In silico identification of novel
cis-regulatory elements
Publicly available and own Arabidopsis thaliana microarray data are processed and stored in the
PathoPlant database. Using an in-house
developed query software, genes being induced at certain abiotic and biotic stimuli are identified.
Promoter regions 1000 bp upstream of the transcription start, if known, or alternatively relative
to the translational start are extracted. Promoter sequences are screened for overrepresented
sequence motifs using BEST
(Binding-site Estimation Suite of Tools) software, which combines four commonly used motif-finding
programs, AlignACE, BioProspector, CONSENSUS, and MEME, as well as the optimization program
BioOptimizer. Novel overrepresented motifs are determined with the
STAMP web server that compares
the motif sequences with known motif sequences and transcription factor (TF) binding sites.
The genomic context of the motifs is further examined using the
AthaMap database that displays TF binding
sites in the genome of A. thaliana. Putative stress-responsive motifs will subsequently
be used by the other project partners and will further be analyzed bioinformatically in a
phylogenetic footprinting approach as well as experimentally
using an in vivo assay system.
printer-friendly version