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Files in this Data Supplement:
Fig. S1. Conservation of the col upstream region and embryonic expression. (A) Col expression in stage 9-15 D. vir embryos, as visualised by Col antibody staining. (B) VISTA plot (Couronne et al., 2003) of the D. melanogaster col upstream region aligned with genomic sequences from D. yakuba, D. ananassae, D. pseudobscura, D. mojavensis and D. virilis. A window size of 100 bp was used. Regions greater than 70% identical are shown in orange; the col 5′ coding exon is in blue. The relative positions of the 5′ ends of P9cl, P5cl and P2.6cl and conserved motifs 1-10 are indicated.
Fig. S2. Conserved sequence motifs in the 2.6 kb col upstream region. Nucleotide sequence of the D. mel col upstream region from −2626 (P2.6cl) to +560 that corresponds to the fusion site with lacZ in Pcl reporter genes (see Fig. 1A). The col transcription start site and initiator ATG (+513) are indicated in bold red. The 5′ restriction sites (Xho1, Swa1, Xmn1, EcoR1) used for cloning of different fragments of the col promoter are in italics; the name of the corresponding reporter construct is indicated in the margin. The >20 bp sequence motifs conserved at the same relative positions in D. mel, D. pseudobscura and D. vir are shaded in blue and numbered from 1 to 10, as indicated in the margin; additional shorter conserved motifs are shaded in grey. Putative binding sites for the TFs MyoD/Nautilus (GACAGCTGTC) (Huang et al., 1996; Kophengnavong et al., 2000; Zhang et al., 1999), Twist homodimers (CATATG) (Ip et al., 1992; Kophengnavong et al., 2000; Castanon et al., 2001), EBF/Collier (TTCC/TCNNGGGAA) (Travis et al., 1993) and Mef2 (TCAAAAATAGA) (Andres et al., 1995) are in bold and underlined in red. Annotation is limited here to those sites found at conserved positions in the six Drosophila species used in our comparisons (see Fig. S1). The Mef2 site is only partly conserved in D. vir.
References
Couronne, O., Poliakov, A., Bray, N., Ishkhanov, T., Ryaboy, D., Rubin, E., Pachter, L. and Dubchak, I. (2003). Strategies and tools for whole-genome alignments. Genome Res. 13, 73-80.
Zhang, J. M., Chen, L., Krause, M., Fire, A. and Paterson, B. M. (1999). Evolutionary conservation of MyoD function and differential utilization of E proteins. Dev. Biol. 208, 465-472.
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