Dehydration stress extends mRNA 3'' untranslated regions with noncoding RNA functions in Arabidopsis

The 3'' untranslated regions (3'' UTRs) of mRNAs play important roles in the regulation of mRNA localization, translation, and stability. Alternative cleavage and polyadenylation (APA) generates mRNAs with different 3'' UTRs, but the involvement of this process in stress response has not been clarified. Here, we report that a subset of stress-related genes exhibits 3'' UTR extensions of their mRNAs during dehydration stress. These extended 3'' UTRs have characteristics of long noncoding RNAs and likely do not interact with miRNAs. Functional studies using T-DNA insertion mutants reveal that they can function as antisense transcripts to repress expression levels of sense genes from the opposite strand, or can activate the transcription of downstream genes from the same strand. Poly(A) signal analysis reveal that mRNAs with 3'' UTR extensions have weaker poly(A) signals than mRNAs without 3'' UTR extensions. Finally, we show that their biogenesis is partially dependent on a trans-acting factor FPA. Taken together, we report that dehydration stress could induce mRNA 3'' UTR extensions, and elucidate a novel function for these stress-induced 3'' UTR extensions as long noncoding RNAs in the regulation of their neighboring genes. Overall design: To study the effects of stress on APA, we performed ssRNA-seq on Arabidopsis seedlings grown in normal, ABA-treated, and dehydration-stressed conditions. We collected samples at two time points (1 h and 3 h) for each treatment and for each time point we had three biological replicates.