The Local Density of H3K9me3 Dictates The Stability of HP1a Condensates-mediated Genomic Interactions

The human genome can be demarcated into different domains based on distinct epigenetic states. The trimethylation of histone H3 lysine 9 (H3K9me3) is essential for the formation of constitutive heterochromatin nanodomains. It is unclear what degrees or densities of H3K9me3 in genomic regions are required for their stable interactions. We demonstrate that the levels of H3K9me3 at the loci are positively correlated with their association with HP1a condensates. Epigenetic perturbation-induced Genome organization (EpiGo)-KRAB introduces ~20 kilobases of H3K9me3 at the TCF3 locus, which is sufficient to establish a stable association between TCF3 and HP1a condensates. In addition, EpiGo-mediated H3K9me3 also led to stable genomic interaction between IDR3 and TCF3. In sum, these data suggest that the density of H3K9me3 could dictate the stability of interactions between genomic loci and HP1a condensates. Here we utilize CRISPR-based DNA imaging to investigate the role of endogenous or ectopic H3K9me3 in chromatin dynamics and genomic interactions. Three loci (IDR3, TCF3 and PR1) with distinct levels of H3K9me3 were chosen to examine the genomic interactions and their association with endogenous HP1a condensates, a heterochromatin marker.