Functionally Coherent Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling

Abstract

BackgroundCell identity is governed by gene expression, regulated by Transcription Factor (TF) binding at cis-regulatory modules. Decoding the relationship TF binding patterns 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 neutral is a current challenge. We studied cell identity in the context of Epithelial to Mesenchymal Transition (EMT), a cell programme fundamental for normal embryonic development that contributes to tumour progression and fibrosis.\n\nResultsWe developed the NetNC software for discovery of functionally coherent TF targets. NetNC was applied to analyse gene regulation by the EMT TFs Snail, Twist in early embryogenesis and also to modENCODE HOT regions. 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 NetNC analysis predicted new gene functions; for example, evidencing networks that reshape Waddingtons landscape during EMT-like phenotype switching. Predicted invasion roles for SNX29, ATG3, UNK and IRX4 were validated using a tractable cell model.\n\nConclusionsWe found extensive neutral TF binding across the nine datasets examined and showed that NetNC performs well in identifying functionally coherent targets. HOT regions had comparatively high functional coherence. Our results illuminate conserved molecular networks that regulate epithelial remodelling in development and disease, with potential implications for precision medicine.