Journal: eLife

Article Title: A global change in RNA polymerase II pausing during the Drosophila midblastula transition

doi: 10.7554/eLife.00861

Figure Lengend Snippet: ( A ) Promoter analysis of all previously identified gene groups. Shown is the enrichment of known core promoter elements found in promoters with dispersed initiation or focused initiation, as well as in the binding motifs for GAGA factor (GAF) and Zelda. Only occurrences close to the known location of the motif relative to the TSS were scored (see ). The star indicates significant enrichment (orange) or depletion (black). Note that the three pre-MBT groups with different Pol II pausing patterns are enriched for distinct core promoter elements. ( B ) The top two known motifs identified by de novo motif analysis for active pre-MBT genes and active MBT genes. The analysis was performed with MEME on the 200 bp long region centered on the TSS. The number of occurrences, p-value and the density distributions relative to the TSS of the identified motifs are shown on the right. Note that all motifs are found with the highest frequency at the expected location but that the DPE/MTE/PB is less specific and more frequently found at positions where it is unlikely to be functional. DOI: http://dx.doi.org/10.7554/eLife.00861.014

Article Snippet: Using MEME v4.8.1 ( ) the fasta files were processed using the following parameters: -mod zoops -dna -nmotifs 50 -revcomp -maxw 12 -maxsize 5000000 -oc meme/ The resulting motifs were then compared against the TRANSFAC 2011.4 database and the listed above using the TOMTOM tool also from the MEME suite.

Techniques: Binding Assay, Functional Assay