Extraction of Functional Binding Sites from Unique Regulatory Regions: The Drosophila Early Developmental Enhancers

Abstract

The early developmental enhancers of Drosophila melanogaster comprise one of the most sophisticated regulatory systems in higher eukaryotes. An elaborate code in their DNA sequence translates both maternal and early embryonic regulatory signals into spatial distribution of transcription factors. One of the most striking features of this code is the redundancy of binding sites for these transcription factors (BSTF). Using this redundancy, we explored the possibility of predicting functional binding sites in a single enhancer region without any prior consensus/matrix description or evolutionary sequence comparisons. We developed a conceptually simple algorithm, Scanseq, that employs an original statistical evaluation for identifying the most redundant motifs and locates the position of potential BSTF in a given regulatory region. To estimate the biological relevance of our predictions, we built thorough literature-based annotations for the best-known Drosophila developmental enhancers and we generated detailed distribution maps for the most robust binding sites. The high statistical correlation between the location of BSTF in these experiment-based maps and the location predicted in silico by Scanseq confirmed the relevance of our approach. We also discuss the definition of true binding sites and the possible biological principles that govern patterning of regulatory regions and the distribution of transcriptional signals.

Quantitative contributions of CtBP-dependent and -independent repression activities of Knirps

“…Sequence analysis of the eve gene indicates that there are more high-affinity Knirps binding sites within the eve stripe 3/7 element than in the 4/6 enhancer, consistent with relative sensitivities of these elements that we determined experimentally (Fig. 3) (Papatsenko et al, 2002;Berman et al, 2002). Removal of some of the Knirps binding sites in the eve stripe 3/7 enhancer reduces the sensitivity of this element to the Knirps gradient (Clyde et al, 2003).…”

Nucleosome-mediated cooperativity between transcription factors

“…(i.e., 4-6 sites per nucleosome) (2). Similarly, the cis-regulatory system of endo16 in sea urchins has about 50 sites localized within 2.3 Kb and grouped into seven clusters of five to 10 sites (4).…”

“…protein-DNA interactions | promoter | enhancer | histone | Monod-Wyman-Changeux I n higher eukaryotes, cis-regulatory regions are 200 to 3,000 base pairs (bps) in length and may contain clusters of 3 to 50 TF binding sites (TFBSs) (1)(2)(3)(4). The arrangement, identity, and affinity of the sites determine the function of the regulatory region.…”

Social behavior and comparative genomics: new genes or new gene regulation?

“…This will involve new techniques to identify regulatory sequences from the honey bee genome using the Drosophila sequence (Berman et al 2002) and new enhancer prediction algorithms to identify novel candidate cisregulatory sequences in the honey bee genome (Ishihara et al 2000;Papatsenko et al 2002).…”