N6-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis

Abstract

N⁶-methyladenosine (m⁶A) is a dynamic, reversible, covalently modified ribonucleotide that occurs predominantly toward 3' ends of eukaryotic mRNAs and is essential for their proper function and regulation. In Arabidopsis thaliana, many RNAs contain at least one m⁶A site, yet the transcriptome-wide function of m⁶A remains mostly unknown. Here, we show that many m⁶A-modified mRNAs in Arabidopsis have reduced abundance in the absence of this mark. The decrease in abundance is due to transcript destabilization caused by cleavage occurring 4 or 5 nt directly upstream of unmodified m⁶A sites. Importantly, we also find that, upon agriculturally relevant salt treatment, m⁶A is dynamically deposited on and stabilizes transcripts encoding proteins required for salt and osmotic stress response. Overall, our findings reveal that m⁶A generally acts as a stabilizing mark through inhibition of site-specific cleavage in plant transcriptomes, and this mechanism is required for proper regulation of the salt-stress-responsive transcriptome.

Keywords: N(6)-methyladenosine; RNA cleavage; RNA covalent modifications; RNA degradation; RNA stability; m(6)A; mRNA; ribonuclease.