title: Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis.
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 intron retaining CCA1 isoforms and altered their phasing to different times of day. Both abiotic and biotic stresses such as drought or P. syringae infection induced 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. Altogether, 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 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.
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, 97331, USA filichks@onid.orst.edu.
authors.forename: Sergei A
authors.initials: SA
authors.lastname: Filichkin
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA.
authors.forename: Jason S
authors.initials: JS
authors.lastname: Cumbie
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA.
authors.forename: J Palitha
authors.initials: JP
authors.lastname: Dharmawadhana
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, 97331, USA.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Jaiswal
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, 97331, USA.
authors.forename: Jeff H
authors.initials: JH
authors.lastname: Chang
authors.affiliation: Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.
authors.forename: Saiprasad G
authors.initials: SG
authors.lastname: Palusa
authors.affiliation: Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.
authors.forename: A S N
authors.initials: AS
authors.lastname: Reddy
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, 97331, USA.
authors.forename: Molly
authors.initials: M
authors.lastname: Megraw
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, 97331, USA Donald Danforth Plant Science Center, Saint Louis, Missouri, 63132, USA tmockler@danforthcenter.org.
authors.forename: Todd C
authors.initials: TC
authors.lastname: Mockler
keywords: Arabidopsis; CCA1; LHY; Pseudomonas syringae; RVE2; SR45; alternative splicing; circadian clock; environmental stress; intron retention; nonsense mRNAs; nonsense mediated mRNA decay (NMD); temperature stress