Evidence of pioneer factor activity of an oncogenic fusion transcription factor

Recent characterizations of pioneer transcription factors provide insights into their structures and patterns of chromatin recognition associated with their roles in cell fate commitment and transformation. Intersecting with these basic science concepts, identification of pioneer factors (PFs) fused together as driver translocations in childhood cancers raises questions of whether these fusions retain the fundamental ability to invade repressed chromatin, consistent with their monomeric PF constituents. This study defines the cellular and chromatin localization of PAX3-FOXO1, an oncogenic driver of childhood rhabdomyosarcoma (RMS), derived from a fusion of PFs. To quantitatively define its chromatin-targeting functions and capacity to drive epigenetic reprogramming, we developed a ChIP-seq workflow with per-cell normalization (pc-ChIP-seq). Our quantitative localization studies address structural variation in RMS genomes and reveal insights into inactive chromatin localization of PAX3-FOXO1. Taken together, our studies are consistent with pioneer function for a driver oncoprotein in RMS, with repressed chromatin binding and nucleosome-motif targeting. [Display omitted] •The fusion oncoprotein PAX3-FOXO1 binds to both active and repressed chromatin•PAX3-FOXO1-binding sites are adjacent to H3K9me3 domains•PAX3-FOXO1 engages partial DNA motifs at early timepoints•PAX3-FOXO1 can bind stably to inaccessible chromatin without inducing accessibility Molecular Genetics; Systems biology; Transcriptomics