundamental tool for insight and discovery in plant-microbe interactions for centuries. From classical light and electron microscopy to corresponding specialized methods for sample preparation and cellular contrasting agents, these approaches have become routine components in the toolkit of plant and microbiology scientists alike to visualize, probe and understand the nature of host-microbe relationships. Over the last three decades, three-dimensional perspectives led by the development of electron tomography, and especially, confocal techniques continue to provide remarkable clarity and spatial detail of tissue and cellular phenomena. Confocal and electron microscopy provide novel revelations that are now commonplace in medium and large institutions. However, many other cutting-edge technologies and sample preparation workflows are relatively unexploited yet offer tremendous potential for unprecedented advancement in our understanding of the inner workings of pathogenic, beneficial, and symbiotic plant-microbe interactions. Here, we highlight key applications, benefits, and challenges of contemporary advanced imaging platforms for plant-microbe systems with special emphasis on several recently developed approaches, such as light-sheet, single molecule, super-resolution, and adaptive optics microscopy, as well as ambient and cryo-volume electron microscopy, X-ray microscopy, and cryo-electron tomography. Furthermore, the potential for complementary sample preparation methodologies, such as optical clearing, expansion microscopy, and multiplex imaging, will be reviewed. Our ultimate goal is to stimulate awareness of these powerful cutting-edge technologies and facilitate their appropriate application and adoption to solve important and unresolved biological questions in the field. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Kirk J Czymmek
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
- Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
| | - Keith E Duncan
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
| | - Howard Berg
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
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4
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Wu C, Hsieh K, Yeh S, Lu Y, Chen L, Ku MSB, Li W. Simultaneous detection of miRNA and mRNA at the single-cell level in plant tissues. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:136-149. [PMID: 36148792 PMCID: PMC9829392 DOI: 10.1111/pbi.13931] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/02/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Detecting the simultaneous presence of a microRNA (miRNA) and a mRNA in a specific tissue can provide support for the prediction that the miRNA regulates the mRNA. Although two such methods have been developed for mammalian tissues, they have a low signal-noise ratio and/or poor resolution at the single-cell level. To overcome these drawbacks, we develop a method that uses sequence-specific miRNA-locked nucleic acid (LNA) and mRNA-LNA probes. Moreover, it augments the detection signal by rolling circle amplification, achieving a high signal-noise ratio at the single-cell level. Dot signals are counted for determining the expression levels of mRNA and miRNA molecules in specific cells. We show a high sequence specificity of our miRNA-LNA probe, revealing that it can discriminate single-base mismatches. Numerical quantification by our method is tested in transgenic rice lines with different gene expression levels. We conduct several applications. First, the spatial expression profiling of osa-miR156 and OsSPL12 in rice leaves reveals their specific expression in mesophyll cells. Second, studying rice and its mutant lines with our method reveals opposite expression patterns of miRNA and its target mRNA in tissues. Third, the dynamic expression profiles of ZmGRF8 and zma-miR396 during maize leaf development provide evidence that zma-miR396 regulates the preferential spatial expression of ZmGRF8 in bundle sheath cells. Finally, our method can be scaled up to simultaneously detect multiple miRNAs and mRNAs in a tissue. Thus, it is a sensitive and versatile technique for studying miRNA regulation of plant tissue development.
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Affiliation(s)
- Chi‐Chih Wu
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
| | | | - Su‐Ying Yeh
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
| | - Yen‐Ting Lu
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
| | - Liang‐Jwu Chen
- Institute of Molecular Biology, National Chung Hsing UniversityTaichungTaiwan
| | - Maurice S. B. Ku
- Department of Agricultural BiotechnologyNational Chiayi UniversityChaiyiTaiwan
- School of Biological SciencesWashington State UniversityPullmanWAUSA
| | - Wen‐Hsiung Li
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
- Department of Ecology and EvolutionUniversity of ChicagoChicagoILUSA
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5
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Zhou X, Huang K, Teng C, Abdelgawad A, Batish M, Meyers BC, Walbot V. 24-nt phasiRNAs move from tapetal to meiotic cells in maize anthers. THE NEW PHYTOLOGIST 2022; 235:488-501. [PMID: 35451503 DOI: 10.1111/nph.18167] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
In maize, 24-nt phased, secondary small interfering RNAs (phasiRNAs) are abundant in meiotic stage anthers, but their distribution and functions are not precisely known. Using laser capture microdissection, we analyzed tapetal cells, meiocytes and other somatic cells at several stages of anther development to establish the timing of 24-PHAS precursor transcripts and the 24-nt phasiRNA products. By integrating RNA and small RNA profiling plus single-molecule and small RNA FISH (smFISH or sRNA-FISH) spatial detection, we demonstrate that the tapetum is the primary site of 24-PHAS precursor and Dcl5 transcripts and the resulting 24-nt phasiRNAs. Interestingly, 24-nt phasiRNAs accumulate in all cell types, with the highest levels in meiocytes, followed by tapetum. Our data support the conclusion that 24-nt phasiRNAs are mobile from tapetum to meiocytes and to other somatic cells. We discuss possible roles for 24-nt phasiRNAs in anther cell types.
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Affiliation(s)
- Xue Zhou
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Kun Huang
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19716, USA
- Dana-Farber Cancer Institute Molecular Imaging Core, 360 Longwood Ave, Boston, MA, 02215, USA
| | - Chong Teng
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Ahmed Abdelgawad
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
- Division of Plant Sciences, University of Missouri - Columbia, Columbia, MO, 65211, USA
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
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6
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Tang Y, Yan X, Gu C, Yuan X. Biogenesis, Trafficking, and Function of Small RNAs in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:825477. [PMID: 35251095 PMCID: PMC8891129 DOI: 10.3389/fpls.2022.825477] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/19/2022] [Indexed: 05/03/2023]
Abstract
Small RNAs (sRNAs) encoded by plant genomes have received widespread attention because they can affect multiple biological processes. Different sRNAs that are synthesized in plant cells can move throughout the plants, transport to plant pathogens via extracellular vesicles (EVs), and transfer to mammals via food. Small RNAs function at the target sites through DNA methylation, RNA interference, and translational repression. In this article, we reviewed the systematic processes of sRNA biogenesis, trafficking, and the underlying mechanisms of its functions.
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Affiliation(s)
- Yunjia Tang
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaoning Yan
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Chenxian Gu
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaofeng Yuan
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
- Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
- *Correspondence: Xiaofeng Yuan,
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7
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Pokhrel S, Huang K, Bélanger S, Zhan J, Caplan JL, Kramer EM, Meyers BC. Pre-meiotic 21-nucleotide reproductive phasiRNAs emerged in seed plants and diversified in flowering plants. Nat Commun 2021; 12:4941. [PMID: 34400639 PMCID: PMC8368212 DOI: 10.1038/s41467-021-25128-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 07/24/2021] [Indexed: 02/07/2023] Open
Abstract
Plant small RNAs are important regulatory elements that fine-tune gene expression and maintain genome integrity by silencing transposons. Reproductive organs of monocots produce abundant phased, small interfering RNAs (phasiRNAs). The 21-nt reproductive phasiRNAs triggered by miR2118 are highly enriched in pre-meiotic anthers, and have been found in multiple eudicot species, in contrast with prior reports of monocot specificity. The 24-nt reproductive phasiRNAs are triggered by miR2275, and are highly enriched during meiosis in many angiosperms. Here, we report the widespread presence of the 21-nt reproductive phasiRNA pathway in eudicots including canonical and non-canonical microRNA (miRNA) triggers of this pathway. In eudicots, these 21-nt phasiRNAs are enriched in pre-meiotic stages, a spatiotemporal distribution consistent with that of monocots and suggesting a role in anther development. Although this pathway is apparently absent in well-studied eudicot families including the Brassicaceae, Solanaceae and Fabaceae, our work in eudicots supports an earlier singular finding in spruce, a gymnosperm, indicating that the pathway of 21-nt reproductive phasiRNAs emerged in seed plants and was lost in some lineages.
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Affiliation(s)
- Suresh Pokhrel
- grid.34424.350000 0004 0466 6352Donald Danforth Plant Science Center, Saint Louis, MO USA ,grid.134936.a0000 0001 2162 3504Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO USA
| | - Kun Huang
- grid.33489.350000 0001 0454 4791Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE USA
| | - Sébastien Bélanger
- grid.34424.350000 0004 0466 6352Donald Danforth Plant Science Center, Saint Louis, MO USA
| | - Junpeng Zhan
- grid.34424.350000 0004 0466 6352Donald Danforth Plant Science Center, Saint Louis, MO USA ,grid.263817.9Department of Biology and Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, Guangdong China
| | - Jeffrey L. Caplan
- grid.33489.350000 0001 0454 4791Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE USA
| | - Elena M. Kramer
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Blake C. Meyers
- grid.34424.350000 0004 0466 6352Donald Danforth Plant Science Center, Saint Louis, MO USA ,grid.134936.a0000 0001 2162 3504Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO USA
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8
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Liang Y, Zhu W, Chen S, Qian J, Li L. Genome-Wide Identification and Characterization of Small Peptides in Maize. FRONTIERS IN PLANT SCIENCE 2021; 12:695439. [PMID: 34220917 PMCID: PMC8244733 DOI: 10.3389/fpls.2021.695439] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/20/2021] [Indexed: 05/06/2023]
Abstract
Small peptides (sPeptides), <100 amino acids (aa) long, are encoded by small open reading frames (sORFs) often found in the 5' and 3' untranslated regions (or other parts) of mRNAs, in long non-coding RNAs, or transcripts from introns and intergenic regions; various sPeptides play important roles in multiple biological processes. In this study, we conducted a comprehensive study of maize (Zea mays) sPeptides using mRNA sequencing, ribosome profiling (Ribo-seq), and mass spectrometry (MS) on six tissues (each with at least two replicates). To identify maize sORFs and sPeptides from these data, we set up a robust bioinformatics pipeline and performed a genome-wide scan. This scan uncovered 9,388 sORFs encoding peptides of 2-100 aa. These sORFs showed distinct genomic features, such as different Kozak region sequences, higher specificity of translation, and high translational efficiency, compared with the canonical protein-coding genes. Furthermore, the MS data verified 2,695 sPeptides. These sPeptides perfectly discriminated all the tissues and were highly associated with their parental genes. Interestingly, the parental genes of sPeptides were significantly enriched in multiple functional gene ontology terms related to abiotic stress and development, suggesting the potential roles of sPeptides in the regulation of their parental genes. Overall, this study lays out the guidelines for genome-wide scans of sORFs and sPeptides in plants by integrating Ribo-seq and MS data and provides a more comprehensive resource of functional sPeptides in maize and gives a new perspective on the complex biological systems of plants.
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Affiliation(s)
| | | | | | | | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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9
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Meitha K, Esyanti RR, Iriawati, Hanisia RH, Rohyani. Green pesticide: Tapping to the promising roles of plant secreted small RNAs and responses towards extracellular DNA. Noncoding RNA Res 2021; 6:42-50. [PMID: 33778217 PMCID: PMC7970063 DOI: 10.1016/j.ncrna.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/02/2021] [Accepted: 02/07/2021] [Indexed: 12/19/2022] Open
Abstract
The diverse roles of non-coding RNA and DNA in cross-species communication is yet to be revealed. Once thought to only involve intra-specifically in regulating gene expression, the evidence that these genetic materials can also modulate gene expression between species that belong to different kingdoms is accumulating. Plants send small RNAs to the pathogen or parasite when they are being attacked, targeting essential mRNAs for infection or parasitism of the hosts. However, the same survival mechanism is also deployed by the pathogen or parasite to destabilize plant immune responses. In plants, it is suggested that exposure to extracellular self-DNA impedes growth, while to extracellular non-self-DNA induces the modulation of reactive oxygen species, expression of resistance related genes, epigenetic mechanism, or suppression of disease severity. Exploring the potential of secreted RNA and extracellular DNA as a green pesticide could be a promising alternative if we are to provide food for the future global population without further damaging the environment. Hence, some studies on plant secreted RNA and responses towards extracellular DNA are discussed in this review. The precise mode of action of entry and the following cascade of signaling once the plant cell is exposed to secreted RNA or extracellular DNA could be an interesting topic for future research.
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Affiliation(s)
- Karlia Meitha
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Rizkita Rachmi Esyanti
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Iriawati
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Ristag Hamida Hanisia
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Rohyani
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
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10
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Huang K, Demirci F, Batish M, Treible W, Meyers BC, Caplan JL. Quantitative, super-resolution localization of small RNAs with sRNA-PAINT. Nucleic Acids Res 2020; 48:e96. [PMID: 32716042 PMCID: PMC7498346 DOI: 10.1093/nar/gkaa623] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 06/24/2020] [Accepted: 07/13/2020] [Indexed: 12/21/2022] Open
Abstract
Small RNAs are non-coding RNAs that play important roles in the lives of both animals and plants. They are 21- to 24-nt in length and ∼10 nm in size. Their small size and high diversity have made it challenging to develop detection methods that have sufficient resolution and specificity to multiplex and quantify. We created a method, sRNA-PAINT, for the detection of small RNAs with 20 nm resolution by combining the super-resolution method, DNA-based points accumulation in nanoscale topography (DNA-PAINT), and the specificity of locked nucleic acid (LNA) probes for the in situ detection of multiple small RNAs. The method relies on designing probes to target small RNAs that combine DNA oligonucleotides (oligos) for PAINT with LNA-containing oligos for hybridization; therefore, we developed an online tool called ‘Vetting & Analysis of RNA for in situ Hybridization probes’ (VARNISH) for probe design. Our method utilizes advances in DNA-PAINT methodologies, including qPAINT for quantification, and Exchange-PAINT for multiplexing. We demonstrated these capabilities of sRNA-PAINT by detecting and quantifying small RNAs in different cell layers of early developmental stage maize anthers that are important for male sexual reproduction.
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Affiliation(s)
- Kun Huang
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA.,Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
| | - Feray Demirci
- FiDoSoft Software Consulting, Redmond, WA 98052, USA
| | - Mona Batish
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Wayne Treible
- Department of Computer and Information Sciences, University of Delaware, Newark, DE 19716, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA.,University of Missouri - Columbia, Division of Plant Sciences, 52 Agriculture Lab, Columbia, MO 65211, USA
| | - Jeffrey L Caplan
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA.,Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
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11
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Wójcik AM. Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis. Int J Mol Sci 2020; 21:E4969. [PMID: 32674459 PMCID: PMC7420248 DOI: 10.3390/ijms21144969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
During early plant embryogenesis, some of the most fundamental decisions on fate and identity are taken making it a fascinating process to study. It is no surprise that higher plant embryogenesis was intensively analysed during the last century, while somatic embryogenesis is probably the most studied regeneration model. Encoded by the MIRNA, short, single-stranded, non-coding miRNAs, are commonly present in all Eukaryotic genomes and are involved in the regulation of the gene expression during the essential developmental processes such as plant morphogenesis, hormone signaling, and developmental phase transition. During the last few years dedicated to miRNAs, analytical methods and tools have been developed, which have afforded new opportunities in functional analyses of plant miRNAs, including (i) databases for in silico analysis; (ii) miRNAs detection and expression approaches; (iii) reporter and sensor lines for a spatio-temporal analysis of the miRNA-target interactions; (iv) in situ hybridisation protocols; (v) artificial miRNAs; (vi) MIM and STTM lines to inhibit miRNA activity, and (vii) the target genes resistant to miRNA. Here, we attempted to summarise the toolbox for functional analysis of miRNAs during plant embryogenesis. In addition to characterising the described tools/methods, examples of the applications have been presented.
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Affiliation(s)
- Anna Maria Wójcik
- University of Silesia in Katowice, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
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12
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Markey FB, Parashar V, Batish M. Methods for spatial and temporal imaging of the different steps involved in RNA processing at single-molecule resolution. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1608. [PMID: 32543077 DOI: 10.1002/wrna.1608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/26/2022]
Abstract
RNA plays a quintessential role as a messenger of information from genotype (DNA) to phenotype (proteins), as well as acts as a regulatory molecule (noncoding RNAs). All steps in the journey of RNA from synthesis (transcription), splicing, transport, localization, translation, to its eventual degradation, comprise important steps in gene expression, thereby controlling the fate of the cell. This lifecycle refers to the majority of RNAs (primarily mRNAs), but not other RNAs such as tRNAs. Imaging these processes in fixed cells and in live cells has been an important tool in developing an understanding of the regulatory steps in RNAs journey. Single-cell and single-molecule imaging techniques enable a much deeper understanding of cellular biology, which is not possible with bulk studies involving RNA isolated from a large pool of cells. Classic techniques, such as fluorescence in situ hybridization (FISH), as well as more recent aptamer-based approaches, have provided detailed insights into RNA localization, and have helped to predict the functions carried out by many RNA species. However, there are still certain processing steps that await high-resolution imaging, which is an exciting and upcoming area of research. In this review, we will discuss the methods that have revolutionized single-molecule resolution imaging in general, the steps of RNA processing in which these methods have been used, and new emerging technologies. This article is categorized under: RNA Export and Localization > RNA Localization RNA Methods > RNA Analyses in Cells RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions.
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Affiliation(s)
- Fatu Badiane Markey
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Vijay Parashar
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Mona Batish
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA.,Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
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13
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Lei X, Liu B. Tapetum-Dependent Male Meiosis Progression in Plants: Increasing Evidence Emerges. FRONTIERS IN PLANT SCIENCE 2020; 10:1667. [PMID: 32010157 PMCID: PMC6979054 DOI: 10.3389/fpls.2019.01667] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/27/2019] [Indexed: 05/28/2023]
Abstract
In higher plants, male meiosis is a key process during microsporogenesis and is crucial for male fertility and seed set. Meiosis involves a highly dynamic organization of chromosomes and cytoskeleton and specifically takes place within sexual cells. However, studies in multiple plant species have suggested that the normal development of tapetum, the somatic cell layer surrounding the developing male meiocytes, is indispensable for the completion of the male meiotic cell cycle. Disrupted tapetum development causes alterations in the expression of a large range of genes involved in male reproduction. Moreover, recent experiments suggest that small RNAs (sRNAs) present in the anthers, including microRNAs (miRNAs) and phased, secondary, small interfering RNAs (phasiRNAs), play a potential but important role in controlling male meiosis, either by influencing the expression of meiotic genes in the meiocytes or through other unclear mechanisms, supporting the hypothesis that male meiosis is non-cell autonomously regulated. In this mini review, we summarize the recorded meiotic defects that occur in plants with defective tapetum development in both Arabidopsis and crops. Thereafter, we outline the latest understanding on the molecular mechanisms that potentially underpin the tapetum-dependent regulation of male meiosis, and we especially discuss the regulatory role of sRNAs. At the end, we propose several outstanding questions that should be addressed in future studies.
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Affiliation(s)
- Xiaoning Lei
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Laboratory of Health Technology Assessment, Fudan University, Shanghai, China
| | - Bing Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
- Key Laboratory for Biotechnology of the State Ethnic Affairs Commission, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
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Huang K, Batish M, Teng C, Harkess A, Meyers BC, Caplan JL. Quantitative Fluorescence In Situ Hybridization Detection of Plant mRNAs with Single-Molecule Resolution. Methods Mol Biol 2020; 2166:23-33. [PMID: 32710401 DOI: 10.1007/978-1-0716-0712-1_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single-molecule FISH (smFISH) has been widely used in animal tissue to localize and quantify RNAs with high specificity. This protocol describes an smFISH method optimized for highly autofluorescent plant tissue. It provides details on fixation buffers and protocols to protect the integrity of plant samples. We also provide smFISH hybridization conditions to detect plant RNA with ~50 fluorescently labeled DNA oligonucleotides. In addition, this protocol provides instructions on linear spectral unmixing of smFISH signal from background autofluorescence by confocal microscopy and a method to quantify the smFISH spots that reflect the copy number of target RNA.
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Affiliation(s)
- Kun Huang
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Mona Batish
- Departments of Biological Sciences and Medical & Molecular Sciences, University of Delaware, Newark, DE, USA
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Alex Harkess
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Jeffrey L Caplan
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
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