Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains

Abstract

On the histone H3 tail, Lys 9 and Lys 27 are both methylation sites associated with epigenetic repression, and reside within a highly related sequence motif ARKS. Here we show that the chromodomain proteins Polycomb (Pc) and HP1 (heterochromatin protein 1) are highly discriminatory for binding to these sites in vivo and in vitro. In Drosophila S2 cells, and on polytene chromosomes, methyl-Lys 27 and Pc are both excluded from areas that are enriched in methyl-Lys 9 and HP1. Swapping of the chromodomain regions of Pc and HP1 is sufficient for switching the nuclear localization patterns of these factors, indicating a role for their chromodomains in both target site binding and discrimination. To better understand the molecular basis for the selection of methyl-lysine binding sites, we solved the 1.8 Å structure of the Pc chromodomain in complex with a H3 peptide bearing trimethyl-Lys 27, and compared it with our previously determined structure of the HP1 chromodomain in complex with a H3 peptide bearing trimethyl-Lys 9. The Pc chromodomain distinguishes its methylation target on the H3 tail via an extended recognition groove that binds five additional residues preceding the ARKS motif. Chromatin structure contains the molecular imprint underlying cell memory and epigenetic inheritance, and emerging evidence suggests that covalent modifications of histones play a major role as carriers of epigenetic information (Felsenfeld and Groudine 2003). Histone modifications can be highly reversible, such as histone acetylation, or more stable, such as histone (lysine) methylation (Zhang and Reinberg 2001;Lachner and Jenuwein 2002). Thus, a wide range of chromatin-based regulatory options is available. These include dynamic marks permitting rapid changes in gene expression in response to physiological and environmental stimuli as well as more permanent indexing systems required for the passage of heritable patterns of epigenetic information from one cell generation to the next (Fischle et al. 2003). The identification of enzyme systems responsible for the steady-state balance of posttranslational histone modifications, together with the discovery of binding modules that "read" covalent marks on histones, have been key for our present understanding of gene regulation in the context of the chromatin polymer.Bromodomains have been the first modules implicated in the read-out of histone marks. They show affinity for acetylated lysines in histone and nonhistone proteins (for review, see Zeng and Zhou 2002), and local recruitment of bromodomain factors to certain regions of chromatin might function in mediating acetyl-histone-encoded antisilencing (Ladurner et al. 2003). In contrast, a second conserved module found in a variety of chromosomal proteins, the chromodomain, has been implicated in binding to methylated lysines on the histone tails (Bannister et al. 2001;Jacobs et al. 2001;Lachner et al. 2001). Indeed, recently a biochemical pathway of gene repression by heterochromatin assembly, involving methylation of Lys 9 of H3 by SE...

The four Rs of RNA-directed evolution

“…These promoters have a low level of transcriptional activity, give rise to short dsRNA products 41,42 and produce methylation of histone H3 at Lys27 (ref. 43). Involvement of RISC in the silencing of PREs is supported by its dependence on piwi, an argonaute family member 42 .…”

Linking the epigenetic ‘language’ of covalent histone modifications to cancer

“…Insights into SET domain structure and mode of catalysis are beginning to emerge (Min et al, 2002). 'ON' and 'OFF' methyl marks are 'read' by chromodomain-containing proteins, such as heterochromatin protein 1 (HP1) and Polycomb (Pc) ( Figure 1A), and it is becoming clear that these proteins specifically recognise Received 29 September 2003; accepted 11 November 2003 methyl marks, depending on their location in the histones (Fischle et al, 2003c).…”

“…Marks that correlate with gene silencing are methylation of lysines 9 and 27, generated by the HMTs SUV39H1 and EZH2, respectively (red ¼ 'OFF' marks). 'Readers' of these repressive marks are HP1 for lysine 9 methylation and Pc for lysine 27 methylation (Fischle et al, 2003c). Serines, adjacent to lysines 9 and 27, are shown to be phosphorylated by Aurora B kinase (orange), and might play a role in preventing 'readers' from recognising methyl marks.…”

Structural dynamics of protein lysine methylation and demethylation

“…Methyllysine recognition is achieved by a cage consists of three aromatic residues. The chromodomain of Polycomb, recognizes methylated H3 lysine 27 in a similar way [17,82]. The binding of trimethyl H3 lysine 4 by CHD1 protein involves double chromodomains, again using an aromatic cage (with two aromatic residues) [83].…”

“…There are currently many known sites of lysine and arginine methylation on histones, and additional sites of modification are still being uncovered. Methylation at these sites, in combination with other modifications (or demodifications) at nearby residues, generates "modification cassettes" [15,16] that yield distinct patterns on chromatin for signaling downstream events [17]. The best-characterized sites of histone methylation are located on the N-terminal tails of histones (such as at Lys-4 and Lys-9 of histone H3 and Arg-3 of histone H4) that protrude from the nucleosome.…”