Large Scale Discovery of Promoter Motifs in Drosophila melanogaster

Abstract

A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs) that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes.

Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex

“…The motif Dpm5 (TGGCAAC), observed at 15.3% of promoters, bears significant identity to the Ohler8 motif (-YGGCARC-) in D. melanogaster (Ohler et al 2002). Dpm5 is enriched at +50 ( Figure 5D); the D. melanogaster Ohler8 motif has an equivalent, but more modest, peak at the same position (Down et al 2007). The cis-regulatory role of Ohler8 is unknown, but it has been validated separately on several occasions since its initial discovery (Fitzgerald et al 2006;Hoskins et al 2011).…”

Juvenile hormone and its receptor, methoprene-tolerant, control the dynamics of mosquito gene expression

“…Along with conservation, the binding sites of many transcription factors show bias for a certain position within the upstream regions, because these transcription factors can act most effectively when at a certain distance from the TSS (29,30). The effect of positional bias for transcription factor binding sites has been observed in insects (31), vertebrates (32,33), and plants (34). In our case, the in silico analysis determined that Metbinding motif variants showed a strong positional bias for the first 300 bases of the promoters of iMet-down-regulated genes.…”

Evolution of genes and genomes on the Drosophila phylogeny

“…This is consistent with previous findings that transcription factor binding sites tend to be found in larger blocks of constraint that cluster to form cis-regulatory modules 150 . To understand selective constraints on nucleotides within cis-regulatory sequences that have direct contact with transcription factors, we estimated the selective constraint for the best match to position weight matrices within each footprint 151 ; core motifs in transcription-factor-binding sites have a mean constraint of 0.773 (0.729-0.814), significantly greater than the mean for the footprints as a whole, and approaching the level of constraint found at non-degenerate coding sites and in ncRNA genes ( Supplementary Fig. 10).…”