Isolation and Analysis of Gene Regulatory Sequences

Abstract

Database‐assisted bioinformatic approaches facilitate the analysis of gene regulatory sequences and allow the identification of putative transcription factor binding sites or common regulatory motifs in similarly expressed genes. These approaches complement experiments that identify specific regulatory sites. They may be easily established if the respective transcription factors responsible for gene expression have already been cloned and annotated to the databases. In this chapter we summarise recent results on transcriptional regulation in plants and describe the most abundant transcription factor families of Arabidopsis thaliana . We summarise experimental approaches to delineate gene regulatory sequences that should precede a database‐assisted analysis. The plant cis‐regulatory DNA element database PLACE and the transcription factor databases PlantCARE and TRANSFAC® are described, including connected software tools. PlanCARE is a plant specific database and TRANSFAC® covers transcription factors of all eukaryotes. The content and use of the TRANSFAC® database is presented in detail. Furthermore, we give examples on the identification of putative transcription factor binding sites in previously identified regulatory sequences and compile other databases that are relevant for the identification of regulatory sequences.

Integration of Bioinformatics and Synthetic Promoters Leads to the Discovery of Novel Elicitor-Responsive cis-Regulatory Sequences in Arabidopsis

“…Motif groups showing high similarity to known cis-regulatory sequences are indicated by the designation of the corresponding TF family and the lowest E value. Wingender, 2001;Hehl et al, 2004;Hehl and Bülow, 2008;Brady and Provart, 2009;Priest et al, 2009;Usadel et al, 2009). One approach is the detection of conserved sequences within coregulated genes.…”