02093nas a2200241   4500000000100000000000100001008004100002260001300043100002100056700001700077700002700094700001900121700001500140700002100155700001200176700001700188700001700205245012000222300001100342490000600353520147800359022001401837       2015                            d  c2015 Feb1 aSergei Filichkin1 aJason Cumbie1 aPalitha Dharmawardhana1 aPankaj Jaiswal1 aJeff Chang1 aSaiprasad Palusa1 aA Reddy1 aMolly Megraw1 aTodd Mockler00aEnvironmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis.  a207-270 v83 aEnvironmental 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.  a1752-9867