- Luna-Zurita, Luis;
- Stirnimann, Christian U;
- Glatt, Sebastian;
- Kaynak, Bogac L;
- Thomas, Sean;
- Baudin, Florence;
- Samee, Abul Hassan;
- He, Daniel;
- Small, Eric M;
- Mileikovsky, Maria;
- Nagy, Andras;
- Holloway, Alisha K;
- Pollard, Katherine S;
- Müller, Christoph W;
- Bruneau, Benoit G
Transcription factors (TFs) are thought to function with partners to achieve specificity and precise quantitative outputs. In the developing heart, heterotypic TF interactions, such as between the T-box TF TBX5 and the homeodomain TF NKX2-5, have been proposed as a mechanism for human congenital heart defects. We report extensive and complex interdependent genomic occupancy of TBX5, NKX2-5, and the zinc finger TF GATA4 coordinately controlling cardiac gene expression, differentiation, and morphogenesis. Interdependent binding serves not only to co-regulate gene expression but also to prevent TFs from distributing to ectopic loci and activate lineage-inappropriate genes. We define preferential motif arrangements for TBX5 and NKX2-5 cooperative binding sites, supported at the atomic level by their co-crystal structure bound to DNA, revealing a direct interaction between the two factors and induced DNA bending. Complex interdependent binding mechanisms reveal tightly regulated TF genomic distribution and define a combinatorial logic for heterotypic TF regulation of differentiation.