RT Journal Article SR Electronic T1 Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis JF bioRxiv FD Cold Spring Harbor Laboratory SP 604199 DO 10.1101/604199 A1 David C. Tack A1 Zhao Su A1 Yunqing Yu A1 Philip C. Bevilacqua A1 Sarah M. Assmann YR 2019 UL http://biorxiv.org/content/early/2019/04/09/604199.abstract AB RNA structures are influenced by their physico-chemical environment. Few studies have assessed genome-wide impacts of abiotic stresses on in vivo RNA structure, however, and none have investigated tissue-specificity. We applied our Structure-seq method to assess in vivo mRNA secondary structure in Arabidopsis shoots and roots under control and salt stress conditions. Structure-seq utilizes dimethyl sulfate (DMS) for in vivo transcriptome-wide covalent modification of accessible As and Cs, i.e. those lacking base pairing and protection. Tissue type was a strong determinant of DMS reactivity, indicating tissue-specificity of RNA structuromes. Both tissues exhibited a significant inverse correlation between salt stress-induced changes in transcript reactivity and changes in transcript abundance, implicating changes in RNA structure and accessibility in transcriptome regulation. In mRNAs wherein the 5’UTR, CDS and 3’UTR concertedly increased or decreased in mean reactivity under salinity, this inverse correlation was more pronounced, suggesting that concordant structural changes across the mRNA have the greatest impact on abundance. Transcripts with the greatest and least salt stress-induced changes in DMS reactivity were enriched in genes encoding stress-related functions and included housekeeping functions, respectively. We conclude that secondary structure regulates mRNA abundance, thereby contributing to tissue specificity of the transcriptome and its dynamic adjustment under stress.One Sentence Summary: Transcriptome-wide methods reveal dynamic tissue-specific and salt stress-dependent modulation of mRNA accessibility and structure, and correlated mRNA abundance changes.