An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

Profiling the genomic binding activity of regulatory proteins in multiple cell types is important for understanding cellular function, as a single regulator can bind to distinct sets of genomic targets depending on the cellular context in which it is expressed. Characterizing the determinants of such differential binding specificity is key to understanding how a single regulator can play multiple roles during development and other dynamic cellular processes. For example, pre-existing chromatin context such as chromatin accessibility or the binding of other regulators may determine the binding of some developmental transcription factors TFs [1,2], while other pioneer TFs may find their binding targets independently of the established chromatin state [3]. In order to reliably characterize such condition-specific regulatory activity, we require methods that can integrate analysis across multiple related experiments in a principled way.