TY - JOUR
T1 - Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis
AU - Tack, David C.
AU - Su, Zhao
AU - Yu, Yunqing
AU - Bevilacqua, Philip C.
AU - Assmann, Sarah M.
N1 - Funding Information:
This research was supported by National Science Foundation grant IOS-1339282 to P.C.B. and S.M.A. We thank Dr. Elizabeth Jolley and Megan Sylvia for reading the manuscript and providing feedback.
Publisher Copyright:
© 2020 Tack et al.
PY - 2020
Y1 - 2020
N2 - 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.
AB - 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.
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U2 - 10.1261/rna.072850.119
DO - 10.1261/rna.072850.119
M3 - Article
C2 - 31937672
AN - SCOPUS:85082148283
SN - 1355-8382
VL - 26
SP - 492
EP - 511
JO - RNA
JF - RNA
IS - 4
ER -