Transcriptome-wide analysis of pseudouridylation of mRNA and non-coding RNAs in Arabidopsis
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Pseudouridine (Ψ) is widely distributed in mRNA and various non-coding RNAs in yeast and mammals, and the specificity of its distribution has been determined. However, knowledge about Ψs in the RNAs of plants, particularly in mRNA, is lacking. In this study, we performed genome-wide pseudouridine-sequencing in Arabidopsis and for the first time identified hundreds of Ψ sites in mRNA and multiple Ψ sites in non-coding RNAs. Many predicted and novel Ψ sites in rRNA and tRNA were detected. mRNA...[Show more]
dc.contributor.author | Sharwood, Robert | |
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dc.date.accessioned | 2022-11-30T23:17:08Z | |
dc.date.available | 2022-11-30T23:17:08Z | |
dc.identifier.issn | 0022-0957 | |
dc.identifier.uri | http://hdl.handle.net/1885/281438 | |
dc.description.abstract | Pseudouridine (Ψ) is widely distributed in mRNA and various non-coding RNAs in yeast and mammals, and the specificity of its distribution has been determined. However, knowledge about Ψs in the RNAs of plants, particularly in mRNA, is lacking. In this study, we performed genome-wide pseudouridine-sequencing in Arabidopsis and for the first time identified hundreds of Ψ sites in mRNA and multiple Ψ sites in non-coding RNAs. Many predicted and novel Ψ sites in rRNA and tRNA were detected. mRNA was extensively pseudouridylated, but with Ψs being under-represented in 3′-untranslated regions and enriched at position 1 of triple codons. The phenylalanine codon UUC was the most frequently pseudouridylated site. Some Ψs present in chloroplast 23S, 16S, and 4.5S rRNAs in wild-type Col-0 were absent in plants with a mutation of SVR1 (Suppressor of variegation 1), a chloroplast pseudouridine synthase gene. Many plastid ribosomal proteins and photosynthesis-related proteins were significantly reduced in svr1 relative to the wild-type, indicating the roles of SVR1 in chloroplast protein biosynthesis in Arabidopsis. Our results provide new insights into the occurrence of pseudouridine in Arabidopsis RNAs and the biological functions of SVR1, and will pave the way for further exploiting the mechanisms underlying Ψ modifications in controlling gene expression and protein biosynthesis in plants. | |
dc.description.sponsorship | This work was supported by the Ministry of Agriculture of China (2016ZX08009-003) and National Program on Key Basic Research Project (973 Program, 2012CB1143001). | |
dc.format.mimetype | application/pdf | |
dc.language.iso | en_AU | |
dc.publisher | Oxford University Press | |
dc.rights | © 2019 The authors | |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | |
dc.source | Journal of Experimental Botany | |
dc.subject | Arabidopsis thaliana | |
dc.subject | proteome | |
dc.subject | Ψ-sequence | |
dc.subject | pseudouridine | |
dc.subject | pseudouridine synthases (PUSs) | |
dc.subject | suppressor of variegation 1 (SVR1) | |
dc.subject | transcriptome | |
dc.title | Transcriptome-wide analysis of pseudouridylation of mRNA and non-coding RNAs in Arabidopsis | |
dc.type | Journal article | |
local.description.notes | Imported from ARIES | |
local.identifier.citationvolume | 70 | |
dc.date.issued | 2019 | |
local.identifier.absfor | 310400 - Evolutionary biology | |
local.identifier.ariespublication | u3102795xPUB5381 | |
local.publisher.url | https://academic.oup.com/ | |
local.type.status | Published Version | |
local.contributor.affiliation | Sharwood, Robert, College of Science, ANU | |
local.bibliographicCitation.issue | 19 | |
local.bibliographicCitation.startpage | 5089 | |
local.bibliographicCitation.lastpage | 5100 | |
local.identifier.doi | 10.1093/jxb/erz273 | |
dc.date.updated | 2021-11-28T07:30:27Z | |
local.identifier.scopusID | 2-s2.0-85073304698 | |
dcterms.accessRights | Open Access | |
dc.provenance | This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com | |
dc.rights.license | Creative Commons Attribution licence | |
Collections | ANU Research Publications |
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