Heterochromatin protein 1 (HP1) family members (␣, , and ␥) bind histone H3 methylated at Lys-9, leading to gene silencing and heterochromatin formation. Several previous reports have suggested that HP1s are posttranslationally modified, yet sites of modification have not yet been exhaustively determined. Here we perform the first comprehensive proteomic analysis of all HP1 isoforms using tandem mass spectrometry. Our data reveal that all HP1 isoforms are highly modified in a manner analogous to histones including phosphorylation, acetylation, methylation, and formylation, including several sites having multiple different types of modifications. Additionally, many of these modifications are found in both the chromo-and chromoshadow domains, suggesting that they may have an important role in modulating HP1 interactions or functions. These studies are the first to systematically map the abundant sites of covalent modifications on HP1 isoforms and provide the foundation for future investigations to test whether these modifications are essential in heterochromatin maintenance or other nuclear processes. Molecular & Cellular Proteomics 8: 2432-2442, 2009.The mammalian HP1␣, , and ␥ proteins are a family of chromatin-associated proteins that are homologs of the Drosophila heterochromatin protein 1 (HP1) 1 , originally identified as a protein required for position effect variegation. Position effect variegation is the silencing phenomenon that occurs when a block of euchromatin is placed adjacent to a region of heterochromatin (1). HP1␣, , and ␥ proteins all contain a N-terminal chromodomain (CD) and a C-terminal chromoshadow domain (CSD) that are linked together by a flexible hinge region (2). The CD in HP1 is one of many specialized domains found in a number of other chromatin-associated proteins that recognizes histone post-translational modifications (PTMs). In particular, x-ray crystallographic studies have demonstrated that the HP1 chromodomain binds directly to the histone H3 protein trimethylated on Lys-9 (3).The C-terminal CSD domain is structurally similar to the CD and is thought to be responsible for dimerization and interactions with other proteins. The mammalian HP1␣, , and ␥ proteins have been shown to form both homo-and heterodimers with each other (4). Although the HP1␣, , and ␥ proteins have similar structures and dimerize with each other, studies suggest they have non-overlapping functions. As the name implies, the HP1 proteins are generally associated with constitutive heterochromatic loci; however, HP1␥ localizes with both hetero-and euchromatin (5). Moreover, although microscopy analysis has demonstrated that HP1␣ and HP1 localize together at many heterochromatic loci, they do not completely overlap, further suggesting that they can function independently (6). Furthermore, HP1␥ was found to be associated with the DNA of actively transcribed genes by chromatin immunoprecipitation (7).All three of the mammalian HP1 proteins can complex with the co-repressor protein, KAP-1/Tif1. Interestingly,...