01594nas a2200193 4500008004100000022001400041245003200055210003100087260000900118300001100127490000800138520108700146653001401233653003001247653002601277100001801303700003001321856004901351 2010 eng d a1940-602900aMicroRNA promoter analysis.0 aMicroRNA promoter analysis c2010 a149-610 v5923 a

In this chapter, we present a brief overview of current knowledge about the promoters of plant microRNAs (miRNAs), and provide a step-by-step guide for predicting plant miRNA promoter elements using known transcription factor binding motifs. The approach to promoter element prediction is based on a carefully constructed collection of Positional Weight Matrices (PWMs) for known transcription factors (TFs) in Arabidopsis. A key concept of the method is to use scoring thresholds for potential binding sites that are appropriate to each individual transcription factor. While the procedure can be applied to search for Transcription Factor Binding Sites (TFBSs) in any pol-II promoter region, it is particularly practical for the case of plant miRNA promoters where upstream sequence regions and binding sites are not readily available in existing databases. The majority of the material described in this chapter is available for download at http://microrna.gr.

[Link to Tools and Supplementary Materials]

10aMicroRNAs10aPromoter Regions, Genetic10aTranscription Factors1 aMegraw, Molly1 aHatzigeorgiou, Artemis, G uhttps://megraw.cgrb.oregonstate.edu/node/325