Histone H3.3K27M Regulates the Chromatin Landscape in Diffuse Intrinsic Pontine Glioma

Diffuse intrinsic pontine glioma (DIPG) is a fatal pediatric brain tumor with the average survival being only a year. To date the only treatment is radiotherapy, but it is not very effective leaving a need to better understand DIPG biology to develop more effective treatment methods. About 80% of DIPGs have a point mutation in one allele of H3F3A, one of two genes that codes for histone variant H3.3, resulting in lysine 27 being mutated to methionine. The H3.3K27M mutation is thought to be one of the first mutations to take place in DIPG tumorigenesis and results in the global depletion of the repressive mark H3K27me3 and an increase in the activating mark H3K27ac. In order to further investigate the effects of H3.3K27M and its subsequent abrogation on normal histone post-translational modifications (PTMs) patterns, we used CRISPR-Cas9 to revert H3.3K27M back to wild-type H3.3 in two patient DIPG cell lines. Here I used ATAC-seq in these isogenic cell lines to study the unique chromatin structure and function at work in DIPG tumors, including specifically what features are due to the H3.3K27M mutation as opposed to other mutations DIPGs are known to have. H3.3K27M results in increased chromatin accessibility surrounding genes that regulate neurogenesis and neuronal development, processes that have been found to be key in DIPG tumor formation and maintenance. The binding sites of several transcription factors including NOTCH signaling factor ASCL1 are enriched in unique open chromatin regions in K27M cells. This provides further support for drug treatments targeting NOTCH signaling and ASCL1. Overall, these studies indicate that both wildtype and mutant H3.3 are key regulators of chromatin dynamics and that K27M likely drives aberrant transcription in DIPG in part through altered chromatin structure