Heterochromatin and Polycomb-associated regions are distinct forms of epigenetically silenced chromatin.
(A) Heterochromatin is marked by H3K9me3 deposited by the suppressor of variegation (SUV) 39-homologue enzymes (SUV39H1 and SUV39H2). These enzymes preferentially bind already monomethylated substrate (H3K9me1). H3K9me3 is recognised by heterochromatin protein 1 (HP1) which self-oligomerizes causing compaction of chromatin and rendering it inaccessible to the transcriptional machinery. HP1 in turn recruits SUV4-20H enzymes which deposit another histone mark of heterochromatin H3K20me3. (B) Polycomb-associated regions are particularly involved in cell-type-specific silencing of developmentally regulated genes and are marked by H3K27me3 deposited by the Polycomb repressive complex (PRC) 2 and H2A119ub1 deposited by the PRC1 complex. Polycomb-associated regions block transcription initiation but can remain accessible to the binding of transcription factors, unlike heterochromatin.