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 A 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.