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High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

Abstract

The binding of some transcription factors has been shown to diverge substantially between closely related species. Here we show that the binding of the developmental transcription factor Twist is highly conserved across six Drosophila species, revealing strong functional constraints at its enhancers. Conserved binding correlates with sequence motifs for Twist and its partners, permitting the de novo discovery of their combinatorial binding. It also includes over 10,000 low-occupancy sites near the detection limit, which tend to mark enhancers of later developmental stages. These results suggest that developmental enhancers can be highly evolutionarily constrained, presumably because of their complex combinatorial nature.

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Figure 1: Evolutionary constraints on Twist binding across six Drosophila species.
Figure 2: High conservation of functional Twist binding across six Drosophila species.
Figure 3: Preferential conservation of clustered binding peaks.
Figure 4: Twist binding depends on the sequence motifs of Twist and its partner transcription factors.
Figure 5: Conservation of low-occupancy peaks.

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Acknowledgements

We would like to thank E. Furlong (European Molecular Biology Laboratory (EMBL)) and M. Levine (University of California Berkeley) for generously providing Twist antibodies; B. Dickson, W. Lugmayr, R. Revilla (IMP), C. Schlötterer (University of Veterinary Medicine Vienna), M. Levine (University of California Berkeley) and R. Krumlauf (Stowers Institute for Medical Research) for discussions, help and advice. A.F.B. was supported by the Austrian Ministry for Science and Research through the Genome Research in Austria (GEN-AU) Bioinformatics Integration Network III. J.Z. is a Pew scholar. A.S. is supported by an European Research Council (ERC) Starting Grant from the European Community's Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 242922.

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Authors and Affiliations

Authors

Contributions

Q.H. performed the ChIP experiments and library preparation, and J.J., A.P., M.G. and J.Z. established the ChIP-Seq pipeline. B.P. and J.P. raised the different Drosophila species, harvested the embryos and staged them, A.F.B. and A.S. analyzed the data, and Q.H., A.F.B., A.S. and J.Z. wrote the manuscript.

Corresponding authors

Correspondence to Alexander Stark or Julia Zeitlinger.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–19 and Supplementary Tables 1–6, 8–10 and 14–16. (PDF 2930 kb)

Supplementary Table 7

Conservation of D. melanosgaster Twist binding peaks in six Drosophila species (XLS 390 kb)

Supplementary Table 11

Quantitative changes of Twist binding peaks in all six Drosophila species (XLS 2360 kb)

Supplementary Table 12

GO analysis of invariant vs. variant peaks (XLS 446 kb)

Supplementary Table 13

GO analysis of genes near Twist binding peaks (XLS 588 kb)

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He, Q., Bardet, A., Patton, B. et al. High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat Genet 43, 414–420 (2011). https://doi.org/10.1038/ng.808

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