The chromatin signaling pathway: diverse mechanisms of recruitment of histone-modifying enzymes and varied biological outcomes

Abstract

Posttranslational modifications of histones are coupled in the regulation of the cellular processes involving chromatin, such as transcription, replication, repair, and genome stability. Recent biochemical and genetic studies have clearly demonstrated that many aspects of chromatin, in addition to posttranslational modifications of histones, provide surfaces that can interact with effectors and the modifying machineries in a context-dependent manner, all as a part of the "chromatin signaling pathway." Here, we have reviewed recent findings on the molecular basis for the recruitment of the chromatin-modifying machineries and their diverse and varied biological outcomes.

Figure 1. Coactivator and Corepressors are histone-modifying enzymes

(A) The histone acetyltransferase, Gcn5, as part of the SAGA complex, is recruited to genes by a variety of transcriptional activators such as the sequence-specific binding protein Gal4. Acetylation of histone H3 through recruitment of Gcn5 by Gal4 synergizes with nucleosome remodeling activities leading to the recruitment of RNA Pol II. (B) The histone deacetylase HDAC1 can be recruited to genes as part of the SMRT/NCOR complexes by sequence-specific DNA-binding proteins such as Retinoic acid receptors (RXR/RAR). Deacetylation of histones facilitates reassembly of compact chromatin for transcriptional repression.

Figure 2. Recruitment of histone-modifying activities by RNA Pol II

The histone H3K4 methyltransferase, Set1, as part of COMPASS, is recruited to genes through interaction with the Polymerase-associated factor (Paf1) complex (1) (Krogan et al., 2003a; Wood et al., 2003). H3K4 trimethylation is found at the start sites of the transcription of active genes, as well as “poised” genes with stalled RNA Pol II (Gilmour, 2009). Upon release of RNA Pol II by phosphorylation of its C-terminal domain (CTD) at serine 2 (P-Ser2), numerous factors associate with the phosphorylated C-terminal domain including the histone H3K36 methyltransferase Set2 (Xiao et al., 2003) (2). Set2 can be recruited through interactions with both the CTD of Pol II and the Paf1 complex (Krogan et al., 2003b; Xiao et al., 2003).

Figure 3. Recruitment of histone-modifying activities by preexisting histone modifications

Methylation of histone H3K36 in the body of actively transcribed genes (see Figure 2) can be bound by the chromodomain-containing protein, Eaf3, as part of the Rpd3S deacetylase complex. This process helps to reposition nucleosomes in the wake of transcribing RNA Pol II. In the absence of Rpd3S, nucleosomes are misplaced, resulting in the exposure of cryptic start sites that can lead to the formation of aberrant transcription. Thus, recruitment of Rpd3S by a histone modification placed by passing RNA polymerase complexes can maintain transcriptional fidelity. However, at most genes, Rpd3S can be recruited directly through the interaction with the Serine 5 phosphorylated form of the RNA Pol II CTD (Govind et al., 2010, F. Robert, unpublished data). These findings indicate that the relative contribution of H3K36 methylation and CTD phosphorylation on the recruitment of Rpd3S can be gene specific and context dependent.

Figure 4. Recruitment by DNA sequences

In humans, CpG islands are found near the promoters of 60–70 % of genes (Illingworth and Bird, 2009). While cytosines within CpG dinucleotides are frequently methylated, in CpG islands cytosines are largely unmethylated. (A) A number of proteins bearing a zinc finger of the CXXC class preferentially bind unmethylated CpG islands. These proteins are associated with a variety of histone-modifying activities including the H3K4 methyltransferases, MLL and Set1/COMPASS, and the H3K36 demethylase, KDM2A (Clouaire and Stancheva, 2008). MBD1 has two zinc fingers that bind methylated DNA and a third of the CXXC class that binds unmethylated DNA. MBD1 is associated with H3K9 methyltransferase activities and is thought to help coordinate silencing by DNA and histone methylations (Sarraf and Stancheva, 2004). (B) A recent study demonstrated that CpG islands were major sites of recruitment of CXXC1 (Cfp1) and H3K4 methylation via mammalian COMPASS, independent of the transcriptional status of the nearby gene (Thomson et al., 2010). (C) In another recent manuscript, KDM2A, an H3K36 demethylase, was found to be targeted to CpG islands via its CXXC motif. Since H3K36 methylation can recruit histone deacetylases (Figure 3), removal of H3K36 methylation in CpG islands could maintain CpG islands in an open, permissive state (Blackledge et al., 2010).

Figure 5. The same histone modification implemented by different complexes can have different consequences

(A) Mammalian Set1/COMPASS is recruited to chromatin of transcriptionally active genes through interaction with the Paf1 Complex (1) (Krogan et al., 2003a), where it is only capable of implementing H3K4 monomethylation. Upon H2B monoubiquitination (H2Bub) by Rad6/Bre1 (2), WDR82 (Cps35 in yeast) interacts with chromatin and associates with COMPASS (3), enabling the complex to trimethylate H3K4 (4), whose presence at promoters is a mark of actively transcribed genes (see Figure 2). (B) MLL is part of a COMPASS-like complex that shares many subunits, but importantly lacks WDR82, and therefore, its methyltransferase activity is likely to be independent of H2Bub. MLL, like its Drosophila homolog Trithorax, is well known for its role in activating Hox genes. Recruitment of MLL via Menin and sequence-specific binding factors could help activate transcription of its target loci by mediating trimethylation of H3K4 (1) which can form a binding site for TAF3, a component of TFIID in the pre-initiation complexes (PIC) (2), thereby, mediating recruitment or stabilization and the basal machinery (PIC) and RNA Pol II (3) (Vermeulen et al., 2007; Wang et al., 2009). Thus, H3K4 trimethylation implemented by the MLL complexes is instructive for transcription (Wang et al., 2009), while H3K4 trimethylation implemented by Set1/COMPASS may be recruited subsequent to initiation of transcription by PIC and RNA Pol II through the H2Bub-WDR82 pathway (Wu et al., 2008; Wang et al., 2009).