HP1 can act independently of H3K9 methylation to promote heterochromatin focus formation, gene repression, and organogenesis.

Abstract

Histone post-translational modifications (PTMs) segregate genomes into heterochromatin and euchromatin by recruiting readers, such as Heterochromatin Protein 1, which binds methylation of histone H3 lysine 9 (H3K9me). Here, we report H3K9me-independent functions for the C. elegans HP1 orthologue HPL-2 and the H3K9 methyltransferase MET-2/SETDB1. The two colocalize in H3K9me-containing subnuclear foci independently of the PTM and each other. Their combined loss additively disrupts gene repression and organogenesis. A mutant HPL-2 deficient for H3K9me binding maintains localization to heterochromatin foci, restricts cell-fate decisions, and represses developmental genes, dependent on its multi-zinc-finger ligand, LIN-13. MET-2, catalytically active or not, requires its cofactor LIN-65 to form foci and silence genes in vivo. Molecular dynamics simulations and in vitro assays suggest that cofactor-driven condensate assemblies underlie H3K9me-independent focus formation in vivo, which correlates with gene silencing during organogenesis. This study defines two parallel, PTM-independent pathways through which a writer and reader can repress developmentally regulated genes.