Heterochromatin represents a cytologically visible state of heritable gene repression. In the yeast, Schizosaccharomyces pombe, the swi6 gene encodes a heterochromatin protein 1 (HP1)-like chromodomain protein that localizes to heterochromatin domains, including the centromeres, telomeres, and the donor mating-type loci, and is involved in silencing at these loci. We identify here the functional domains of swi6p and demonstrate that the chromodomain from a mammalian HP1-like protein, M31, can functionally replace that of swi6p, showing that chromodomain function is conserved from yeasts to humans. Site-directed mutagenesis, based on a modeled three-dimensional structure of the swi6p chromodomain, shows that the hydrophobic amino acids which lie in the core of the structure are critical for biological function. Gel filtration, gel overlay experiments, and mass spectroscopy show that HP1 proteins can self-associate, and we suggest that it is as oligomers that HP1 proteins are incorporated into heterochromatin complexes that silence gene activity.The highly conserved heterochromatin protein 1 (HP1) class of chromobox genes (HP1) encode structural adapters whose probable role is to assemble a variety of macromolecular complexes in chromatin (30). The possible functions of these complexes are wide-ranging and include roles in transcriptional repression (12,36,54,55), transgene silencing (17, 26), chromosome segregation (14, 31), recruitment of silent genes to heterochromatin (7, 54), localization of heterochromatin to the nuclear periphery (67), and sex chromosome inactivation during mammalian spermatogenesis (44).The swi6 gene in Schizosaccharomyces pombe is a nonessential gene that is required for the recombination-suppression and silencing which encompasses the mat2-K-mat3 region (33). Cloning of the gene showed that swi6 is a member of the HP1 class of chromobox genes (38), suggesting that the recombination-suppression and silencing are due to the packaging of the mat2-K-mat3 region into a heterochromatin-like complex that renders the region inaccessible to the transcriptional and recombination machinery (38,63). Other trans-acting factors that are required for repression at the silent loci include rik1, clr1, clr2, clr3, clr4, and clr6 (34, 64). rik1, clr1, and clr4 are thought to encode structural components of the heterochromatin-like complex, while clr3 and clr6 share considerable homology with histone deacetylases (20). Along with the silent mating-type loci, swi6p is also involved in silencing at the fission yeast centromeres and telomeres (14, 47) and plays a role in chromosome segregation at anaphase (14).HP1 proteins are characterized by the possession of both a classical chromodomain (CD) and a chromo shadow domain (CSD) (2) linked by a variable intervening region (IVR) or "hinge" (16). In addition, a stretch of acidic amino acids immediately precedes the CD of HP1 proteins (see Fig. 1A). The solution structure of the CD from the murine HP1-like heterochromatin-associated protein, M31 (also known as mH...