A two-way analysis of Dichaete and SoxN binding in two species of Drosophila reveals that the majority of conserved intervals are commonly bound by both TFs, leading us to identify a list of conserved, common group B Sox targets, while an analysis of uniquely bound conserved intervals provides indications as to the features that differentiate Dichaete and SoxN functions during development.
Since 14-3-3 14-3-3 14-3-3essed in T cells and 14-3-3 θ (or τ) was initially identified as an isoform that uniquely bound active but not inactive Vpr mutants [ 11, 28], we focused on the θ isoform and observed a partial reduction (50–60%) in Vpr-induced G2,M arrest upon 14-3-3 θ knockdown as indicated by the decreased ratio of G2,M to G1 cells (Fig. 1B,C).
In addition, we have recently analysed the genomics of SoxN in the Drosophila embryo and find very substantial overlap between Dichaete and SoxN binding as well as a repertoire of genes uniquely bound by each gene (EF and SR, in preparation).
Additionally, a de novo motif search in the uniquely bound SoxN intervals uncovered a motif corresponding to Ultraspiracle (Usp), a TF involved in several aspects of neuron morphogenesis [ 97, 98].
In PFAM, each ligand is uniquely bound to a protein domain (Supplementary Fig. 1), in other words one entry per domain ligand combination.
Interestingly, DNA packaging, which has been suggested to be a function of E2F4 in murine cells [27], was enriched as a functional category in the genes uniquely bound by E2f4 in mouse (Figure 2D, Figure S7).
KEGG pathway analysis revealed a shortlist of genes whose promoters uniquely bound MYCN in the over expressing state and who are members of established signalling pathways which are dysregulated in cancer.
Dichaete has previously been shown to bind together with Ventral veins lacking (Vvl) in the midline [ 50, 56]; we have identified an enriched motif for the hindgut-specific factor Byn in uniquely bound, conserved Dichaete intervals, which may represent a similar interaction.
Nonetheless, despite the overall high level of binding conservation, the increase in conservation at commonly bound sites compared to uniquely bound sites, with 94% of commonly-bound D. simulans sites being conserved in D. melanogaster, is striking and highly significant.
Approximately 80% of the bound genes that had homologs in the second species were uniquely bound in the first species; only a fifth of the bound homologous genes shared E2F4 binding between species.
