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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 yet been clari...

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Autores principales: Sun, Hai-Xi, Li, Yan, Niu, Qi-Wen, Chua, Nam-Hai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538558/
https://www.ncbi.nlm.nih.gov/pubmed/28522613
http://dx.doi.org/10.1101/gr.218669.116
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author Sun, Hai-Xi
Li, Yan
Niu, Qi-Wen
Chua, Nam-Hai
author_facet Sun, Hai-Xi
Li, Yan
Niu, Qi-Wen
Chua, Nam-Hai
author_sort Sun, Hai-Xi
collection PubMed
description 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 yet 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 act as antisense transcripts to repress expression levels of sense genes from the opposite strand or can activate the transcription or lead to read-through transcription of their downstream genes. Further analysis suggests that transcripts with 3′ UTR extensions have weaker poly(A) signals than those 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 transcript 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.
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spelling pubmed-55385582018-02-01 Dehydration stress extends mRNA 3′ untranslated regions with noncoding RNA functions in Arabidopsis Sun, Hai-Xi Li, Yan Niu, Qi-Wen Chua, Nam-Hai Genome Res Research 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 yet 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 act as antisense transcripts to repress expression levels of sense genes from the opposite strand or can activate the transcription or lead to read-through transcription of their downstream genes. Further analysis suggests that transcripts with 3′ UTR extensions have weaker poly(A) signals than those 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 transcript 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. Cold Spring Harbor Laboratory Press 2017-08 /pmc/articles/PMC5538558/ /pubmed/28522613 http://dx.doi.org/10.1101/gr.218669.116 Text en © 2017 Sun et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Research
Sun, Hai-Xi
Li, Yan
Niu, Qi-Wen
Chua, Nam-Hai
Dehydration stress extends mRNA 3′ untranslated regions with noncoding RNA functions in Arabidopsis
title Dehydration stress extends mRNA 3′ untranslated regions with noncoding RNA functions in Arabidopsis
title_full Dehydration stress extends mRNA 3′ untranslated regions with noncoding RNA functions in Arabidopsis
title_fullStr Dehydration stress extends mRNA 3′ untranslated regions with noncoding RNA functions in Arabidopsis
title_full_unstemmed Dehydration stress extends mRNA 3′ untranslated regions with noncoding RNA functions in Arabidopsis
title_short Dehydration stress extends mRNA 3′ untranslated regions with noncoding RNA functions in Arabidopsis
title_sort dehydration stress extends mrna 3′ untranslated regions with noncoding rna functions in arabidopsis
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538558/
https://www.ncbi.nlm.nih.gov/pubmed/28522613
http://dx.doi.org/10.1101/gr.218669.116
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