Transcription factor binding specificities

Supplemental Figure 5: Binding specificities of maternal and gap transcription factors

Supplemental Data: Binding sites used to build binding models:

• Bicoid
• Caudal
• Hunchback
• Kruppel
• Knirps

Supplemental data: Background file (b-file) used for aligning binding sequences with MEME. The b-file supplies n-th order Markov probabilities of non-coding DNA in Drosophila, which MEME uses as a null model when searching for statistically significant alignments.

Searching for clusters near even-skipped

Figure 1: Distribution of predicted transcription factor binding sites near even-skipped.

Supplemental data: CONSENSUS was used to search for sites with high predicted affinity for our TFs. The exact command used is as follows:
patser-v3b -a fly_intergen.consensus.alph -c -d2 -f seqfile.cons -l 4 -m PWM.file. Frequency matrices of the format required for the PWM.file files are availble at the bottom of the TF report in our TF database.

Binding site clustering can identify many CRMs in a test set containing 19 examples

Supplemental Table 1: A table detailing 19 example CRMs known to be regulated by combinations of the maternal effect and gap transcription factors described above.

Supplemental Data: A fasta file containing sequences for these 19 CRMs

Supplemental Figure 6: Genomic plots showing significant binding site clusters adjacent to the 9 genes containging these 19 CRMs

• hunchback
• knirps
• Kruppel
• even-skipped
• hairy
• runt
• abdominal-A
• spalt
• Ultrabithorax

Assessing the specificity of binding site clusters

Figure 2: Results of genome-wide search for binding site clusters

Supplemental Data: Genomic plots for all significant clusters of binding sites (note: These whole-genome scans were done with PWMs trained on all available binding sequences. Therefore, they do not always match those from Supplemental Figure 6 above, which were scanned using PWMs that ommitted sequences derived from the example CRMs themselves.)

• clusters of 12 or more sites
• clusters of 13 or more sites
• clusters of 14 or more sites
• clusters of 15 or more sites
• clusters of 16 or more sites
• clusters of 17 or more sites
• clusters of 18 or more sites

Investigating novel clusters of binding sites

Supplemental Table 2: Describes the genes flanking 28 novel binding site clusters identified in whole-genome searches. Embryonic expression patterns (whole mount RNA in-situ and microarray) for these 49 genes these genes.

Figure 3: A condensed version of Supplemental Table 2, showing only those clusters adjacent to genes with a gap or striped expression pattern

Supplemental Figure 7: Binding site plots for each of the 28 novel binding site clusters identified in whole-genome searches

Figure 4: A novel enhancer controlling posterior expression of giant