title: Bioinformatic Identification of Conserved Cis-Sequences in Coregulated Genes.
abstract: Bioinformatics tools can be employed to identify conserved cis-sequences in sets of coregulated plant genes because more and more gene expression and genomic sequence data become available. Knowledge on the specific cis-sequences, their enrichment and arrangement within promoters, facilitates the design of functional synthetic plant promoters that are responsive to specific stresses. The present chapter illustrates an example for the bioinformatic identification of conserved Arabidopsis thaliana cis-sequences enriched in drought stress-responsive genes. This workflow can be applied for the identification of cis-sequences in any sets of coregulated genes. The workflow includes detailed protocols to determine sets of coregulated genes, to extract the corresponding promoter sequences, and how to install and run a software package to identify overrepresented motifs. Further bioinformatic analyses that can be performed with the results are discussed.
authors.affiliation: Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany. lorenz.buelow@julius-kuehn.de.
authors.forename: Lorenz
authors.initials: L
authors.lastname: Bülow
authors.affiliation: Institut für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Hehl
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D012984:Software
keywords: AthaMap; BEST; Cis-elements; Cis-regulatory sequences; Coregulated genes; Overrepresented motifs; PathoPlant; Promoter sequences; TAIR