Biochemical and Cellular Libraries Reveal Cancer-Associated Histone Mutations That Perturb Nucleosome Structure and Inhibit Cell Differentiation

Recent whole genome sequencing data mining efforts have revealed thousands of mutations in histones, the DNA-packaging proteins in eukaryotic genomes, across a wide range of cancer types. These occur in all four core histones in both the unstructured tail and folded globular domains and remain largely uncharacterized. Here we used two high-throughput approaches, a DNA-barcoded mononucleosome library and a humanized yeast library, to profile the biochemical and cellular effects of these mutations. We identified cancer-associated mutations in the histone globular domains that enhance fundamental chromatin remodeling processes, nucleosome sliding and histone exchange, and are lethal in yeast. In mammalian cells these mutations promote cancer phenotypes, upregulating cancer-associated gene pathways and inhibiting cellular differentiation by altering expression of lineage-specific transcription factors. This work represents the first comprehensive functional analysis of the histone mutational landscape in human cancers, and leads to a model in which histone mutations that perturb nucleosome remodeling can contribute to the development of cancer phenotypes.