Computational approaches identify novel transcription factor combinations that promote corticospinal axon growth after injury

Abstract

Transcription factors (TFs) act as powerful levers to regulate neural physiology and can be targeted to improve cellular responses to injury or disease. Because TFs often depend on cooperative activity, a major challenge is to identify and deploy optimal sets. Here we developed a novel bioinformatics pipeline, centered on TF co-occupancy of regulatory DNA, and used it to predict factors that improve axon growth in corticospinal tract (CST) axons when combined with a known pro-regenerative TF, Klf6. Assays of neurite outgrowth confirmed cooperative activity by 12 candidates, and in vivo testing showed strong promotion of CST growth upon combined expression of Klf6 and Nr5a2. Transcriptional profiling of CST neurons identified Klf6/Nr5a2-responsive gene networks involved in macromolecule biosynthesis and DNA repair. These data identify novel TF combinations that promote enhanced CST growth, clarify the transcriptional correlates, and provide a bioinformatics roadmap to detect TF synergy.