Conserved chromosomal HP1 proteins capable of binding to histone H3 methylated 
at lysine 9 are believed to provide a dynamic platform for the recruitment 
and/or spreading of various regulatory proteins involved in diverse chromosomal 
processes. The fission yeast Schizosaccharomyces pombe HP1 family members Chp2 
and Swi6 are important for heterochromatin assembly and transcriptional 
silencing, but their precise roles are not fully understood. Here, we show that 
Swi6 and Chp2 associate with histone deacetylase (HDAC) protein complexes 
containing class I HDAC Clr6 and class II HDAC Clr3 (a component of Snf2/HDAC 
repressor complex), which are critical for transcriptional silencing of 
centromeric repeats targeted by the heterochromatin machinery. Mapping of RNA 
polymerase (Pol) II distribution in single and double mutant backgrounds 
revealed that Swi6 and Chp2 proteins and their associated HDAC complexes have 
overlapping functions in limiting Pol II occupancy across pericentromeric 
heterochromatin domains. The purified Swi6 fraction also contains factors 
involved in various chromosomal processes such as chromatin remodeling and DNA 
replication. Also, Swi6 copurifies with Mis4 protein, a cohesin loading factor 
essential for sister chromatid cohesion, and with centromere-specific histone H3 
variant CENP-A, which is incorporated into chromatin in a 
heterochromatin-dependent manner. These analyses suggest that among other 
functions, HP1 proteins associate with chromatin-modifying factors that in turn 
cooperate to assemble repressive chromatin; thus, precluding accessibility of 
underlying DNA sequences to transcriptional machinery.