02503nas a2200325   4500008004100000022001400041245012000055210006900175260001300244300001100257490000600268520148900274653002501763653001601788653002501804653002101829653003801850653001201888653003301900100002501933700002101958700002801979700002002007700001902027700002502046700001802071700001802089700002102107856004902128       2015                        eng d  a1752-986700aEnvironmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis.0 aEnvironmental stresses modulate abundance and timing of alternat  c2015 Feb  a207-270 v83 a<p>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&nbsp;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.</p>10aAlternative Splicing10aArabidopsis10aArabidopsis Proteins10aCircadian Clocks10aGene Expression Regulation, Plant10aIntrons10aNonsense Mediated mRNA Decay1 aFilichkin, Sergei, A1 aCumbie, Jason, S1 aDharmawardhana, Palitha1 aJaiswal, Pankaj1 aChang, Jeff, H1 aPalusa, Saiprasad, G1 aReddy, A, S N1 aMegraw, Molly1 aMockler, Todd, C  uhttps://megraw.cgrb.oregonstate.edu/node/31502171nas a2200217   4500008004100000022001400041245012000055210006900175260001500244520145100259100002501710700002101735700002701756700002001783700001901803700002501822700001801847700001801865700002101883856004901904       2014                        eng d  a1752-986700aEnvironmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis.0 aEnvironmental Stresses Modulate Abundance and Timing of Alternat  c2014 Nov 33 a<p>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.</p>1 aFilichkin, Sergei, A1 aCumbie, Jason, S1 aDharmawadhana, Palitha1 aJaiswal, Pankaj1 aChang, Jeff, H1 aPalusa, Saiprasad, G1 aReddy, A, S N1 aMegraw, Molly1 aMockler, Todd, C  uhttps://megraw.cgrb.oregonstate.edu/node/317