Natural antisense transcripts of MIR398 genes suppress microR398 processing and attenuate plant thermotolerance

Li, Yajie; Li, Xiaorong; Yang, Jun; He, Yuqing

doi:10.1038/s41467-020-19186-x

Cited by 54 publications

(61 citation statements)

References 81 publications

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“…In particular, lncNATs are correlated with the response to various abiotic and biotic stresses [29,34,37]. For example, a recent study in Arabidopsis revealed that NATs affect plant thermotolerance [38].…”

Section: Introductionmentioning

confidence: 99%

Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

Zhang

et al. 2021

Preprint

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Background Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa L.), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although many rice domestication related traits, such as seed shattering and plant architecture, have been intensively studied at the phenotypic and genomic levels, further investigation is needed to understand the molecular basis of phenotypic differences between cultivated and wild rice. Drought stress is one of the most severe abiotic stresses affecting rice growth and production. Adaptation to drought stress involves a cascade of genes and regulatory factors that form complex networks. Long noncoding natural antisense transcripts (lncNATs), a class of long noncoding RNAs (lncRNAs), regulate the corresponding sense transcripts and play an important role in plant growth and development. However, the contribution of lncNATs to drought stress response in wild rice remains largely unknown. Results Here, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis of Nipponbare (O. sativa ssp. japonica) and two O. nivara accessions (BJ89 and BJ278) to determine the role of lncNATs in drought stress response in wild rice. A total of 1,246 lncRNAs were identified, including 1,091 coding–noncoding NAT pairs, of which 50 were expressed only in Nipponbare, and 77 were expressed only in BJ89 and/or BJ278. Of the 1,091 coding–noncoding NAT pairs, 240 were differentially expressed between control and drought stress conditions. Among these 240 NAT pairs, 12 were detected only in Nipponbare, and 187 were detected uniquely in O. nivara. Furthermore, 10 of the 240 coding–noncoding NAT pairs were correlated with genes previously demonstrated to be involved in stress response; among these, nine pairs were uniquely found in O. nivara, and one pair was shared between O. nivara and Nipponbare. Conclusion We identified lncNATs associated with drought stress response in cultivated rice and O. nivara. These results will improve our understanding of the function of lncNATs in drought tolerance and accelerate rice breeding.

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Section: Introductionmentioning

confidence: 99%

Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

Zhang

et al. 2021

Preprint

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“…As a primary catalyst of oxygen free radicals, superoxide dismutase plays an important role in the stress tolerance of rice. Many studies have revealed that increased expression of SOD improves stress tolerance in plants (Liu et (Li et al 2020), however the protein level expression of SODs are not reported in rice. In our study, a rabbit polyclonal antibody against OsCu/Zn SOD was used to test its expression under high-temperature.…”

Section: Discussionmentioning

confidence: 99%

“…MiR398 exhibits strong homology betreen Arabidopsis thaliana and rice. Many studies have shown that Cu/Zn SOD in rice is also regulated by miR398 (Balyan et al 2017; Yao et al 2014; Li et al 2019) and there are muti-level regulation among Natural antisense transcripts of MIR398, miRNA and SOD in Arabidopsis thaliana (Li et al 2020), however the protein level expression of SODs are not reported in rice. In our study, a rabbit polyclonal antibody against OsCu/Zn SOD was used to test its expression under high-temperature.…”

Section: Rabbit Anti-oscu/zn Sod Is Cross Reactive With Sod From Tomamentioning

confidence: 99%

Development and Optimization of Rabbit Polyclonal Antibodies for Cu/ZnSOD detection in Rice (Oryza sativa L.)

Xiong

Pan

Luo

et al. 2021

Preprint

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Superoxide dismutase (SOD) activity is an important measure of plant stress tolerance used in cultivar improvement. At present, we are unaware of any widely available immunological reagents for the detection of SOD in Oryza sativa (common Asian rice) or other plants. In this study, we used insilico B-cell epitope prediction tools to generate peptides which were immunized into rabbits to yield polyclonal antibodies against Cu/Zn SODs. Immunoblotting demonstrated that the antibody specifically recognized both native and denatured Cu/Zn SODs in rice. In addition, this antibody can confirm the expression tendency of endogenous OsCu/Zn SODs under heat stress by immunoblotting, and has a positive reaction in tomato leaf extracts, as well as human Hela cells. Chloroplast content of Cu/Zn SODs in rice can be identified by ELISA indirect competition method using this antibody. These results suggest that this Cu/Zn SOD rabbit polyclonal antibody may be a useful tool for elucidating the biological functions of Cu/Zn SODs in plants.

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“…Knock-down of NAT398b/c promotes the accumulation of MIR398b and MIR398c, while the overexpression of NAT398b and NAT398c represses the processing of miR398. Notably, the overexpression of siRNAs derived from NAT398 overlapping transcripts, so-called nat-siR398, reduces the levels of pri-miR398b and pri-miR398c [37].…”

Section: Lncrnas As Precursors Of Small Regulatory Rnasmentioning

confidence: 99%

Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations

Fonouni‐Farde

Ariel

Crespi

2021

ncRNA

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The first reference to the “C-value paradox” reported an apparent imbalance between organismal genome size and morphological complexity. Since then, next-generation sequencing has revolutionized genomic research and revealed that eukaryotic transcriptomes contain a large fraction of non-protein-coding components. Eukaryotic genomes are pervasively transcribed and noncoding regions give rise to a plethora of noncoding RNAs with undeniable biological functions. Among them, long noncoding RNAs (lncRNAs) seem to represent a new layer of gene expression regulation, participating in a wide range of molecular mechanisms at the transcriptional and post-transcriptional levels. In addition to their role in epigenetic regulation, plant lncRNAs have been associated with the degradation of complementary RNAs, the regulation of alternative splicing, protein sub-cellular localization, the promotion of translation and protein post-translational modifications. In this review, we report and integrate numerous and complex mechanisms through which long noncoding transcripts regulate post-transcriptional gene expression in plants.

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Natural antisense transcripts of MIR398 genes suppress microR398 processing and attenuate plant thermotolerance

Cited by 54 publications

References 81 publications

Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

Development and Optimization of Rabbit Polyclonal Antibodies for Cu/ZnSOD detection in Rice (Oryza sativa L.)

Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations

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