02853nas a2200373 4500008004100000022001400041245012300055210006900178260001600247300001100263490000800274520174600282653001602028653002502044653001802069653002302087653002802110653001902138653001602157653001702173100002502190700001802215700001802233700001902251700001602270700002102286700002102307700001802328700002202346700002502368700001802393700002002411856004802431 2015 eng d a1477-912900aThe cyclophilin A DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation.0 acyclophilin A DIAGEOTROPICA gene affects auxin transport in both c2015 Feb 15 a712-210 v1423 a
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.
10aArabidopsis10aBiological Transport10aCyclophilin A10aIndoleacetic Acids10aLycopersicon esculentum10aPlant Proteins10aPlant Roots10aPlant Shoots1 aIvanchenko, Maria, G1 aZhu, Jinsheng1 aWang, Bangjun1 aMedvecká, Eva1 aDu, Yunlong1 aAzzarello, Elisa1 aMancuso, Stefano1 aMegraw, Molly1 aFilichkin, Sergei1 aDubrovsky, Joseph, G1 aFriml, Jiří1 aGeisler, Markus uhttp://megraw.cgrb.oregonstate.edu/node/31602502nas a2200325 4500008004100000022001400041245012000055210006900175260001300244300001100257490000600268520148900274653002501763653001601788653002501804653002101829653003801850653001201888653003301900100002501933700002101958700002801979700002002007700001902027700002502046700001802071700001802089700002102107856004802128 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 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.
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 uhttp://megraw.cgrb.oregonstate.edu/node/31502177nas a2200277 4500008004100000022001400041245011900055210006900174260000900243300000800252490000700260520133000267653001601597653001701613653001801630653001901648653001601667653003001683653002701713653001301740653003401753100002101787700002501808700001801833856004801851 2015 eng d a1471-216400aNanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.0 aNanoCAGEXL and CapFilter an approach to genome wide identificati c2015 a5970 v163 aBACKGROUND: Identifying the transcription start sites (TSS) of genes is essential for characterizing promoter regions. Several protocols have been developed to capture the 5' 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.
RESULTS: 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.
CONCLUSION: nanoCAGE-XL together with CapFilter allows for genome wide identification of high confidence transcription start sites in large eukaryotic genomes.
[Link to Protocol, Additional Data, and Supplementary Materials]
10aArabidopsis10aGenes, Plant10aGenome, Plant10aNanotechnology10aPlant Roots10aPromoter Regions, Genetic10aSequence Analysis, DNA10aSoftware10aTranscription Initiation Site1 aCumbie, Jason, S1 aIvanchenko, Maria, G1 aMegraw, Molly uhttp://megraw.cgrb.oregonstate.edu/node/31102910nas a2200457 4500008004100000022001400041245011200055210006900167260001300236300001200249490000700261520157400268653001601842653002501858653001801883653002101901653001501922653003801937653001801975653002001993653002202013653001602035653003002051653001902081653001502100653002702115653002402142653001302166653002602179653003402205100001602239700002102255700002302276700001302299700002002312700001702332700002202349700001502371700001802386856004802404 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 aUnderstanding 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 uhttp://megraw.cgrb.oregonstate.edu/node/31901717nas a2200325 4500008004100000022001400041245012600055210006900181260000900250300000800259490000700267520073000274653001501004653001201019653001601031653002601047653002801073653003101101653002901132653001101161653001401172653003401186653003001220653001301250653002601263100001801289700002101307700001501328856004801343 2013 eng d a1474-760X00aSustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.0 aSustainedinput switches for transcription factors and microRNAs c2013 aR850 v143 aWaRSwap 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.
10aAlgorithms10aAnimals10aArabidopsis10aComputational Biology10aDrosophila melanogaster10aGene Expression Regulation10aGene Regulatory Networks10aHumans10aMicroRNAs10aMolecular Sequence Annotation10aNucleic Acid Conformation10aSoftware10aTranscription Factors1 aMegraw, Molly1 aMukherjee, Sayan1 aOhler, Uwe uhttp://megraw.cgrb.oregonstate.edu/node/32002378nas a2200433 4500008004100000022001400041245006200055210005700117260001500174300001100189490000800200520113300208653001601341653002501357653001801382653002701400653001601427653003001443653001601473653003301489653002701522653003201549653001301581653001501594653001501609653002901624100002401653700002301677700001801700700002701718700001901745700002101764700002301785700001501808700002801823700002301851700002201874856004801896 2012 eng d a1091-649000aThe protein expression landscape of the Arabidopsis root.0 aprotein expression landscape of the Arabidopsis root c2012 May 1 a6811-80 v1093 aBecause 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.
10aArabidopsis10aArabidopsis Proteins10aBase Sequence10aChromatography, Liquid10aDNA Primers10aGene Expression Profiling10aPlant Roots10aPlants, Genetically Modified10aProtein Array Analysis10aProtein Interaction Mapping10aProteome10aProteomics10aRNA, Plant10aTandem Mass Spectrometry1 aPetricka, Jalean, J1 aSchauer, Monica, A1 aMegraw, Molly1 aBreakfield, Natalie, W1 aThompson, Will1 aGeorgiev, Stoyan1 aSoderblom, Erik, J1 aOhler, Uwe1 aMoseley, Martin, Arthur1 aGrossniklaus, Ueli1 aBenfey, Philip, N uhttp://megraw.cgrb.oregonstate.edu/node/32102389nas a2200433 4500008004100000022001400041245007000055210006600125260001600191300000800207490000600215520115000221653001601371653002501387653003001412653002901442653001401471653001601485653003101501653002001532653002601552653003301578100002201611700001801633700001801651700002501669700001601694700001901710700001601729700001501745700002901760700001501789700002201804700001501826700001701841700002701858700002201885856004801907 2011 eng d a1744-429200aA stele-enriched gene regulatory network in the Arabidopsis root.0 asteleenriched gene regulatory network in the Arabidopsis root c2011 Jan 18 a4590 v73 aTightly 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.
10aArabidopsis10aArabidopsis Proteins10aGene Expression Profiling10aGene Regulatory Networks10aMicroRNAs10aPlant Roots10aReproducibility of Results10aSystems Biology10aTranscription Factors10aTwo-Hybrid System Techniques1 aBrady, Siobhan, M1 aZhang, Lifang1 aMegraw, Molly1 aMartinez, Natalia, J1 aJiang, Eric1 aYi, Charles, S1 aLiu, Weilin1 aZeng, Anna1 aTaylor-Teeples, Mallorie1 aKim, Dahae1 aAhnert, Sebastian1 aOhler, Uwe1 aWare, Doreen1 aWalhout, Albertha, J M1 aBenfey, Philip, N uhttp://megraw.cgrb.oregonstate.edu/node/32201853nas a2200337 4500008004100000022001400041245005600055210005500111260001300166300001100179490000700190520089800197653001601095653001801111653001801129653002301147653002801170653001701198653001401215653003001229653001301259653002601272653003401298100001801332700001901350700002401369700002101393700002301414700003001437856004801467 2006 eng d a1355-838200aMicroRNA promoter element discovery in Arabidopsis.0 aMicroRNA promoter element discovery in Arabidopsis c2006 Sep a1612-90 v123 aIn 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.
10aArabidopsis10aBase Sequence10aBinding Sites10aDatabases, Genetic10aFeedback, Physiological10aGenes, Plant10aMicroRNAs10aPromoter Regions, Genetic10aTATA Box10aTranscription Factors10aTranscription Initiation Site1 aMegraw, Molly1 aBaev, Vesselin1 aRusinov, Ventsislav1 aJensen, Shane, T1 aKalantidis, Kriton1 aHatzigeorgiou, Artemis, G uhttp://megraw.cgrb.oregonstate.edu/node/331