Abstract
Here we present a quantitative and predictive model of the transcriptional readout of the proximal 1.7 kb of the control region of the Drosophila melanogaster gene even skipped (eve). The model is based on the positions and sequence of individual binding sites on the DNA and quantitative, time-resolved expression data at cellular resolution. These data demonstrated new expression features, first reported here. The model correctly predicts the expression patterns of mutations in trans, as well as point mutations, insertions and deletions in cis. It also shows that the nonclassical expression of stripe 7 driven by this fragment is activated by the protein Caudal (Cad), and repressed by the proteins Tailless (Tll) and Giant (Gt).
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Acknowledgements
We thank P. Gergen for comments on the manuscript. E.M., H.J., J.J., A.K. and J.R. were supported by US National Institutes of Health grant 2 ROI RR07801. D.S., H.J. and S.H. were supported in part by contract W-7405-ENG-36 from the US Department of Energy. H.J. received partial support from the State University of New York.
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Supplementary information
Supplementary Fig. 1
Matrix representing the quenching function q(d) for the 34-site model. (PDF 30 kb)
Supplementary Fig. 2
Expression data of transcription factors and lacZ mRNA. (PDF 55 kb)
Supplementary Fig. 3
Model output. (PDF 102 kb)
Supplementary Fig. 4
Parameter distribution. (PDF 41 kb)
Supplementary Fig. 5
Graphical analysis of expression in the posterior region of the embryo. (PDF 47 kb)
Supplementary Fig. 6
Regulatory analysis of expression near 64% AP position. (PDF 69 kb)
Supplementary Fig. 7
Regulatory analysis of stripe 2 formation. (PDF 55 kb)
Supplementary Table 1
Binding sites used in modeling. (PDF 87 kb)
Supplementary Table 2
Root mean square (rms) scores of models. (PDF 42 kb)
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Janssens, H., Hou, S., Jaeger, J. et al. Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nat Genet 38, 1159–1165 (2006). https://doi.org/10.1038/ng1886
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DOI: https://doi.org/10.1038/ng1886
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