Breakers and amplifiers in chromatin circuitry: acetylation and ubiquitination control the heterochromatin machinery

Abstract

Eukaryotic genomes are segregated into active euchromatic and repressed heterochromatic compartments. Gene regulatory networks, chromosomal structures, and genome integrity rely on the timely and locus-specific establishment of active and silent states to protect the genome and provide the basis for cell division and specification of cellular identity. Here, we focus on the mechanisms and molecular machinery that establish heterochromatin in Schizosaccharomyces pombe and compare it with Saccharomyces cerevisiae and the mammalian polycomb system. We present recent structural and mechanistic evidence, which suggests that histone acetylation protects active transcription by disrupting the positive feedback loops used by the heterochromatin machinery and that H2A and H3 monoubiquitination actively drives heterochromatin, whereas H2B monoubiquitination mobilizes the defenses to quench heterochromatin.

Figure 1

S. pombe heterochromatin complexes combine RNAi and chromatin modifiers anchored to the H3K9me2/3 platform. (a) The model of the RITS complex based on the crystal structures of the Chp1 chromodomain (PDBID:3G7L) and the Chp1-Tas3 subcomplex shows how Ago1 (model) and siRNAs are connected to H3K9me2/3 [17,65]. Although homology with mammalian silencing complexes has long been elusive, recent structural work on the mammalian HUSH silencing complex has revealed a similar architecture to the RITS complex [66]. CD: chromodomain. (b) The model based on crystal structures of the nucleosome remodeling and deacetylation complex SHREC shows how the building blocks assemble on the Clr1 scaffold into a remodeler module targeted to H3K9me2/3 and an HDAC module guided by the MBD-like Clr2 subunit [26,38]. Arb2: Arb2 domain. (c) Proposed structure of the CLRC complex, which is closely related to Cul4-ring ligases (CRL4) and targeted by the WD40 protein Dos1 to the ubiquitination target histone H3 lysine 14. Clr4 is a subunit of CLRC and recognizes the ligation product H3K14ub, which strongly stimulates H3K9 methyltransferase activity. However, it remains poorly understood how Clr4 associates with the E3 ligase [23]. LIM: LIM domain.

Figure 2

H3K14 is central in the compartmentalization of S. pombe chromatin. (a) The interconnected chromatin marks H2Bub, H3K4me, H3K9ac, and H3K14ac mark loci of active gene transcription due to the full complement of elongation factors that is associated with elongating PolII. H3K9 and H3K14 acetylation directly suppresses heterochromatin formation on actively transcribed genes through inhibition of the CLRC complex. Transparent nucleosomes indicate increased histone turnover by the RSC remodeler and histone chaperones like Nap1, which contributes to maintenance of euchromatin. All tails and modifications in blue refer to H3. (b) SHREC and Sir2 recruitment is necessary to provide a ‘blank’ template where heterochromatin can form through recruitment of CLRC by RITS and other mechanisms. Licensing of H3K9 methylation by H3K14ub allows for the establishment of heterochromatic feedback loops that rely on the chromodomain proteins of the RITS, SHREC, and CLRC complexes (see Fig. 1).

Figure 3

H4K16ac and H3K79me repel Sir3 in S. cerevisiae: (a) H4K16ac repels Sir3–nucleosome binding. In heterochromatin, Sir2 deacetylates H4K16ac in an NAD-dependent manner, allowing stable binding of Sir3 to the NCP by the interaction of H4K16 with a negatively charged pocket of Sir3. The Sir3 BAH domain is shown in complex with both sides of the NCP disk surface (PDB: 3TU4) [67]. (b) Dot1 histone methyltransferase docks onto the nucleosome acidic patch and makes contacts with H2BK123ub and H4K16ac that stimulate SAM-dependent- transfer of a methyl group to generate H3K79me, a marker of euchromatin. Dot1 in complex with the H4K16ac NCP disk surface is shown, (PDB:7K6Q) [50].

Figure 4

Ubiquitin and H3K27me3 promote polycomb silencing. (a) The crystal structure of PRC2 (PDBID:5KJH) reveals how the H3K27me3 peptide bound to Eed communicates with the Ezh2 SET domain (blue) through the Suz12 SRM (pink) and SAL (green) domains. This was adapted from Ref. [59]. (b) H2AK119ub is recognized by the JARID2 and AEBP2 subunits of PRC2 (PDBID:6WKR) [63]. (c) Feedback between PRC1 and PRC2 drives transcriptional repression. PRC1 deposits H2AK119ub, which, together with H3K27me-mediated stimulation through EED, guides PRC2 H3K27 methyltransferase activity. H3K27 me further recruits PRC1 through the Cbx chromodomain.