The recent completion of the Arabidopsis thaliana genome provides an opportunity to examine features of genes and their potential control regions on a genomic scale. Regions of the sequence upstream of all transcribed regions, here referred to as genes, were examined as well as sequences corresponding to the genes themselves. The upstream regions extended to the previous gene or to 1500 nucleotides upstream, whichever occurred first. Motifs nine nucleotides long were analyzed. Motifs that are important elements in a functional promoter are likely to be found in promoters more frequently than in genes themselves, We therefore examined motifs that had high normalized ratios of occurrences in upstream sequences versus gene sequences.
Several hundred candidate motifs with high ratios have been identified. Some of these motifs also show preferred upstream locations with respect to their adjacent genes. Motifs with very low ratios are being examined as well.
A subset of genes known to be circadian clock regulated was also studied. Specific known clock regulatory elements are found both upstream of these clock genes but also upstream of many other genes not known to be clock regulated. We have identified some candidate elements that may be useful in defining clock regulated genes.
The poster panels were arranged as shown here. Click on a Panel below to see that panel.
Panel 1: Introduction and GGCCCATTA Motif
Panel 2: Analysis of GGCCCATTA Motif
Panel 3: Identifying Motifs By Standard Deviation
panel 4: Identifying Motifs By Chi Squared Analysis
Panel 5: Analysis of Clock Gene Promoter Elements
Panel 6: Summary