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

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.

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/31502735nas a2200301 4500008004100000022001400041245016300055210006900218260001300287300001300300490000700313520173600320653001002056653003002066653003802096653004402134653002802178653001702206653002702223653001002250100002602260700002102286700001602307700002102323700001802344700002202362856004902384 2014 eng d a1460-243100aA comparative study of ripening among berries of the grape cluster reveals an altered transcriptional programme and enhanced ripening rate in delayed berries.0 acomparative study of ripening among berries of the grape cluster c2014 Nov a5889-9020 v653 a

Transcriptional studies in relation to fruit ripening generally aim to identify the transcriptional states associated with physiological ripening stages and the transcriptional changes between stages within the ripening programme. In non-climacteric fruits such as grape, all ripening-related genes involved in this programme have not been identified, mainly due to the lack of mutants for comparative transcriptomic studies. A feature in grape cluster ripening (Vitis vinifera cv. Pinot noir), where all berries do not initiate the ripening at the same time, was exploited to study their shifted ripening programmes in parallel. Berries that showed marked ripening state differences in a véraison-stage cluster (ripening onset) ultimately reached similar ripeness states toward maturity, indicating the flexibility of the ripening programme. The expression variance between these véraison-stage berry classes, where 11% of the genes were found to be differentially expressed, was reduced significantly toward maturity, resulting in the synchronization of their transcriptional states. Defined quantitative expression changes (transcriptional distances) not only existed between the véraison transitional stages, but also between the véraison to maturity stages, regardless of the berry class. It was observed that lagging berries complete their transcriptional programme in a shorter time through altered gene expressions and ripening-related hormone dynamics, and enhance the rate of physiological ripening progression. Finally, the reduction in expression variance of genes can identify new genes directly associated with ripening and also assess the relevance of gene activity to the phase of the ripening programme.

10aFruit10aGene Expression Profiling10aGene Expression Regulation, Plant10aOligonucleotide Array Sequence Analysis10aPlant Growth Regulators10aTime Factors10aTranscription, Genetic10aVitis1 aGouthu, Satyanarayana1 aO'Neil, Shawn, T1 aDi, Yanming1 aAnsarolia, Mitra1 aMegraw, Molly1 aDeluc, Laurent, G uhttps://megraw.cgrb.oregonstate.edu/node/31802911nas a2200457 4500008004100000022001400041245011200055210006900167260001300236300001200249490000700261520157400268653001601842653002501858653001801883653002101901653001501922653003801937653001801975653002001993653002202013653001602035653003002051653001902081653001502100653002702115653002402142653001302166653002602179653003402205100001602239700002102255700002302276700001302299700002002312700001702332700002202349700001502371700001802386856004902404 2014 eng d a1532-298X00aPaired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.0 aPairedend analysis of transcription start sites in Arabidopsis r c2014 Jul a2746-600 v263 a

Understanding plant gene promoter architecture has long been a challenge due to the lack of relevant large-scale data sets and analysis methods. Here, we present a publicly available, large-scale transcription start site (TSS) data set in plants using a high-resolution method for analysis of 5' ends of mRNA transcripts. Our data set is produced using the paired-end analysis of transcription start sites (PEAT) protocol, providing millions of TSS locations from wild-type Columbia-0 Arabidopsis thaliana whole root samples. Using this data set, we grouped TSS reads into "TSS tag clusters" and categorized clusters into three spatial initiation patterns: narrow peak, broad with peak, and weak peak. We then designed a machine learning model that predicts the presence of TSS tag clusters with outstanding sensitivity and specificity for all three initiation patterns. We used this model to analyze the transcription factor binding site content of promoters exhibiting these initiation patterns. In contrast to the canonical notions of TATA-containing and more broad "TATA-less" promoters, the model shows that, in plants, the vast majority of transcription start sites are TATA free and are defined by a large compendium of known DNA sequence binding elements. We present results on the usage of these elements and provide our Plant PEAT Peaks (3PEAT) model that predicts the presence of TSSs directly from sequence.

[Link to Additional Data and Supplementary Materials]

10aArabidopsis10aArabidopsis Proteins10aBinding Sites10aCluster Analysis10aDNA, Plant10aGene Expression Regulation, Plant10aGenome, Plant10aModels, Genetic10aNucleotide Motifs10aPlant Roots10aPromoter Regions, Genetic10aRNA, Messenger10aRNA, Plant10aSequence Analysis, DNA10aSpecies Specificity10aTATA Box10aTranscription Factors10aTranscription Initiation Site1 aMorton, Taj1 aPetricka, Jalean1 aCorcoran, David, L1 aLi, Song1 aWinter, Cara, M1 aCarda, Alexa1 aBenfey, Philip, N1 aOhler, Uwe1 aMegraw, Molly uhttps://megraw.cgrb.oregonstate.edu/node/319