N⁶‐methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis

Abstract

After transcription, a messenger RNA (mRNA) is further post‐transcriptionally regulated by several features including RNA secondary structure and covalent RNA modifications (specifically N 6 ‐methyladenosine, m 6 A). Both RNA secondary structure and m 6 A have been demonstrated to regulate mRNA stability and translation and have been independently linked to plant responses to soil salinity levels. However, the effect of m 6 A on regulating RNA secondary structure and the combinatorial interplay between these two RNA features during salt stress response has yet to be studied. Here, we globally identify RNA‐protein interactions and RNA secondary structure during systemic salt stress. This analysis reveals that RNA secondary structure changes significantly during salt stress, and that it is independent of global changes in RNA‐protein interactions. Conversely, we find that m 6 A is anti‐correlated with RNA secondary structure in a condition‐dependent manner, with salt‐specific m 6 A correlated with a decrease in mRNA secondary structure during salt stress. Taken together, we suggest that salt‐specific m 6 A deposition and the associated loss of RNA secondary structure results in increases in mRNA stability for transcripts encoding abiotic stress response proteins and ultimately increases in protein levels from these stabilized transcripts. In total, our comprehensive analyses reveal important post‐transcriptional regulatory mechanisms involved in plant long‐term salt stress response and adaptation.

Genome-Wide Investigation of N6-Methyladenosine Regulatory Genes and Their Roles in Tea (Camellia sinensis) Leaves During Withering Process

“…Under external stress, the increase of m6A marks in the 5' untranslated region (UTR) promoted the translation of drought-resistant mRNA ( Meyer et al, 2015 ). Meanwhile, m6A RNA methylation can also alleviate the damage of abiotic stress via modulating mRNA abundance, splicing, stability, and decay ( Zhou et al, 2015 , 2018 ; Duan et al, 2017 ; Kramer et al, 2020 ). Additionally, recent studies have shown that the dynamic redistribution of m6A levels under stress leads to m6A marks mainly enriched in genes related to primary and secondary metabolisms ( Liu et al, 2020 ).…”

Novel insights into the pervasive role of RNA structure in post-transcriptional regulation of gene expression in plants

“…A similar study in Arabidopsis found that RNA structures in both shoot and root were globally refolded in response to salt stress, leading to an inverse change of RNA abundance [41]. In contrast, protein interaction profile sequencing (PIP-seq), a method that simultaneously identifies protein-bound regions on a transcriptome-wide scale to examine global patterns of in vitro RNA secondary structure, reached the opposite conclusion following systemic salt stress in Arabidopsis [42]. They observed that N 6 -methyladenosine (m 6 A) RNA changes anti-correlated with alterations of RNA secondary structures in response to salt stress [42].…”

“…They observed that N 6 -methyladenosine (m 6 A) RNA changes anti-correlated with alterations of RNA secondary structures in response to salt stress [42]. Interestingly, the salt-specific m6A deposition and the associated weak RNA secondary structure resulted in increases in mRNA stability [42]. These contrasting results might be due to the different time periods employed for salt treatment [41,42].…”

“…In contrast, protein interaction profile sequencing (PIP-seq), a method that simultaneously identifies protein-bound regions on a transcriptome-wide scale to examine global patterns of in vitro RNA secondary structure, reached the opposite conclusion following systemic salt stress in Arabidopsis [ 42 ]. They observed that N 6 -methyladenosine (m 6 A) RNA changes anti-correlated with alterations of RNA secondary structures in response to salt stress [ 42 ]. Interestingly, the salt-specific m6A deposition and the associated weak RNA secondary structure resulted in increases in mRNA stability [ 42 ].…”

RNA N6-Methyladenosine Responds to Low-Temperature Stress in Tomato Anthers

“…Recent evidences demonstrated that m 6 A also participates in plant responses to various abiotic stresses. In Arabidopsis, changed m 6 A deposition affects RNA secondary structure under salt stress, resulting in increased stability of mRNA transcripts of abiotic stress response genes (Kramer et al, 2020). Additionally, ALKBH6 (eraser) mutation results in increased salt, drought, and heat stress sensitivity during seed germination (Huong et al, 2020).…”