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. 2015 Feb;8(2):207-27.
doi: 10.1016/j.molp.2014.10.011. Epub 2015 Jan 8.

Environmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis

Sergei A Filichkin  1 , Jason S Cumbie  2 , Palitha Dharmawardhana  2 , Pankaj Jaiswal  3 , Jeff H Chang  3 , Saiprasad G Palusa  4 , A S N Reddy  4 , Molly Megraw  3 , Todd C Mockler  5
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Free article

Environmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis

Sergei A Filichkin et al. Mol Plant. 2015 Feb.
Free article

Abstract

Environmental stresses profoundly altered accumulation of nonsense mRNAs including intron-retaining (IR) transcripts in Arabidopsis. Temporal patterns of stress-induced IR mRNAs were dissected using both oscillating and non-oscillating transcripts. Broad-range thermal cycles triggered a sharp increase in the long IR CCA1 isoforms and altered their phasing to different times of day. Both abiotic and biotic stresses such as drought or Pseudomonas syringae infection induced a similar increase. Thermal stress induced a time delay in accumulation of CCA1 I4Rb transcripts, whereas functional mRNA showed steady oscillations. Our data favor a hypothesis that stress-induced instabilities of the central oscillator can be in part compensated through fluctuations in abundance and out-of-phase oscillations of CCA1 IR transcripts. Taken together, our results support a concept that mRNA abundance can be modulated through altering ratios between functional and nonsense/IR transcripts. SR45 protein specifically bound to the retained CCA1 intron in vitro, suggesting that this splicing factor could be involved in regulation of intron retention. Transcriptomes of nonsense-mediated mRNA decay (NMD)-impaired and heat-stressed plants shared a set of retained introns associated with stress- and defense-inducible transcripts. Constitutive activation of certain stress response networks in an NMD mutant could be linked to disequilibrium between functional and nonsense mRNAs.

Keywords: Arabidopsis; alternative splicing; circadian clock; environmental stress; intron retention; nonsense-mediated mRNA decay (NMD).

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