MicroRNA promoter element discovery in Arabidopsis.

@article{citeulike:812862, 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.}, address = {1Center for Bioinformatics and Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.}, author = {Megraw, Molly and Baev, Vesselin and Rusinov, Ventsislav and Jensen, Shane T T. and Kalantidis, Kriton and Hatzigeorgiou, Artemis G G. }, citeulike-article-id = {812862}, doi = {10.1261/rna.130506}, issn = {1355-8382}, journal = {RNA}, keywords = {bioinformatics, expression-regulation, mirna, motifs, promoter}, month = {August}, posted-at = {2007-11-18 00:04:14}, priority = {4}, title = {MicroRNA promoter element discovery in Arabidopsis.}, url = {http://dx.doi.org/10.1261/rna.130506}, year = {2006} }

TY - JOUR ID - citeulike:812862 L3 - citeulike-article-id:812862 TI - MicroRNA promoter element discovery in Arabidopsis. JF - RNA AD - 1Center for Bioinformatics and Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. SN - 1355-8382 N2 - 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. KW - bioinformatics KW - expression-regulation KW - mirna KW - motifs KW - promoter AU - Megraw, Molly AU - Baev, Vesselin AU - Rusinov, Ventsislav AU - Jensen, Shane T AU - Kalantidis, Kriton AU - Hatzigeorgiou, Artemis G PY - 2006/08/03/ UR - http://dx.doi.org/10.1261/rna.130506 ER -