Interrogating the role of the histone mark H3K9me3 in D. melanogaster Genome Organization and Gene Regulation

Organization of chromatin in three-dimensional (3D) space impacts DNA-templated events by controlling the accessibility of transcriptional machinery to the underlying DNA sequence. Despite its importance in regulating genome function, the mechanisms controlling 3D architecture remain poorly understood. Here, we examine the contribution of histone post-translational modifications (PTMs), a feature of chromatin that is highly correlated with 3D genome organization, but whose role has not been directly tested. In particular, we interrogate the role for the heterochromatin-correlate, histone H3 lysine 9 trimethylation (H3K9me3), in governing 3D organization of the D. melanogaster genome. We directly test the contribution of H3K9me3 by using a genetic platform in which the endogenous histone gene locus has been deleted and replaced with transgenic versions encoding non modifiable histone H3K9. H3K9me3 provides a binding site for heterochromatin protein 1 (HP1), which has been implicated in liquid-liquid phase separation, a biophysical property that separates molecules in 3D space. Given this property of HP1 and it’s localization to H3K9me3, we hypothesize H3K9me3 demarcates regions of the genome that become physically separated from other regions of the genome. We perform a comprehensive analysis of genomics data, including HiC and RNA-seq, from H3K9me3-deficient D. melanogaster to assess the direct impact of H3K9me3 loss to 3D organization.