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Transcriptome-Wide Analysis of RNA m6A Methylation and Gene Expression Changes Among Two Arabidopsis Ecotypes and Their Reciprocal Hybrids

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Title: Transcriptome-Wide Analysis of RNA m6A Methylation and Gene Expression Changes Among Two Arabidopsis Ecotypes and Their Reciprocal Hybrids
Authors: Zhihui Xu, Xiaobo Shi, Mengmei Bao, Xiaoqian Song, Yuxia Zhang, Haiyan Wang, Hairong Xie, Fei Mao, Shuai Wang, Hongmei Jin, Suomeng Dong, Feng Zhang, Zhe Wu, Yufeng Wu
Source: Frontiers in Plant Science, Vol 12 (2021)
Publisher Information: Frontiers Media S.A., 2021.
Publication Year: 2021
Collection: LCC:Plant culture
Subject Terms: RNA m6A methylation, hybrid, heterosis, Arabidopsis, RNA modification dynamics, Plant culture, SB1-1110
More Details: The remodeling of transcriptome, epigenome, proteome, and metabolome in hybrids plays an important role in heterosis. N(6)-methyladenosine (m6A) methylation is the most abundant type of post-transcriptional modification for mRNAs, but the pattern of inheritance from parents to hybrids and potential impact on heterosis are largely unknown. We constructed transcriptome-wide mRNA m6A methylation maps of Arabidopsis thaliana Col-0 and Landsberg erecta (Ler) and their reciprocal F1 hybrids. Generally, the transcriptome-wide pattern of m6A methylation tends to be conserved between accessions. Approximately 74% of m6A methylation peaks are consistent between the parents and hybrids, indicating that a majority of the m6A methylation is maintained after hybridization. We found a significant association between differential expression and differential m6A modification, and between non-additive expression and non-additive methylation on the same gene. The overall RNA m6A level between Col-0 and Ler is clearly different but tended to disappear at the allelic sites in the hybrids. Interestingly, many enriched biological functions of genes with differential m6A modification between parents and hybrids are also conserved, including many heterosis-related genes involved in biosynthetic processes of starch. Collectively, our study revealed the overall pattern of inheritance of mRNA m6A modifications from parents to hybrids and a potential new layer of regulatory mechanisms related to heterosis formation.
Document Type: article
File Description: electronic resource
Language: English
ISSN: 1664-462X
Relation: https://www.frontiersin.org/articles/10.3389/fpls.2021.685189/full; https://doaj.org/toc/1664-462X
DOI: 10.3389/fpls.2021.685189
Access URL: https://doaj.org/article/24119658f1e44efead4898617d49d187
Accession Number: edsdoj.24119658f1e44efead4898617d49d187
Database: Directory of Open Access Journals
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  Data: Transcriptome-Wide Analysis of RNA m6A Methylation and Gene Expression Changes Among Two Arabidopsis Ecotypes and Their Reciprocal Hybrids
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  Data: <searchLink fieldCode="AR" term="%22Zhihui+Xu%22">Zhihui Xu</searchLink><br /><searchLink fieldCode="AR" term="%22Xiaobo+Shi%22">Xiaobo Shi</searchLink><br /><searchLink fieldCode="AR" term="%22Mengmei+Bao%22">Mengmei Bao</searchLink><br /><searchLink fieldCode="AR" term="%22Xiaoqian+Song%22">Xiaoqian Song</searchLink><br /><searchLink fieldCode="AR" term="%22Yuxia+Zhang%22">Yuxia Zhang</searchLink><br /><searchLink fieldCode="AR" term="%22Haiyan+Wang%22">Haiyan Wang</searchLink><br /><searchLink fieldCode="AR" term="%22Hairong+Xie%22">Hairong Xie</searchLink><br /><searchLink fieldCode="AR" term="%22Fei+Mao%22">Fei Mao</searchLink><br /><searchLink fieldCode="AR" term="%22Shuai+Wang%22">Shuai Wang</searchLink><br /><searchLink fieldCode="AR" term="%22Hongmei+Jin%22">Hongmei Jin</searchLink><br /><searchLink fieldCode="AR" term="%22Suomeng+Dong%22">Suomeng Dong</searchLink><br /><searchLink fieldCode="AR" term="%22Feng+Zhang%22">Feng Zhang</searchLink><br /><searchLink fieldCode="AR" term="%22Zhe+Wu%22">Zhe Wu</searchLink><br /><searchLink fieldCode="AR" term="%22Yufeng+Wu%22">Yufeng Wu</searchLink>
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  Data: Frontiers in Plant Science, Vol 12 (2021)
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  Data: <searchLink fieldCode="DE" term="%22RNA+m6A+methylation%22">RNA m6A methylation</searchLink><br /><searchLink fieldCode="DE" term="%22hybrid%22">hybrid</searchLink><br /><searchLink fieldCode="DE" term="%22heterosis%22">heterosis</searchLink><br /><searchLink fieldCode="DE" term="%22Arabidopsis%22">Arabidopsis</searchLink><br /><searchLink fieldCode="DE" term="%22RNA+modification+dynamics%22">RNA modification dynamics</searchLink><br /><searchLink fieldCode="DE" term="%22Plant+culture%22">Plant culture</searchLink><br /><searchLink fieldCode="DE" term="%22SB1-1110%22">SB1-1110</searchLink>
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  Data: The remodeling of transcriptome, epigenome, proteome, and metabolome in hybrids plays an important role in heterosis. N(6)-methyladenosine (m6A) methylation is the most abundant type of post-transcriptional modification for mRNAs, but the pattern of inheritance from parents to hybrids and potential impact on heterosis are largely unknown. We constructed transcriptome-wide mRNA m6A methylation maps of Arabidopsis thaliana Col-0 and Landsberg erecta (Ler) and their reciprocal F1 hybrids. Generally, the transcriptome-wide pattern of m6A methylation tends to be conserved between accessions. Approximately 74% of m6A methylation peaks are consistent between the parents and hybrids, indicating that a majority of the m6A methylation is maintained after hybridization. We found a significant association between differential expression and differential m6A modification, and between non-additive expression and non-additive methylation on the same gene. The overall RNA m6A level between Col-0 and Ler is clearly different but tended to disappear at the allelic sites in the hybrids. Interestingly, many enriched biological functions of genes with differential m6A modification between parents and hybrids are also conserved, including many heterosis-related genes involved in biosynthetic processes of starch. Collectively, our study revealed the overall pattern of inheritance of mRNA m6A modifications from parents to hybrids and a potential new layer of regulatory mechanisms related to heterosis formation.
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        Value: 10.3389/fpls.2021.685189
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      – Text: English
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      – SubjectFull: RNA m6A methylation
        Type: general
      – SubjectFull: hybrid
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      – SubjectFull: heterosis
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      – SubjectFull: Arabidopsis
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      – SubjectFull: RNA modification dynamics
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      – TitleFull: Transcriptome-Wide Analysis of RNA m6A Methylation and Gene Expression Changes Among Two Arabidopsis Ecotypes and Their Reciprocal Hybrids
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