The plant epitranscriptome: revisiting pseudouridine and 2′‐O‐methyl RNA modifications
Summary There is growing evidence that post‐transcriptional RNA modifications are highly dynamic and can be used to improve crop production. Although more than 172 unique types of RNA modifications have been identified throughout the kingdom of life, we are yet to leverage upon the understanding to...
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| Veröffentlicht in: | Plant biotechnology journal 2022-07, Vol.20 (7), p.1241-1256 |
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| creator | Ramakrishnan, Muthusamy Rajan, K. Shanmugha Mullasseri, Sileesh Palakkal, Sarin Kalpana, Krishnan Sharma, Anket Zhou, Mingbing Vinod, Kunnummal Kurungara Ramasamy, Subbiah Wei, Qiang |
| description | Summary
There is growing evidence that post‐transcriptional RNA modifications are highly dynamic and can be used to improve crop production. Although more than 172 unique types of RNA modifications have been identified throughout the kingdom of life, we are yet to leverage upon the understanding to optimize RNA modifications in crops to improve productivity. The contributions of internal mRNA modifications such as N6‐methyladenosine (m6A) and 5‐methylcytosine (m5C) methylations to embryonic development, root development, leaf morphogenesis, flowering, fruit ripening and stress response are sufficiently known, but the roles of the two most abundant RNA modifications, pseudouridine (Ψ) and 2′‐O‐methylation (Nm), in the cell remain unclear due to insufficient advances in high‐throughput technologies in plant development. Therefore, in this review, we discuss the latest methods and insights gained in mapping internal Ψ and Nm and their unique properties in plants and other organisms. In addition, we discuss the limitations that remain in high‐throughput technologies for qualitative and quantitative mapping of these RNA modifications and highlight future challenges in regulating the plant epitranscriptome.
Fine‐tuning of RNA modifications has recently been proposed to improve crop production, and these post‐transcriptional RNA modifications have been shown to be highly dynamic. In this review, we summarize recent findings on available technologies for mapping pseudouridine and 2′‐O‐methyl groups and their functional significance. |
| doi_str_mv | 10.1111/pbi.13829 |
| format | Article |
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There is growing evidence that post‐transcriptional RNA modifications are highly dynamic and can be used to improve crop production. Although more than 172 unique types of RNA modifications have been identified throughout the kingdom of life, we are yet to leverage upon the understanding to optimize RNA modifications in crops to improve productivity. The contributions of internal mRNA modifications such as N6‐methyladenosine (m6A) and 5‐methylcytosine (m5C) methylations to embryonic development, root development, leaf morphogenesis, flowering, fruit ripening and stress response are sufficiently known, but the roles of the two most abundant RNA modifications, pseudouridine (Ψ) and 2′‐O‐methylation (Nm), in the cell remain unclear due to insufficient advances in high‐throughput technologies in plant development. Therefore, in this review, we discuss the latest methods and insights gained in mapping internal Ψ and Nm and their unique properties in plants and other organisms. In addition, we discuss the limitations that remain in high‐throughput technologies for qualitative and quantitative mapping of these RNA modifications and highlight future challenges in regulating the plant epitranscriptome.
Fine‐tuning of RNA modifications has recently been proposed to improve crop production, and these post‐transcriptional RNA modifications have been shown to be highly dynamic. In this review, we summarize recent findings on available technologies for mapping pseudouridine and 2′‐O‐methyl groups and their functional significance.</description><identifier>ISSN: 1467-7644</identifier><identifier>EISSN: 1467-7652</identifier><identifier>DOI: 10.1111/pbi.13829</identifier><identifier>PMID: 35445501</identifier><language>eng</language><publisher>England: John Wiley & Sons, Inc</publisher><subject>2′‐O‐methylation ; 5-Methylcytosine ; Adenosine ; Agricultural production ; Corn ; Crop production ; DNA methylation ; Embryogenesis ; Embryonic development ; Embryonic growth stage ; epitranscriptomics ; Flowering ; Flowers & plants ; Gene expression ; Mammals ; Mapping ; Methylation ; Morphogenesis ; N6-methyladenosine ; next‐generation sequencing ; Plants - genetics ; Plants - metabolism ; Population ; Proteins ; pseudouridine ; Pseudouridine - genetics ; Pseudouridine - metabolism ; Review ; Rice ; Ripening ; RNA ; RNA - metabolism ; RNA modifications ; RNA Processing, Post-Transcriptional - genetics ; Root development ; Stem cells ; Transcriptome - genetics ; Transfer RNA</subject><ispartof>Plant biotechnology journal, 2022-07, Vol.20 (7), p.1241-1256</ispartof><rights>2022 The Authors. published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.</rights><rights>2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.</rights><rights>COPYRIGHT 2022 John Wiley & Sons, Inc.</rights><rights>2022. This work is published under http://creativecommons.org/licenses/by-nc/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4829-f1b3b588e3f569c735a12ae5fd4a484a6e4deb0f7a4d804778d67c49398c45123</citedby><cites>FETCH-LOGICAL-c4829-f1b3b588e3f569c735a12ae5fd4a484a6e4deb0f7a4d804778d67c49398c45123</cites><orcidid>0000-0003-4826-9802 ; 0000-0002-6819-2956 ; 0000-0001-7819-339X ; 0000-0001-5674-4410 ; 0000-0001-5180-2087 ; 0000-0001-6828-9195</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fpbi.13829$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fpbi.13829$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>230,314,776,780,860,881,1411,11542,27903,27904,45553,45554,46030,46454</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35445501$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ramakrishnan, Muthusamy</creatorcontrib><creatorcontrib>Rajan, K. Shanmugha</creatorcontrib><creatorcontrib>Mullasseri, Sileesh</creatorcontrib><creatorcontrib>Palakkal, Sarin</creatorcontrib><creatorcontrib>Kalpana, Krishnan</creatorcontrib><creatorcontrib>Sharma, Anket</creatorcontrib><creatorcontrib>Zhou, Mingbing</creatorcontrib><creatorcontrib>Vinod, Kunnummal Kurungara</creatorcontrib><creatorcontrib>Ramasamy, Subbiah</creatorcontrib><creatorcontrib>Wei, Qiang</creatorcontrib><title>The plant epitranscriptome: revisiting pseudouridine and 2′‐O‐methyl RNA modifications</title><title>Plant biotechnology journal</title><addtitle>Plant Biotechnol J</addtitle><description>Summary
There is growing evidence that post‐transcriptional RNA modifications are highly dynamic and can be used to improve crop production. Although more than 172 unique types of RNA modifications have been identified throughout the kingdom of life, we are yet to leverage upon the understanding to optimize RNA modifications in crops to improve productivity. The contributions of internal mRNA modifications such as N6‐methyladenosine (m6A) and 5‐methylcytosine (m5C) methylations to embryonic development, root development, leaf morphogenesis, flowering, fruit ripening and stress response are sufficiently known, but the roles of the two most abundant RNA modifications, pseudouridine (Ψ) and 2′‐O‐methylation (Nm), in the cell remain unclear due to insufficient advances in high‐throughput technologies in plant development. Therefore, in this review, we discuss the latest methods and insights gained in mapping internal Ψ and Nm and their unique properties in plants and other organisms. In addition, we discuss the limitations that remain in high‐throughput technologies for qualitative and quantitative mapping of these RNA modifications and highlight future challenges in regulating the plant epitranscriptome.
Fine‐tuning of RNA modifications has recently been proposed to improve crop production, and these post‐transcriptional RNA modifications have been shown to be highly dynamic. In this review, we summarize recent findings on available technologies for mapping pseudouridine and 2′‐O‐methyl groups and their functional significance.</description><subject>2′‐O‐methylation</subject><subject>5-Methylcytosine</subject><subject>Adenosine</subject><subject>Agricultural production</subject><subject>Corn</subject><subject>Crop production</subject><subject>DNA methylation</subject><subject>Embryogenesis</subject><subject>Embryonic development</subject><subject>Embryonic growth stage</subject><subject>epitranscriptomics</subject><subject>Flowering</subject><subject>Flowers & plants</subject><subject>Gene expression</subject><subject>Mammals</subject><subject>Mapping</subject><subject>Methylation</subject><subject>Morphogenesis</subject><subject>N6-methyladenosine</subject><subject>next‐generation sequencing</subject><subject>Plants - genetics</subject><subject>Plants - metabolism</subject><subject>Population</subject><subject>Proteins</subject><subject>pseudouridine</subject><subject>Pseudouridine - genetics</subject><subject>Pseudouridine - metabolism</subject><subject>Review</subject><subject>Rice</subject><subject>Ripening</subject><subject>RNA</subject><subject>RNA - metabolism</subject><subject>RNA modifications</subject><subject>RNA Processing, Post-Transcriptional - genetics</subject><subject>Root development</subject><subject>Stem cells</subject><subject>Transcriptome - genetics</subject><subject>Transfer RNA</subject><issn>1467-7644</issn><issn>1467-7652</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp1kd1qFDEUxwdR7Ide-AIy4I292O3ke8YLYS1-FIoVqXdCyCQnuykzyTSZqexdH8Fn8ZH6JKZOXVQwISQkv_M_5-RfFM9QtUR5HA-tWyJS4-ZBsY8oFwvBGX64O1O6VxykdFlVGHHGHxd7hFHKWIX2i68XGyiHTvmxhMGNUfmkoxvG0MOrMsK1S250fl0OCSYTpuiM81Aqb0p8e_Pj9ub7eV49jJttV37-uCr7YJx1Wo0u-PSkeGRVl-Dp_X5YfHn39uLkw-Ls_P3pyepsoWkuemFRS1pW10As440WhCmEFTBrqKI1VRyogbayQlFTV1SI2nChaUOaWlOGMDksXs-6w9T2YDT43Egnh-h6FbcyKCf_fvFuI9fhWjaYIiKaLPDyXiCGqwnSKHuXNHT5XyBMSWLOCOYCkbtcL_5BL_O3-NxepmokCGkoz9RyptaqA-m8DTmvztNA73TwYF2-XwmKGKkoETngaA7QMaQUwe6qR5W8M1lmk-UvkzP7_M92d-RvVzNwPAPfcpbt_5Xkpzens-RPnqC0Qg</recordid><startdate>202207</startdate><enddate>202207</enddate><creator>Ramakrishnan, Muthusamy</creator><creator>Rajan, K. Shanmugha</creator><creator>Mullasseri, Sileesh</creator><creator>Palakkal, Sarin</creator><creator>Kalpana, Krishnan</creator><creator>Sharma, Anket</creator><creator>Zhou, Mingbing</creator><creator>Vinod, Kunnummal Kurungara</creator><creator>Ramasamy, Subbiah</creator><creator>Wei, Qiang</creator><general>John Wiley & Sons, Inc</general><general>John Wiley and Sons Inc</general><scope>24P</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>L6V</scope><scope>LK8</scope><scope>M7P</scope><scope>M7S</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-4826-9802</orcidid><orcidid>https://orcid.org/0000-0002-6819-2956</orcidid><orcidid>https://orcid.org/0000-0001-7819-339X</orcidid><orcidid>https://orcid.org/0000-0001-5674-4410</orcidid><orcidid>https://orcid.org/0000-0001-5180-2087</orcidid><orcidid>https://orcid.org/0000-0001-6828-9195</orcidid></search><sort><creationdate>202207</creationdate><title>The plant epitranscriptome: revisiting pseudouridine and 2′‐O‐methyl RNA modifications</title><author>Ramakrishnan, Muthusamy ; Rajan, K. Shanmugha ; Mullasseri, Sileesh ; Palakkal, Sarin ; Kalpana, Krishnan ; Sharma, Anket ; Zhou, Mingbing ; Vinod, Kunnummal Kurungara ; Ramasamy, Subbiah ; Wei, Qiang</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4829-f1b3b588e3f569c735a12ae5fd4a484a6e4deb0f7a4d804778d67c49398c45123</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>2′‐O‐methylation</topic><topic>5-Methylcytosine</topic><topic>Adenosine</topic><topic>Agricultural production</topic><topic>Corn</topic><topic>Crop production</topic><topic>DNA methylation</topic><topic>Embryogenesis</topic><topic>Embryonic development</topic><topic>Embryonic growth stage</topic><topic>epitranscriptomics</topic><topic>Flowering</topic><topic>Flowers & plants</topic><topic>Gene expression</topic><topic>Mammals</topic><topic>Mapping</topic><topic>Methylation</topic><topic>Morphogenesis</topic><topic>N6-methyladenosine</topic><topic>next‐generation sequencing</topic><topic>Plants - genetics</topic><topic>Plants - metabolism</topic><topic>Population</topic><topic>Proteins</topic><topic>pseudouridine</topic><topic>Pseudouridine - genetics</topic><topic>Pseudouridine - metabolism</topic><topic>Review</topic><topic>Rice</topic><topic>Ripening</topic><topic>RNA</topic><topic>RNA - metabolism</topic><topic>RNA modifications</topic><topic>RNA Processing, Post-Transcriptional - genetics</topic><topic>Root development</topic><topic>Stem cells</topic><topic>Transcriptome - genetics</topic><topic>Transfer RNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ramakrishnan, Muthusamy</creatorcontrib><creatorcontrib>Rajan, K. 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Shanmugha</au><au>Mullasseri, Sileesh</au><au>Palakkal, Sarin</au><au>Kalpana, Krishnan</au><au>Sharma, Anket</au><au>Zhou, Mingbing</au><au>Vinod, Kunnummal Kurungara</au><au>Ramasamy, Subbiah</au><au>Wei, Qiang</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The plant epitranscriptome: revisiting pseudouridine and 2′‐O‐methyl RNA modifications</atitle><jtitle>Plant biotechnology journal</jtitle><addtitle>Plant Biotechnol J</addtitle><date>2022-07</date><risdate>2022</risdate><volume>20</volume><issue>7</issue><spage>1241</spage><epage>1256</epage><pages>1241-1256</pages><issn>1467-7644</issn><eissn>1467-7652</eissn><abstract>Summary
There is growing evidence that post‐transcriptional RNA modifications are highly dynamic and can be used to improve crop production. Although more than 172 unique types of RNA modifications have been identified throughout the kingdom of life, we are yet to leverage upon the understanding to optimize RNA modifications in crops to improve productivity. The contributions of internal mRNA modifications such as N6‐methyladenosine (m6A) and 5‐methylcytosine (m5C) methylations to embryonic development, root development, leaf morphogenesis, flowering, fruit ripening and stress response are sufficiently known, but the roles of the two most abundant RNA modifications, pseudouridine (Ψ) and 2′‐O‐methylation (Nm), in the cell remain unclear due to insufficient advances in high‐throughput technologies in plant development. Therefore, in this review, we discuss the latest methods and insights gained in mapping internal Ψ and Nm and their unique properties in plants and other organisms. In addition, we discuss the limitations that remain in high‐throughput technologies for qualitative and quantitative mapping of these RNA modifications and highlight future challenges in regulating the plant epitranscriptome.
Fine‐tuning of RNA modifications has recently been proposed to improve crop production, and these post‐transcriptional RNA modifications have been shown to be highly dynamic. In this review, we summarize recent findings on available technologies for mapping pseudouridine and 2′‐O‐methyl groups and their functional significance.</abstract><cop>England</cop><pub>John Wiley & Sons, Inc</pub><pmid>35445501</pmid><doi>10.1111/pbi.13829</doi><tpages>1256</tpages><orcidid>https://orcid.org/0000-0003-4826-9802</orcidid><orcidid>https://orcid.org/0000-0002-6819-2956</orcidid><orcidid>https://orcid.org/0000-0001-7819-339X</orcidid><orcidid>https://orcid.org/0000-0001-5674-4410</orcidid><orcidid>https://orcid.org/0000-0001-5180-2087</orcidid><orcidid>https://orcid.org/0000-0001-6828-9195</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Plant biotechnology journal, 2022-07, Vol.20 (7), p.1241-1256 |
| issn | 1467-7644 1467-7652 |
| language | eng |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Wiley Online Library Journals Frontfile Complete; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Wiley-Blackwell Open Access Titles |
| subjects | 2′‐O‐methylation 5-Methylcytosine Adenosine Agricultural production Corn Crop production DNA methylation Embryogenesis Embryonic development Embryonic growth stage epitranscriptomics Flowering Flowers & plants Gene expression Mammals Mapping Methylation Morphogenesis N6-methyladenosine next‐generation sequencing Plants - genetics Plants - metabolism Population Proteins pseudouridine Pseudouridine - genetics Pseudouridine - metabolism Review Rice Ripening RNA RNA - metabolism RNA modifications RNA Processing, Post-Transcriptional - genetics Root development Stem cells Transcriptome - genetics Transfer RNA |
| title | The plant epitranscriptome: revisiting pseudouridine and 2′‐O‐methyl RNA modifications |
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