Physical nature of chromatin boundary elements

Identify and characterize the physical mechanisms and molecular structures that act as boundary elements halting the propagation of H3K9me3-driven methylation waves (mediated by HP1 recruitment of SUV39H1 methylase) along one-dimensional arrays of nucleosomes, in order to explain how spreading is confined within heterochromatin domains.

Background

Classical one-dimensional models of epigenetic mark propagation posit that HP1 binds to H3K9me3-marked nucleosomes and recruits SUV39H1, catalyzing methylation of neighboring nucleosomes until a boundary element is reached. While such models reproduce domain-like structures, the actual physical identity and mechanism of these boundary elements have not been established.

This paper proposes that the sharp surface of a PAC-induced condensate could serve as the physical realization of boundary elements, but the general physical nature of boundary elements in vivo remains an explicitly stated unresolved issue in the literature and in the paper’s framing.