Pioneer activity of an oncogenic fusion transcription factor at inaccessible chromatin

Abstract

Recent characterizations of pioneer transcription factors have led to new insights into their structures and patterns of chromatin recognition that are instructive for understanding their role in cell fate commitment and transformation. Intersecting with these basic science concepts, the 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. In this study, we define the cellular and chromatin localization of the translocation, PAX3-FOXO1, an oncogenic driver of childhood rhabdomyosarcoma (RMS), derived from a genetic fusion of PFs. To quantitatively define its chromatin-targeting functions and capacity to drive epigenetic reprogramming, we developed a new method for ChIP-seq with per-cell normalization (pc-ChIP-seq). Our quantitative localization studies address structural variation in RMS genomes and reveal novel insights into heterochromatin localization of PAX3-FOXO1. From these studies, we report novel pioneer function for the major driver oncogene in RMS, with repressed chromatin binding and nucleosome-motif targeting in human cells.