The plant epitranscriptome: revisiting pseudouridine and 2′-O-methyl RNA modifications

Muthusamy Ramakrishnan; K. Shanmugha Rajan; Sileesh Mullasseri; Sarin Palakkal; Krishnan Kalpana; Anket Sharma; Mingbing Zhou; Kunnummal Kurungara Vinod; Subbiah Ramasamy; Qiang Wei

doi:10.1111/pbi.13829

The plant epitranscriptome: revisiting pseudouridine and 2′-O-methyl RNA modifications

Muthusamy Ramakrishnan, K. Shanmugha Rajan, Sileesh Mullasseri, Sarin Palakkal, Krishnan Kalpana, Anket Sharma, Mingbing Zhou, Kunnummal Kurungara Vinod, Subbiah Ramasamy, Qiang Wei

The Mina and Everard Goodman Faculty of Life Sciences

Research output: Contribution to journal › Review article › peer-review

10 Scopus citations

Abstract

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.

Original language	English
Pages (from-to)	1241-1256
Number of pages	16
Journal	Plant Biotechnology Journal
Volume	20
Issue number	7
DOIs	https://doi.org/10.1111/pbi.13829
State	Published - Jul 2022

Bibliographical note

Publisher Copyright:
© 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Funding

KSR is supported by post‐doctoral fellowships from Koshland Foundation and the Dean, Faculty of Chemistry, Weizmann Institute of Science. The authors apologize to those whose original work(s) could not be included in this review due to space limitations. Figure 1 was created with BioRender.com. The authors are grateful for support from the National Natural Science Foundation of China (32071848), a grant from the Jiangxi ‘Shuangqian’ Program (S2019DQKJ2030), the Natural Science Foundation for Distinguished Young Scholars of Nanjing Forestry University (JC2019004), the Qing Lan Project of Jiangsu Higher Education Institutions, and a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions. This work was also supported by the Metasequoia Faculty Research Start‐up Funding (grant number 163100028) at Bamboo Research Institute, Nanjing Forestry University for the first author MR. The authors are grateful for support from the National Natural Science Foundation of China (32071848), a grant from the Jiangxi ‘Shuangqian’ Program (S2019DQKJ2030), the Natural Science Foundation for Distinguished Young Scholars of Nanjing Forestry University (JC2019004), the Qing Lan Project of Jiangsu Higher Education Institutions, and a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions. This work was also supported by the Metasequoia Faculty Research Start-up Funding (grant number 163100028) at Bamboo Research Institute, Nanjing Forestry University for the first author MR. KSR is supported by post-doctoral fellowships from Koshland Foundation and the Dean, Faculty of Chemistry, Weizmann Institute of Science. The authors apologize to those whose original work(s) could not be included in this review due to space limitations. Figure 1 was created with BioRender.com.

Funders	Funder number
Bamboo Research Institute
Metasequoia Faculty Research Start-up Funding
Natural Science Foundation for Distinguished Young Scholars of Nanjing Forestry University	JC2019004
Qing Lan Project of Jiangsu Higher Education Institutions
Nanjing Forestry University
Koshland Foundation
Weizmann Institute of Science
National Natural Science Foundation of China	S2019DQKJ2030, 32071848
Priority Academic Program Development of Jiangsu Higher Education Institutions	163100028

Keywords

2′-O-methylation
RNA modifications
epitranscriptomics
next-generation sequencing
pseudouridine

Access to Document

10.1111/pbi.13829

Cite this

@article{e64b7973a61e41a9a462dfffed82bb5a,

title = "The plant epitranscriptome: revisiting pseudouridine and 2′-O-methyl RNA modifications",

abstract = "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.",

keywords = "2′-O-methylation, RNA modifications, epitranscriptomics, next-generation sequencing, pseudouridine",

author = "Muthusamy Ramakrishnan and Rajan, {K. Shanmugha} and Sileesh Mullasseri and Sarin Palakkal and Krishnan Kalpana and Anket Sharma and Mingbing Zhou and Vinod, {Kunnummal Kurungara} and Subbiah Ramasamy and Qiang Wei",

note = "Publisher Copyright: {\textcopyright} 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.",

year = "2022",

month = jul,

doi = "10.1111/pbi.13829",

language = "אנגלית",

volume = "20",

pages = "1241--1256",

journal = "Plant Biotechnology Journal",

issn = "1467-7644",

publisher = "Wiley-Blackwell Publishing Ltd",

number = "7",

}

TY - JOUR

T1 - The plant epitranscriptome

T2 - revisiting pseudouridine and 2′-O-methyl RNA modifications

AU - Ramakrishnan, Muthusamy

AU - Rajan, K. Shanmugha

AU - Mullasseri, Sileesh

AU - Palakkal, Sarin

AU - Kalpana, Krishnan

AU - Sharma, Anket

AU - Zhou, Mingbing

AU - Vinod, Kunnummal Kurungara

AU - Ramasamy, Subbiah

AU - Wei, Qiang

PY - 2022/7

Y1 - 2022/7

N2 - 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.

AB - 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.

KW - 2′-O-methylation

KW - RNA modifications

KW - epitranscriptomics

KW - next-generation sequencing

KW - pseudouridine

UR - http://www.scopus.com/inward/record.url?scp=85129740358&partnerID=8YFLogxK

U2 - 10.1111/pbi.13829

DO - 10.1111/pbi.13829

M3 - ???researchoutput.researchoutputtypes.contributiontojournal.systematicreview???

C2 - 35445501

AN - SCOPUS:85129740358

SN - 1467-7644

VL - 20

SP - 1241

EP - 1256

JO - Plant Biotechnology Journal

JF - Plant Biotechnology Journal

IS - 7

ER -

The plant epitranscriptome: revisiting pseudouridine and 2′-O-methyl RNA modifications

Abstract

Bibliographical note

Funding

Keywords

Access to Document

Other files and links

Fingerprint

Cite this