Coherent Transcription Factor Target Networks Illuminate Epithelial Remodelling and Oncogenic Notch

Cell identity is governed by gene expression, regulated by Transcription Factor (TF) binding at cis-regulatory modules. Decoding the relationship between patterns of TF binding and the regulation of cognate target genes is nontrivial, remaining a fundamental limitation in understanding cell decision-making mechanisms. Identification of TF physical binding that is biologically 9neutral9 is a current challenge. We present the 9NetNC9 software for discovery of functionally coherent TF targets, applied to study gene regulation in early embryogenesis. Predicted neutral binding accounted for 50% to >=80% of candidate target genes assigned from significant binding peaks. Novel gene functions and network modules were identified, including regulation of chromatin organisation and crosstalk with notch signalling. Orthologues of predicted TF targets discriminated breast cancer molecular subtypes and our analysis evidenced new tumour biology; for example, predicting networks that reshape Waddington9s landscape during EMT-like phenotype switching. Predicted invasion roles for SNX29, ATG3, UNK and IRX4 were validated using a tractable cell model. This work illuminates conserved molecular networks that regulate epithelial remodelling in development and disease, with potential implications for precision medicine.