02910nas 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 a
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' 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/31901853nas 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