02378nas 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 a
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.
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/32102434nas a2200385 4500008004100000022001400041245005900055210005800114260001300172300001200185490000700197520139400204653001401598653002401612653001201636653001801648653001001666653001101676653001201687653000901699653001401708653002801722653001601750653001901766653004101785653002501826100002001851700001801871700002001889700002001909700001901929700003001948700002201978856004802000 2008 eng d a1362-496200aFrequency and fate of microRNA editing in human brain.0 aFrequency and fate of microRNA editing in human brain c2008 Sep a5270-800 v363 aPrimary transcripts of certain microRNA (miRNA) genes (pri-miRNAs) are subject to RNA editing that converts adenosine to inosine (A-->I RNA editing). However, the frequency of the pri-miRNA editing and the fate of edited pri-miRNAs remain largely to be determined. Examination of already known pri-miRNA editing sites indicated that adenosine residues of the UAG triplet sequence might be edited more frequently. In the present study, therefore, we conducted a large-scale survey of human pri-miRNAs containing the UAG triplet sequence. By direct sequencing of RT-PCR products corresponding to pri-miRNAs, we examined 209 pri-miRNAs and identified 43 UAG and also 43 non-UAG editing sites in 47 pri-miRNAs, which were highly edited in human brain. In vitro miRNA processing assay using recombinant Drosha-DGCR8 and Dicer-TRBP (the human immuno deficiency virus transactivating response RNA-binding protein) complexes revealed that a majority of pri-miRNA editing is likely to interfere with the miRNA processing steps. In addition, four new edited miRNAs with altered seed sequences were identified by targeted cloning and sequencing of the miRNAs that would be processed from edited pri-miRNAs. Our studies predict that approximately 16% of human pri-miRNAs are subject to A-->I editing and, thus, miRNA editing could have a large impact on the miRNA-mediated gene silencing.
10aAdenosine10aAdenosine Deaminase10aAnimals10aBase Sequence10aBrain10aHumans10aInosine10aMice10aMicroRNAs10aMolecular Sequence Data10aRNA Editing10aRNA Precursors10aRNA Processing, Post-Transcriptional10aRNA-Binding Proteins1 aKawahara, Yukio1 aMegraw, Molly1 aKreider, Edward1 aIizasa, Hisashi1 aValente, Louis1 aHatzigeorgiou, Artemis, G1 aNishikura, Kazuko uhttp://megraw.cgrb.oregonstate.edu/node/32701853nas 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