Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis

David C. Tack, Zhao Su, Yunqing Yu, Philip C. Bevilacqua, Sarah M. Assmann

Research output: Contribution to journalArticle

Abstract

Little is known concerning the effects of abiotic factors on in vivo RNA structures. We applied Structure-seq to assess the in vivo mRNA structuromes of Arabidopsis thaliana under salinity stress, which negatively impacts agriculture. Structure-seq utilizes dimethyl sulfate reactivity to identify As and Cs that lack base-pairing or protection. Salt stress refolded transcripts differentially in root versus shoot, evincing tissue specificity of the structurome. Both tissues exhibited an inverse correlation between salt stress-induced changes in transcript reactivity and changes in abundance, with stress-related mRNAs showing particular structural dynamism. This inverse correlation is more pronounced in mRNAs wherein the mean reactivity of the 5′UTR, CDS, and 3′UTR concertedly change under salinity stress, suggesting increased susceptibility to abundance control mechanisms in transcripts exhibiting this phenomenon, which we name "concordancy." Concordant salinity-induced increases in reactivity were notably observed in photosynthesis genes, thereby implicating mRNA structural loss in the well-known depression of photosynthesis by salt stress. Overall, changes in secondary structure appear to impact mRNA abundance, molding the functional specificity of the transcriptome under stress.

Original languageEnglish (US)
Pages (from-to)492-511
Number of pages20
JournalRNA
Volume26
Issue number4
DOIs
StatePublished - Jan 1 2020

All Science Journal Classification (ASJC) codes

  • Molecular Biology

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