(A, B, C) The Drosophila bZIP protein CG30420 recognizes a site that is different from those recognized by its human orthologs ATF2 and ATF7. Box in B indicates the position whose specificity is diverged between fruit fly and human. Note that CG30420 recognizes a 10-mer ATGACGTGAT that is not bound by ATF7. Enrichment of 10-mers in CG30420 and ATF7 experiments is shown in panel C, oval indicates 10-mers preferentially recognized by CG30420. Two-dimensional color scale indicates the score of each k-mer against CG30420 and ATF7 PWM models (red indicates strong match to both, violet and green strong matches to only CG30420 and ATF7, respectively). For replicates and structural analysis, see Figure 7—figure supplement 1. (D, E) The diverged binding specificities between Drosophila and human in nuclear receptor subfamily. Whereas, all human NR1I subfamily genes (VDR, NR1I2, NR1I3) recognize a motif containing direct repeat of a GTTCA motif, Hr96 (NR1J subfamily) recognizes tail-to-tail dimer of a different half-site, GT(G/T)CA. Drosophila knrl (NR0 subfamily), which has no human ortholog, recognizes a G(A/G)(G/T)CA motif, which is not recognized by any human nuclear receptor. The diverged position in NR1 subfamily is indicated by red triangle. Dendrograms in A and D show amino-acid sequence similarity of the DNA-binding domains. (F) Summary of biological roles of TFs with divergent specificities. Cell types and biological functions are indicated in green in Drosophila (left) and human (right). For some TFs with multiple functions (e.g., bZIP and HOX proteins, nuclear receptors), only one divergent role is shown for clarity. In addition to their divergent roles, Hr96 and its orthologs have also shared functionality (xenobiotic responses; (King-Jones et al., 2006; Reschly and Krasowski, 2006)). Note that TFs with novel specificities are often associated with cell types that do not exist in the other organism. References: 1(Lunde et al., 1998); 2(Hsouna et al., 2004); 3(Boll and Noll, 2002); 4(Horner et al., 2009); 5(Schwank et al., 2008); 6(Doumpas et al., 2013); 7(Seong et al., 2011); 8(Gregorieff et al., 2009); 9(Bartel et al., 2000); 10(Lu et al., 2003); 11(Oliveira et al., 2004); 12(Pardee et al., 2011); 13(Zakany and Duboule, 2007); 14(Maekawa et al., 1999); 15(Chen et al., 2012). Raw data and scripts are provided at Figure 7—source data 1.