Eukaryotic transcription factors (TFs) form complexes with various partner proteins to recognize their genomic target sites. Yet, how the DNA sequence determines which TF complex forms at any given site is poorly understood. Here we demonstrate that high-throughput in vitro binding assays coupled with unbiased computational analysis provides unprecedented insight into how complexes of homeodomain proteins adapt their stoichiometry and configuration to the bound DNA. Using inferred knowledge about minor groove width readout, we design targeted protein mutations that destabilize homeodomain binding in a complex-specific manner. By performing parallel SELEX-seq, ChIP-seq, RNA-seq and Hi-C assays, we not only reveal complex-specific functions, but also show that TF binding sites that lack a canonical sequence motif emerge as a consequence of direct interaction with functionally bound sites.
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