<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sparks, E. E.</style></author><author><style face="normal" font="default" size="100%">Drapek, C.</style></author><author><style face="normal" font="default" size="100%">Gaudinier, A.</style></author><author><style face="normal" font="default" size="100%">Li, S.</style></author><author><style face="normal" font="default" size="100%">Ansariola, M.</style></author><author><style face="normal" font="default" size="100%">Shen, N.</style></author><author><style face="normal" font="default" size="100%">Hennacy, J. H.</style></author><author><style face="normal" font="default" size="100%">Zhang, J.</style></author><author><style face="normal" font="default" size="100%">Turco, G.</style></author><author><style face="normal" font="default" size="100%">Petricka, J. J.</style></author><author><style face="normal" font="default" size="100%">Foret, J.</style></author><author><style face="normal" font="default" size="100%">Hartemink, A. J.</style></author><author><style face="normal" font="default" size="100%">Gordan, R.</style></author><author><style face="normal" font="default" size="100%">Megraw, M.</style></author><author><style face="normal" font="default" size="100%">Brady, S. M.</style></author><author><style face="normal" font="default" size="100%">Benfey, P. N.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors</style></title><secondary-title><style face="normal" font="default" size="100%">Dev Cell</style></secondary-title><short-title><style face="normal" font="default" size="100%">Developmental cell</style></short-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Arabidopsis Proteins/ genetics/ metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Arabidopsis/ genetics/growth &amp; development/ metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Computer Simulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Regulatory Networks</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Reporter</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Synthetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Roots/cytology/metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Plants, Genetically Modified</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Repressor Proteins/genetics/metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Trans-Activators/genetics/metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Factors/ genetics/ metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Two-Hybrid System Techniques</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">12/2016</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">https://doi.org/10.1016/j.devcel.2016.09.031</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">39</style></volume><pages><style face="normal" font="default" size="100%">585-596</style></pages><isbn><style face="normal" font="default" size="100%">1878-1551 (Electronic)1534-5807 (Linking)</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Tissue-specific gene expression is often thought to arise from spatially restricted transcriptional cascades. However, it is unclear how expression is established at the top of these cascades in the absence of pre-existing specificity. We generated a transcriptional network to explore how transcription factor expression is established in the Arabidopsis thaliana root ground tissue. Regulators of the SHORTROOT-SCARECROW transcriptional cascade were validated in planta. At the top of this cascade, we identified both activators and repressors of SHORTROOT. The aggregate spatial expression of these regulators is not sufficient to predict transcriptional specificity. Instead, modeling, transcriptional reporters, and synthetic promoters support a mechanism whereby expression at the top of the SHORTROOT-SCARECROW cascade is established through opposing activities of activators and repressors.&lt;/p&gt;</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Filichkin, Sergei A</style></author><author><style face="normal" font="default" size="100%">Cumbie, Jason S</style></author><author><style face="normal" font="default" size="100%">Dharmawardhana, Palitha</style></author><author><style face="normal" font="default" size="100%">Jaiswal, Pankaj</style></author><author><style face="normal" font="default" size="100%">Chang, Jeff H</style></author><author><style face="normal" font="default" size="100%">Palusa, Saiprasad G</style></author><author><style face="normal" font="default" size="100%">Reddy, A S N</style></author><author><style face="normal" font="default" size="100%">Megraw, Molly</style></author><author><style face="normal" font="default" size="100%">Mockler, Todd C</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Environmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis.</style></title><secondary-title><style face="normal" font="default" size="100%">Mol Plant</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Mol Plant</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Alternative Splicing</style></keyword><keyword><style  face="normal" font="default" size="100%">Arabidopsis</style></keyword><keyword><style  face="normal" font="default" size="100%">Arabidopsis Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Circadian Clocks</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">Introns</style></keyword><keyword><style  face="normal" font="default" size="100%">Nonsense Mediated mRNA Decay</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2015 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">207-27</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;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&amp;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.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gouthu, Satyanarayana</style></author><author><style face="normal" font="default" size="100%">O'Neil, Shawn T</style></author><author><style face="normal" font="default" size="100%">Di, Yanming</style></author><author><style face="normal" font="default" size="100%">Ansarolia, Mitra</style></author><author><style face="normal" font="default" size="100%">Megraw, Molly</style></author><author><style face="normal" font="default" size="100%">Deluc, Laurent G</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A comparative study of ripening among berries of the grape cluster reveals an altered transcriptional programme and enhanced ripening rate in delayed berries.</style></title><secondary-title><style face="normal" font="default" size="100%">J Exp Bot</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Exp. Bot.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Fruit</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Growth Regulators</style></keyword><keyword><style  face="normal" font="default" size="100%">Time Factors</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Vitis</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">65</style></volume><pages><style face="normal" font="default" size="100%">5889-902</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;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.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">20</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Morton, Taj</style></author><author><style face="normal" font="default" size="100%">Petricka, Jalean</style></author><author><style face="normal" font="default" size="100%">Corcoran, David L</style></author><author><style face="normal" font="default" size="100%">Li, Song</style></author><author><style face="normal" font="default" size="100%">Winter, Cara M</style></author><author><style face="normal" font="default" size="100%">Carda, Alexa</style></author><author><style face="normal" font="default" size="100%">Benfey, Philip N</style></author><author><style face="normal" font="default" size="100%">Ohler, Uwe</style></author><author><style face="normal" font="default" size="100%">Megraw, Molly</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.</style></title><secondary-title><style face="normal" font="default" size="100%">Plant Cell</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Plant Cell</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Arabidopsis</style></keyword><keyword><style  face="normal" font="default" size="100%">Arabidopsis Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Binding Sites</style></keyword><keyword><style  face="normal" font="default" size="100%">Cluster Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Nucleotide Motifs</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Roots</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Messenger</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Species Specificity</style></keyword><keyword><style  face="normal" font="default" size="100%">TATA Box</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Factors</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Initiation Site</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">26</style></volume><pages><style face="normal" font="default" size="100%">2746-60</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;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&amp;#39; 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 &amp;quot;TSS tag clusters&amp;quot; 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 &amp;quot;TATA-less&amp;quot; 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.&lt;/p&gt;&lt;p&gt;&lt;a href=&quot;http://megraw-dev.cgrb.oregonstate.edu/3PEAT&quot;&gt;[Link to Additional Data and Supplementary Materials]&lt;/a&gt;&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue></record></records></xml>