<?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%">Ivanchenko, Maria G</style></author><author><style face="normal" font="default" size="100%">Zhu, Jinsheng</style></author><author><style face="normal" font="default" size="100%">Wang, Bangjun</style></author><author><style face="normal" font="default" size="100%">Medvecká, Eva</style></author><author><style face="normal" font="default" size="100%">Du, Yunlong</style></author><author><style face="normal" font="default" size="100%">Azzarello, Elisa</style></author><author><style face="normal" font="default" size="100%">Mancuso, Stefano</style></author><author><style face="normal" font="default" size="100%">Megraw, Molly</style></author><author><style face="normal" font="default" size="100%">Filichkin, Sergei</style></author><author><style face="normal" font="default" size="100%">Dubrovsky, Joseph G</style></author><author><style face="normal" font="default" size="100%">Friml, Jiří</style></author><author><style face="normal" font="default" size="100%">Geisler, Markus</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The cyclophilin A DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation.</style></title><secondary-title><style face="normal" font="default" size="100%">Development</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Development</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Arabidopsis</style></keyword><keyword><style  face="normal" font="default" size="100%">Biological Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Cyclophilin A</style></keyword><keyword><style  face="normal" font="default" size="100%">Indoleacetic Acids</style></keyword><keyword><style  face="normal" font="default" size="100%">Lycopersicon esculentum</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Roots</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Shoots</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 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">142</style></volume><pages><style face="normal" font="default" size="100%">712-21</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Cyclophilin A is a conserved peptidyl-prolyl cis-trans isomerase (PPIase) best known as the cellular receptor of the immunosuppressant cyclosporine A. Despite significant effort, evidence of developmental functions of cyclophilin A in non-plant systems has remained obscure. Mutations in a tomato (Solanum lycopersicum) cyclophilin A ortholog, DIAGEOTROPICA (DGT), have been shown to abolish the organogenesis of lateral roots; however, a mechanistic explanation of the phenotype is lacking. Here, we show that the dgt mutant lacks auxin maxima relevant to priming and specification of lateral root founder cells. DGT is expressed in shoot and root, and localizes to both the nucleus and cytoplasm during lateral root organogenesis. Mutation of ENTIRE/IAA9, a member of the auxin-responsive Aux/IAA protein family of transcriptional repressors, partially restores the inability of dgt to initiate lateral root primordia but not the primordia outgrowth. By comparison, grafting of a wild-type scion restores the process of lateral root formation, consistent with participation of a mobile signal. Antibodies do not detect movement of the DGT protein into the dgt rootstock; however, experiments with radiolabeled auxin and an auxin-specific microelectrode demonstrate abnormal auxin fluxes. Functional studies of DGT in heterologous yeast and tobacco-leaf auxin-transport systems demonstrate that DGT negatively regulates PIN-FORMED (PIN) auxin efflux transporters by affecting their plasma membrane localization. Studies in tomato support complex effects of the dgt mutation on PIN expression level, expression domain and plasma membrane localization. Our data demonstrate that DGT regulates auxin transport in lateral root formation.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">4</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%">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%">Cumbie, Jason S</style></author><author><style face="normal" font="default" size="100%">Ivanchenko, Maria G</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%">NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Arabidopsis</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanotechnology</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%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</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%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2015</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">16</style></volume><pages><style face="normal" font="default" size="100%">597</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;BACKGROUND: &lt;/b&gt;Identifying the transcription start sites (TSS) of genes is essential for characterizing promoter regions. Several protocols have been developed to capture the 5&amp;#39; end of transcripts via Cap Analysis of Gene Expression (CAGE) or linker-ligation strategies such as Paired-End Analysis of Transcription Start Sites (PEAT), but often require large amounts of tissue. More recently, nanoCAGE was developed for sequencing on the Illumina GAIIx to overcome these difficulties.&lt;/p&gt;&lt;p&gt;&lt;b&gt;RESULTS: &lt;/b&gt;Here we present the first publicly available adaptation of nanoCAGE for sequencing on recent ultra-high throughput platforms such as Illumina HiSeq-2000, and CapFilter, a computational pipeline that greatly increases confidence in TSS identification. We report excellent gene coverage, reproducibility, and precision in transcription start site discovery for samples from Arabidopsis thaliana roots.&lt;/p&gt;&lt;p&gt;&lt;b&gt;CONCLUSION: &lt;/b&gt;nanoCAGE-XL together with CapFilter allows for genome wide identification of high confidence transcription start sites in large eukaryotic genomes.&lt;/p&gt;&lt;p&gt;&lt;a href=&quot;http://megraw-dev.cgrb.oregonstate.edu/nanocage&quot;&gt;[Link to Protocol, Additional Data, and Supplementary Materials]&lt;/a&gt;&lt;/p&gt;&lt;p&gt;&lt;a href=&quot;http://megraw-dev.cgrb.oregonstate.edu/capfilter&quot;&gt;[Link to CapFilter Software]&lt;/a&gt;&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%">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><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%">Megraw, Molly</style></author><author><style face="normal" font="default" size="100%">Mukherjee, Sayan</style></author><author><style face="normal" font="default" size="100%">Ohler, Uwe</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.</style></title><secondary-title><style face="normal" font="default" size="100%">Genome Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Genome Biol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Algorithms</style></keyword><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Arabidopsis</style></keyword><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Drosophila melanogaster</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Regulatory Networks</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">MicroRNAs</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Annotation</style></keyword><keyword><style  face="normal" font="default" size="100%">Nucleic Acid Conformation</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Factors</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">14</style></volume><pages><style face="normal" font="default" size="100%">R85</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;WaRSwap is a randomization algorithm that for the first time provides a practical network motif discovery method for large multi-layer networks, for example those that include transcription factors, microRNAs, and non-regulatory protein coding genes. The algorithm is applicable to systems with tens of thousands of genes, while accounting for critical aspects of biological networks, including self-loops, large hubs, and target rearrangements. We validate WaRSwap on a newly inferred regulatory network from Arabidopsis thaliana, and compare outcomes on published Drosophila and human networks. Specifically, sustained input switches are among the few over-represented circuits across this diverse set of eukaryotes.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">8</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%">Petricka, Jalean J</style></author><author><style face="normal" font="default" size="100%">Schauer, Monica A</style></author><author><style face="normal" font="default" size="100%">Megraw, Molly</style></author><author><style face="normal" font="default" size="100%">Breakfield, Natalie W</style></author><author><style face="normal" font="default" size="100%">Thompson, J Will</style></author><author><style face="normal" font="default" size="100%">Georgiev, Stoyan</style></author><author><style face="normal" font="default" size="100%">Soderblom, Erik J</style></author><author><style face="normal" font="default" size="100%">Ohler, Uwe</style></author><author><style face="normal" font="default" size="100%">Moseley, Martin Arthur</style></author><author><style face="normal" font="default" size="100%">Grossniklaus, Ueli</style></author><author><style face="normal" font="default" size="100%">Benfey, Philip N</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The protein expression landscape of the Arabidopsis root.</style></title><secondary-title><style face="normal" font="default" size="100%">Proc Natl Acad Sci U S A</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Proc. Natl. Acad. Sci. U.S.A.</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%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Chromatography, Liquid</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Primers</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Roots</style></keyword><keyword><style  face="normal" font="default" size="100%">Plants, Genetically Modified</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Array Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Interaction Mapping</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteome</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteomics</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">Tandem Mass Spectrometry</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 May 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">109</style></volume><pages><style face="normal" font="default" size="100%">6811-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Because proteins are the major functional components of cells, knowledge of their cellular localization is crucial to gaining an understanding of the biology of multicellular organisms. We have generated a protein expression map of the Arabidopsis root providing the identity and cell type-specific localization of nearly 2,000 proteins. Grouping proteins into functional categories revealed unique cellular functions and identified cell type-specific biomarkers. Cellular colocalization provided support for numerous protein-protein interactions. With a binary comparison, we found that RNA and protein expression profiles are weakly correlated. We then performed peak integration at cell type-specific resolution and found an improved correlation with transcriptome data using continuous values. We performed GeLC-MS/MS (in-gel tryptic digestion followed by liquid chromatography-tandem mass spectrometry) proteomic experiments on mutants with ectopic and no root hairs, providing complementary proteomic data. Finally, among our root hair-specific proteins we identified two unique regulators of root hair development.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">18</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%">Brady, Siobhan M</style></author><author><style face="normal" font="default" size="100%">Zhang, Lifang</style></author><author><style face="normal" font="default" size="100%">Megraw, Molly</style></author><author><style face="normal" font="default" size="100%">Martinez, Natalia J</style></author><author><style face="normal" font="default" size="100%">Jiang, Eric</style></author><author><style face="normal" font="default" size="100%">Yi, Charles S</style></author><author><style face="normal" font="default" size="100%">Liu, Weilin</style></author><author><style face="normal" font="default" size="100%">Zeng, Anna</style></author><author><style face="normal" font="default" size="100%">Taylor-Teeples, Mallorie</style></author><author><style face="normal" font="default" size="100%">Kim, Dahae</style></author><author><style face="normal" font="default" size="100%">Ahnert, Sebastian</style></author><author><style face="normal" font="default" size="100%">Ohler, Uwe</style></author><author><style face="normal" font="default" size="100%">Ware, Doreen</style></author><author><style face="normal" font="default" size="100%">Walhout, Albertha J M</style></author><author><style face="normal" font="default" size="100%">Benfey, Philip N</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A stele-enriched gene regulatory network in the Arabidopsis root.</style></title><secondary-title><style face="normal" font="default" size="100%">Mol Syst Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Mol. Syst. Biol.</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%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Regulatory Networks</style></keyword><keyword><style  face="normal" font="default" size="100%">MicroRNAs</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Roots</style></keyword><keyword><style  face="normal" font="default" size="100%">Reproducibility of Results</style></keyword><keyword><style  face="normal" font="default" size="100%">Systems Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Factors</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%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Jan 18</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">459</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Tightly controlled gene expression is a hallmark of multicellular development and is accomplished by transcription factors (TFs) and microRNAs (miRNAs). Although many studies have focused on identifying downstream targets of these molecules, less is known about the factors that regulate their differential expression. We used data from high spatial resolution gene expression experiments and yeast one-hybrid (Y1H) and two-hybrid (Y2H) assays to delineate a subset of interactions occurring within a gene regulatory network (GRN) that determines tissue-specific TF and miRNA expression in plants. We find that upstream TFs are expressed in more diverse cell types than their targets and that promoters that are bound by a relatively large number of TFs correspond to key developmental regulators. The regulatory consequence of many TFs for their target was experimentally determined using genetic analysis. Remarkably, molecular phenotypes were identified for 65% of the TFs, but morphological phenotypes were associated with only 16%. This indicates that the GRN is robust, and that gene expression changes may be canalized or buffered.&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%">Megraw, Molly</style></author><author><style face="normal" font="default" size="100%">Baev, Vesselin</style></author><author><style face="normal" font="default" size="100%">Rusinov, Ventsislav</style></author><author><style face="normal" font="default" size="100%">Jensen, Shane T</style></author><author><style face="normal" font="default" size="100%">Kalantidis, Kriton</style></author><author><style face="normal" font="default" size="100%">Hatzigeorgiou, Artemis G</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">MicroRNA promoter element discovery in Arabidopsis.</style></title><secondary-title><style face="normal" font="default" size="100%">RNA</style></secondary-title><alt-title><style face="normal" font="default" size="100%">RNA</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Arabidopsis</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Binding Sites</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Feedback, Physiological</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">MicroRNAs</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</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%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">1612-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;In this study we present a method of identifying Arabidopsis miRNA promoter elements using known transcription factor binding motifs. We provide a comparative analysis of the representation of these elements in miRNA promoters, protein-coding gene promoters, and random genomic sequences. We report five transcription factor (TF) binding motifs that show evidence of overrepresentation in miRNA promoter regions relative to the promoter regions of protein-coding genes. This investigation is based on the analysis of 800-nucleotide regions upstream of 63 experimentally verified Transcription Start Sites (TSS) for miRNA primary transcripts in Arabidopsis. While the TATA-box binding motif was also previously reported by Xie and colleagues, the transcription factors AtMYC2, ARF, SORLREP3, and LFY are identified for the first time as overrepresented binding motifs in miRNA promoters.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">9</style></issue></record></records></xml>