MicroRNA promoter analysis.

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.

[1]  A. Krishnamachari,et al.  Computational analysis of plant RNA Pol-II promoters. , 2006, Bio Systems.

[2]  Xin Chen,et al.  TRANSFAC: an integrated system for gene expression regulation , 2000, Nucleic Acids Res..

[3]  Curtis E. Dyreson,et al.  Genome analysis Athena : a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences , 2005 .

[4]  Shane T. Jensen,et al.  MicroRNA promoter element discovery in Arabidopsis. , 2006, RNA.

[5]  Sean R. Eddy,et al.  Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .

[6]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[7]  Victor V. Solovyev,et al.  PromH: promoters identification using orthologous genomic sequences , 2003, Nucleic Acids Res..

[8]  B. Meyers,et al.  Construction of small RNA cDNA libraries for deep sequencing. , 2007, Methods.

[9]  Ramana V. Davuluri,et al.  AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors , 2003, BMC Bioinformatics.

[10]  Gary D. Stormo,et al.  DNA binding sites: representation and discovery , 2000, Bioinform..

[11]  Stijn van Dongen,et al.  miRBase: microRNA sequences, targets and gene nomenclature , 2005, Nucleic Acids Res..

[12]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[13]  D. Bartel,et al.  MicroRNAS and their regulatory roles in plants. , 2006, Annual review of plant biology.

[14]  Martin Schindler,et al.  AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana , 2005, Nucleic Acids Res..

[15]  Weixiong Zhang,et al.  Characterization and Identification of MicroRNA Core Promoters in Four Model Species , 2007, PLoS Comput. Biol..

[16]  Scott A. Givan,et al.  Expression of Arabidopsis MIRNA Genes1[w] , 2005, Plant Physiology.

[17]  A. Hatzigeorgiou,et al.  TarBase: A comprehensive database of experimentally supported animal microRNA targets. , 2005, RNA.