Ellen V. Rothenberg Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA Corresponding author: evrothits.caltech.edu Abstract

Transcription factors are defined by their sequence-specific binding to DNA and by their selective impacts on gene expression, depending on specific binding sites. The factor binding motifs in the DNA should thus represent a blueprint of regulatory logic, suggesting that transcription factor binding patterns on the genome (e.g., measured by ChIP-seq) should indicate which target genes the factors are directly controlling. However, although genetic data confirm high impacts of transcription factor perturbation in embryology, transcription factors bind to far more sites than the number of genes they dynamically regulate, when measured by direct perturbation in a given cell type. Also, deletion of carefully chosen transcription factor binding sites often gives disappointingly weak results. In a new study in the previous issue of Genes & Development, Lo and colleagues (pp. 1079–1095) reconcile these contradictions by using an elegant experimental system to directly compare the roles of transcription factor–binding site interaction in gene regulation maintenance with roles of the same factor–site interactions in gene regulation through developmental change. They examine Oct4:Sox2 shared target genes under maintained versus reinduced pluripotency conditions within the same cell clone. The results show that the same factor–site interaction impacts can appear modest in assays in developmental steady-state but are far more important as regulatory catalysts of developmental change.