title: MicroRNA promoter element discovery in Arabidopsis.
abstract: 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.
authors.affiliation: Center for Bioinformatics and Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Molly
authors.initials: M
authors.lastname: Megraw
authors.forename: Vesselin
authors.initials: V
authors.lastname: Baev
authors.forename: Ventsislav
authors.initials: V
authors.lastname: Rusinov
authors.forename: Shane T
authors.initials: ST
authors.lastname: Jensen
authors.forename: Kriton
authors.initials: K
authors.lastname: Kalantidis
authors.forename: Artemis G
authors.initials: AG
authors.lastname: Hatzigeorgiou
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D001665:Binding Sites; D030541:Databases, Genetic; D025461:Feedback, Physiological / Q000235:genetics; D017343:Genes, Plant; D035683:MicroRNAs; D011401:Promoter Regions, Genetic; D016385:TATA Box; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism; D024363:Transcription Initiation Site
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors