RNA methylation in plants: An overview
RNA methylation is an important post-transcriptional modification that influences gene regulation. Over 200 different types of RNA modifications have been identified in plants. In animals, the mystery of RNA methylation has been revealed, and its biological role and applications have become increasi...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1132959/full |
| _version_ | 1811162695620100096 |
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| author | Harshraj Shinde Ambika Dudhate Ulhas S. Kadam Jong Chan Hong Jong Chan Hong |
| author_facet | Harshraj Shinde Ambika Dudhate Ulhas S. Kadam Jong Chan Hong Jong Chan Hong |
| author_sort | Harshraj Shinde |
| collection | DOAJ |
| description | RNA methylation is an important post-transcriptional modification that influences gene regulation. Over 200 different types of RNA modifications have been identified in plants. In animals, the mystery of RNA methylation has been revealed, and its biological role and applications have become increasingly clear. However, RNA methylation in plants is still poorly understood. Recently, plant science research on RNA methylation has advanced rapidly, and it has become clear that RNA methylation plays a critical role in plant development. This review summarizes current knowledge on RNA methylation in plant development. Plant writers, erasers, and readers are highlighted, as well as the occurrence, methods, and software development in RNA methylation is summarized. The most common and abundant RNA methylation in plants is N6-methyladenosine (m6A). In Arabidopsis, mutations in writers, erasers, and RNA methylation readers have affected the plant’s phenotype. It has also been demonstrated that methylated TRANSLATIONALLY CONTROLLED TUMOR PROTEIN 1-messenger RNA moves from shoot to root while unmethylated TCTP1-mRNA does not. Methylated RNA immunoprecipitation, in conjunction with next-generation sequencing, has been a watershed moment in plant RNA methylation research. This method has been used successfully in rice, Arabidopsis, Brassica, and maize to study transcriptome-wide RNA methylation. Various software or tools have been used to detect methylated RNAs at the whole transcriptome level; the majority are model-based analysis tools (for example, MACS2). Finally, the limitations and future prospects of methylation of RNA research have been documented. |
| first_indexed | 2024-04-10T06:33:26Z |
| format | Article |
| id | doaj.art-d8e667347cf5438999c8f864d70372f0 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-10T06:33:26Z |
| publishDate | 2023-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-d8e667347cf5438999c8f864d70372f02023-03-01T04:58:53ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-03-011410.3389/fpls.2023.11329591132959RNA methylation in plants: An overviewHarshraj Shinde0Ambika Dudhate1Ulhas S. Kadam2Jong Chan Hong3Jong Chan Hong4Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United StatesSequencing and Genome Discovery Center, Stowers Institute for Medical Research, Kansas City, MO, United StatesPlant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju-daero, Jinju, Gyeongnam, Republic of KoreaPlant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju-daero, Jinju, Gyeongnam, Republic of KoreaDivision of Plant Sciences, University of Missouri, Columbia, MO, United StatesRNA methylation is an important post-transcriptional modification that influences gene regulation. Over 200 different types of RNA modifications have been identified in plants. In animals, the mystery of RNA methylation has been revealed, and its biological role and applications have become increasingly clear. However, RNA methylation in plants is still poorly understood. Recently, plant science research on RNA methylation has advanced rapidly, and it has become clear that RNA methylation plays a critical role in plant development. This review summarizes current knowledge on RNA methylation in plant development. Plant writers, erasers, and readers are highlighted, as well as the occurrence, methods, and software development in RNA methylation is summarized. The most common and abundant RNA methylation in plants is N6-methyladenosine (m6A). In Arabidopsis, mutations in writers, erasers, and RNA methylation readers have affected the plant’s phenotype. It has also been demonstrated that methylated TRANSLATIONALLY CONTROLLED TUMOR PROTEIN 1-messenger RNA moves from shoot to root while unmethylated TCTP1-mRNA does not. Methylated RNA immunoprecipitation, in conjunction with next-generation sequencing, has been a watershed moment in plant RNA methylation research. This method has been used successfully in rice, Arabidopsis, Brassica, and maize to study transcriptome-wide RNA methylation. Various software or tools have been used to detect methylated RNAs at the whole transcriptome level; the majority are model-based analysis tools (for example, MACS2). Finally, the limitations and future prospects of methylation of RNA research have been documented.https://www.frontiersin.org/articles/10.3389/fpls.2023.1132959/fullRNA methylationsplant developmentwritersgene regulationsoftware |
| spellingShingle | Harshraj Shinde Ambika Dudhate Ulhas S. Kadam Jong Chan Hong Jong Chan Hong RNA methylation in plants: An overview Frontiers in Plant Science RNA methylations plant development writers gene regulation software |
| title | RNA methylation in plants: An overview |
| title_full | RNA methylation in plants: An overview |
| title_fullStr | RNA methylation in plants: An overview |
| title_full_unstemmed | RNA methylation in plants: An overview |
| title_short | RNA methylation in plants: An overview |
| title_sort | rna methylation in plants an overview |
| topic | RNA methylations plant development writers gene regulation software |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1132959/full |
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