Structural Basis of Heterochromatin Formation by Human HP1

Abstract

Heterochromatin plays important roles in transcriptional silencing and genome maintenance by the formation of condensed chromatin structures, which determine the epigenetic status of eukaryotic cells. The trimethylation of histone H3 lysine 9 (H3K9me3), a target of heterochromatin protein 1 (HP1), is a hallmark of heterochromatin formation. However, the mechanism by which HP1 folds chromatin-containing H3K9me3 into a higher-order structure has not been elucidated. Here we report the three-dimensional structure of the H3K9me3-containing dinucleosomes complexed with human HP1α, HP1β, and HP1γ, determined by cryogenic electron microscopy with a Volta phase plate. In the structures, two H3K9me3 nucleosomes are bridged by a symmetric HP1 dimer. Surprisingly, the linker DNA between the nucleosomes does not directly interact with HP1, thus allowing nucleosome remodeling by the ATP-utilizing chromatin assembly and remodeling factor (ACF). The structure depicts the fundamental architecture of heterochromatin.

Local states of chromatin compaction at transcription start sites control transcription levels

“…Thus, HP1a, MBD2b, and histone H1 may all be selectively recruited to their marks. Previous experiments with reconstituted chromatin showed that HP1a bridges two adjacent nucleosomes (Machida et al, 2018), and that histone H1 promotes condensation among three nucleosomes (White et al, 2016). In addition, an in vivo imaging study showed that histone H1 is preferentially incorporated into "clutches" of a few nucleosomes (Ricci et al, 2015).…”

On the relation of phase separation and Hi-C maps to epigenetics

“…(ii), HP1 can act as a "bridge" between H3K9me3-marked nucleosomes (46,74,77) and, (iii), HP1 can also act as a bridge between distantly located loci (73,74), it is unsurprising that the KRAB-ZNF heterochromatin-like domains ("blocks") make far cis-contacts that emerge as the B4 sub compartment in Hi-C maps (105).…”

“…Bridging by HP1 proteins has been definitively demonstrated through elucidation of the three-dimensional structure of H3K9me3-containing di-nucleosomes complexed with human HP1α, β or γ 77 ( Figure 2). Two H3K9me3 nucleosomes are bridged by a symmetric HP1 dimer via the H3K9me3-CD interaction; the linker DNA between the nucleosomes does not directly interact with HP1 77 . in vivo FRAP studies indicate that the binding of HP1 to H3K9me3-marked nucleosomes is dynamic and transient but the rapid and constant exchange with unbound HP1 in the nucleoplasm [55][56][57] would maintain the bridging interactions.…”

“…between H3K9me3-marked nucleosomes 46,74,77 and, (iii), HP1 can also act as a bridge between distantly located loci 73,74 , it is unsurprising that the KRAB-ZNF heterochromatin-like domains ("blocks") make far cis-contacts that emerge as the B4 sub compartment in Hi-C maps 105 . Importantly, treating chromatin fibres as BCPs has been used with considerable success to accurately simulate contact maps derived from Hi-C experiments 154,[163][164][165][166] .…”

“…For one, a liquid droplet would surround chromatin whereas the lacI-HP1a forms a tightly-localised domain at lacO (74). Further, the bridging effects observed in vitro and in vivo are mediated by direct stereospecific interactions requiring the modular domains of HP1 (73,74,77), whereas liquid droplets pull genomic regions together by proxy via surface tension driven coalescence (70).…”