DEV02746 Supplementary Material

Files in this Data Supplement:

• Supplemental Table S1-6 -

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• Supplemental Table S7 -

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• Supplemental Table S8 -

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• Supplemental Figure 1 -

  Fig. S1. In situ hybridization of newly identified Hox downstream genes in arm::Hox embryos. (A) Selected genes responsive to Dfd induction: wingless (wg), giant (gt), CG3097, Muscle protein 20 (Mp20), disconnected (disco), Ance. (B) Selected genes responsive to Scr induction: Heat shock protein 23 (Hsp23), LysE. (C) Selected genes responsive to Antp induction: CG8193, pavarotti (pav), CG17052, Ance. (D) Selected genes responsive to Ubx induction: CG8193, LysE, Hsp23, CG17052, CG3097, Mp20. (E) Selected genes responsive to Abd-A induction: CG3097, Mp20. (F) Selected genes responsive to Abd-B induction: singed (sn), LysE, Hsp23, masquerade (mas), wrapper, Wrinkled (W).

• Supplemental Figure 2 -

  Fig. S2. Description of Hox response element finder. (A) Flow-chart of bioinformatics approach used to identify Hox response elements. (B) Position Frequency Matrix (PFM) and parameters used for identification of clusters of Dfd-binding sites using cis-Analyst are shown. (C) Predicted Dfd response elements do not interact with Ubx, another Hox protein. EMSA with response elements for four predicted direct Dfd target genes − fz2, CG5756, wg and Eip63E − using no protein, translation lysate only (L) and lysate with Ubx protein (U) are shown. As a positive control, an Ubx consensus sequence was used. Under the same experimental conditions, the Ubx consensus sequence is strongly bound by Ubx, whereas all predicted Dfd enhancers do not interact with Ubx protein. cons, Ubx consensus binding sequence (5′-TTAGCGATGATTAATTGCCTCCTT-3′). Asterisk marks unspecific binding of lysate protein.

• Supplemental Figure 3 -

  Fig. S3. In situ hybridization of unique and regional Hox downstream genes in embryos ubiquitously mis-expressing any of the Hox genes used in this study. The expression of three unique Hox downstream genes, as identified in the microarray experiment, is shown in the light gray box. singed (sn) and wrapper are two examples of genes repressed by Abd-B only; ImpL2 is one example that is activated by Abd-B only and not regulated by any other Hox gene. In the dark gray box, one regional Hox downstream gene, as identified in the microarray experiment, is shown. sage is induced by Scr and repressed by Ubx and Abd-A, which is also demonstrated by the in situ hybridization.