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 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.
authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA. Electronic address: filichks@onid.orst.edu.
authors: Sergei A
authors: SA
authors: Filichkin
authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
authors: Jason S
authors: JS
authors: Cumbie
authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
authors: Palitha
authors: P
authors: Dharmawardhana
authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.
authors: Pankaj
authors: P
authors: Jaiswal
authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.
authors: Jeff H
authors: JH
authors: Chang
authors: Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, CO 80523, USA.
authors: Saiprasad G
authors: SG
authors: Palusa
authors: Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, CO 80523, USA.
authors: A S N
authors: AS
authors: Reddy
authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.
authors: Molly
authors: M
authors: Megraw
authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA; Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA. Electronic address: tmockler@danforthcenter.org.
authors: Todd C
authors: TC
authors: Mockler
mesh_terms: D017398:Alternative Splicing / Q000235:genetics / Q000502:physiology; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D057906:Circadian Clocks / Q000235:genetics / Q000502:physiology; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D007438:Introns / Q000235:genetics; D059365:Nonsense Mediated mRNA Decay / Q000235:genetics / Q000502:physiology
chemical_list: D029681:Arabidopsis Proteins
keywords: Arabidopsis; alternative splicing; circadian clock; environmental stress; intron retention; nonsense-mediated mRNA decay (NMD)