Messenger RNA Modifications in Plants

Shen, Lisha; Liang, Zhe; Wong, Chui Eng; Yu, Hao

doi:10.1016/j.tplants.2019.01.005

Cited by 83 publications

(76 citation statements)

References 98 publications

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“…Transcriptional and post-transcriptional regulation, including the activity of small RNAs and DNA methylation, mediates fiber cell development 46 . Modification of m 6 A messenger RNA can stabilize mRNA and promote translation with a role in developmental regulation of plants and animals 47 . In Upland cotton, m 6 A peaks are…”

Section: Expression Network and Mmentioning

confidence: 99%

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

et al. 2020

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olyploidy or whole-genome duplication provides genomic opportunities for evolutionary innovations in many animal groups and all flowering plants 1-5 , including most important crops such as wheat, cotton and canola or oilseed rape 6-8. The common occurrence of polyploidy may suggest its advantage and potential for selection and adaptation 2,3,9 , through rapid genetic and genomic changes as observed in newly formed Brassica napus 10 , Tragopogon miscellus 11 and polyploid wheat 12 , and/or largely epigenetic modifications as in Arabidopsis and cotton polyploids 5,13. Cotton is a powerful model for revealing genomic insights into polyploidy 3 , providing a phylogenetically defined framework of polyploidization (~1.5 million years ago (Ma)) 14 , followed by natural diversification and crop domestication 15. The evolutionary history of the polyploid cotton clade is longer than that of some other allopolyploids, such as hexaploid wheat (~8,000 years) 12 , tetraploid canola (~7,500 years) 16 and tetraploid Tragopogon (~150 years) 11. Polyploidization between an A-genome African species (Gossypium arboreum (Ga)-like) and a D-genome American species (G. raimondii (Gr)-like) in the New World created a new allotetraploid or amphidiploid (AD-genome) cotton clade (Fig. 1a) 14 , which has diversified into five polyploid lineages, G. hirsutum (Gh) (AD) 1 , G. barbadense (Gb) (AD) 2 , G. tomentosum (Gt) (AD) 3 , G. mustelinum (Gm) (AD) 4 and G. darwinii (Gd) (AD) 5. G. ekmanianum and G. stephensii are recently characterized and closely related to Gh 17. Gh and Gb were separately domesticated from perennial shrubs to become annualized Upland and Pima cottons 15. To date, global cotton production provides income for ~100 million families across ~150 countries, with an annual economic impact of ~US$500 billion worldwide 6. However, cotton supply is reduced due to aridification, climate change and pest emergence. Future improvements in cotton and sustainability will involve use of the genomic resources and gene-editing tools becoming available in many crops 9,18,19. Cotton genomes have been sequenced for the D-genome (Gr) 20 and A-genome (Ga) 21 diploids and two cultivated tetraploids 22-26. These analyses have shown structural, genetic and gene expression variation related to fiber traits and stress responses in cultivated

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Section: Expression Network and Mmentioning

confidence: 99%

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

et al. 2020

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“…Non-classical chemical changes, apart from capping and polyadenylation modifications, alter the stability of mRNAs,. More than 160 chemical modifications of mRNAs have been recently reported in A. thaliana, as a whole they are considered the epitranscriptome [76]. These alterations include the methylation of the adenosine and cytosine nucleotides: N6-methyladenosine (m 6 A) and 5-methylcytosine (m 5 C) [77].…”

Section: The Seed Epitranscriptomementioning

confidence: 99%

Reactive Oxygen Species (ROS) and Nucleic Acid Modifications during Seed Dormancy

Katsuya-Gaviria

Caro

Carrillo-Barral

et al. 2020

Plants

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The seed is the propagule of higher plants and allows its dissemination and the survival of the species. Seed dormancy prevents premature germination under favourable conditions. Dormant seeds are only able to germinate in a narrow range of conditions. During after-ripening (AR), a mechanism of dormancy release, seeds gradually lose dormancy through a period of dry storage. This review is mainly focused on how chemical modifications of mRNA and genomic DNA, such as oxidation and methylation, affect gene expression during late stages of seed development, especially during dormancy. The oxidation of specific nucleotides produced by reactive oxygen species (ROS) alters the stability of the seed stored mRNAs, being finally degraded or translated into non-functional proteins. DNA methylation is a well-known epigenetic mechanism of controlling gene expression. In Arabidopsis thaliana, while there is a global increase in CHH-context methylation through embryogenesis, global DNA methylation levels remain stable during seed dormancy, decreasing when germination occurs. The biological significance of nucleic acid oxidation and methylation upon seed development is discussed.

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“…Expansion in scope and refinement of such methods [10][11][12] have now produced maps of several modifications in tissues and cells of diverse origins [13][14][15][16][17], spawning the term 'epitranscriptomics' to mainly (but not exclusively) refer to research into the function of modified nucleosides in mRNA [18]. Challenges exist not only in the accurate detection of these generally sparse modifications but also in ascribing molecular, cellular and organismic functions to these 'epitranscriptomic marks'-in mRNA [19][20][21] as well as in ncRNA [22,23].…”

Section: Introductionmentioning

confidence: 99%

Multiple links between 5-methylcytosine content of mRNA and translation

et al. 2020

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Background: 5-Methylcytosine (m 5 C) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA, where it serves incompletely understood molecular functions. In pursuit of potential links of m 5 C with mRNA translation, we performed polysome profiling of human HeLa cell lysates and subjected RNA from resultant fractions to efficient bisulfite conversion followed by RNA sequencing (bsRNA-seq). Bioinformatic filters for rigorous site calling were devised to reduce technical noise.Results: We obtained~1000 candidate m 5 C sites in the wider transcriptome, most of which were found in mRNA. Multiple novel sites were validated by amplicon-specific bsRNA-seq in independent samples of either human HeLa, LNCaP and PrEC cells. Furthermore, RNAi-mediated depletion of either the NSUN2 or TRDMT1 m 5 C:RNA methyltransferases showed a clear dependence on NSUN2 for the majority of tested sites in both mRNAs and noncoding RNAs. Candidate m 5 C sites in mRNAs are enriched in 5′UTRs and near start codons and are embedded in a local context reminiscent of the NSUN2-dependent m 5 C sites found in the variable loop of tRNA. Analysing mRNA sites across the polysome profile revealed that modification levels, at bulk and for many individual sites, were inversely correlated with ribosome association. Conclusions: Our findings emphasise the major role of NSUN2 in placing the m 5 C mark transcriptome-wide. We further present evidence that substantiates a functional interdependence of cytosine methylation level with mRNA translation. Additionally, we identify several compelling candidate sites for future mechanistic analysis.

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Messenger RNA Modifications in Plants

Cited by 83 publications

References 98 publications

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

Reactive Oxygen Species (ROS) and Nucleic Acid Modifications during Seed Dormancy

Multiple links between 5-methylcytosine content of mRNA and translation

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