The cell uses post-translational modifications of histone proteins to help organize the genome, and these modifications impact transcriptional regulation and other genomic processes. I developed a chemical strategy to incorporate methyl lysine analogues into recombinant histones (Simon et al. Cell, 2007) that is now widely used to study the direct biochemical impact of histone lysine methylation. These reagents have provided insight into the structure and mechanisms underlying chromatin regulation. For example, in collaboration with the Luger and Hansen laboratories we solved high-resolution structures of histone H3 Kc79me2 (where Kc denotes the methyl-lysine analogue) incorporated into histone octamer in the context of a nucleosome (Lu et al. Nat Struct Mol Bio, 2008). We also showed that methylation of one residue of histone H4 (K20) is sufficient to induce chromatin compaction in vitro. With these specifically methylated histones, I worked with many groups to investigate key biological questions, such as the role of histone H3 K27 methylation in the stability of polycomb proteins during replication (Francis et al. Cell, 2009), and how HP1 leads to the formation of heterochromatin fibers in vitro, revealing methylation-dependent oligomerization of HP1 (Canzio et al. Mol Cell, 2011). These methyl lysine analogues are widely used by other labs, and are particularly useful in structural studies of chromatin (e.g., Poepsel et al. Nat Struct Mol Bio 2018).
Our work has also contributed to our understanding of how lncRNAs impact chromatin regulation. It has been suggested that these lncRNAs direct histone-modifying complexes to specific chromatin loci. As a postdoctoral fellow, Matt developed CHART (capture hybridization analysis of RNA targets), a hybridization-based technique that specifically enriches endogenous RNAs along with their targets from reversibly-crosslinked chromatin extracts (Simon et al. PNAS, 2012). In the Simon Lab at Yale, we used CHART to study Xist, revealing a two-step spreading mechanism for the Xist lncRNA that drives dosage compensation in mammals (Simon, Pinter, Fang, et al. Nature, 2013).