MicroRNA promoter element discovery in Arabidopsis.
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.
Megraw
Molly
M
Center for Bioinformatics and Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
Baev
Vesselin
V
Rusinov
Ventsislav
V
Jensen
Shane T
ST
Kalantidis
Kriton
K
Hatzigeorgiou
Artemis G
AG
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
D035683:MicroRNAs; D014157:Transcription Factors