01715nas a2200253   4500008004100000022001400041245011200055210006900167260001300236300001100249490000700260520091500267653002701182653002501209653002101234653003401255653001501289653002601304100002201330700002101352700001801373700002101391856004901412       2015                        eng d  a1879-035600aAlternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress.0 aAlternative splicing in plants directing traffic at the crossroa  c2015 Apr  a125-350 v243 a<p>In recent years, high-throughput sequencing-based analysis of plant transcriptomes has suggested that up to &sim;60% of plant gene loci encode alternatively spliced mature transcripts. These studies have also revealed that alternative splicing in plants can be regulated by cell type, developmental stage, the environment, and the circadian clock. Alternative splicing is coupled to RNA surveillance and processing mechanisms, including nonsense mediated decay. Recently, non-protein-coding transcripts have also been shown to undergo alternative splicing. These discoveries collectively describe a robust system of post-transcriptional regulatory feedback loops which influence RNA abundance. In this review, we summarize recent studies describing the specific roles alternative splicing and RNA surveillance play in plant adaptation to environmental stresses and the regulation of the circadian clock.</p>10aAdaptation, Biological10aAlternative Splicing10aCircadian Clocks10aPlant Physiological Phenomena10aRNA, Plant10aStress, Physiological1 aFilichkin, Sergei1 aPriest, Henry, D1 aMegraw, Molly1 aMockler, Todd, C  uhttps://megraw.cgrb.oregonstate.edu/node/31402911nas 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<p>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&#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 &quot;TSS tag clusters&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 &quot;TATA-less&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.</p><p><a href="http://megraw-dev.cgrb.oregonstate.edu/3PEAT">[Link to Additional Data and Supplementary Materials]</a></p>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/31902379nas a2200433   4500008004100000022001400041245006200055210005700117260001500174300001100189490000800200520113300208653001601341653002501357653001801382653002701400653001601427653003001443653001601473653003301489653002701522653003201549653001301581653001501594653001501609653002901624100002401653700002301677700001801700700002701718700001901745700002101764700002301785700001501808700002801823700002301851700002201874856004901896       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<p>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.</p>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  uhttps://megraw.cgrb.oregonstate.edu/node/321