Heterochromatin protein 1 (HP1) was first described in Drosophila melanogaster 
as a heterochromatin associated protein required for epigenetic gene silencing. 
Most eukaryotes have at least three HP1 homologs that play differential roles in 
heterochromatin and euchromatin. However, despite the fact that the three HP1 
proteins bind to different regions of the genome, several studies show that most 
of the interactions occur in a manner specific to HP1a. In addition, little is 
known about the overall interaction network of the three Drosophila HP1 
homologs, HP1a, HP1b, and HP1c. Here, we performed the first comprehensive 
proteomic analysis of Drosophila HP1 homologs by coupling a double-affinity 
purification approach with MudPIT analysis to identify interacting proteins of 
Drosophila HP1. We discovered 160-310 proteins co-eluted with HP1, including a 
number of novel HP1-binding partners along with the previously identified HP1 
binding proteins. Finally, we showed that slight and unique binding preferences 
might exist between the three HP1 proteins in Drosophila. These studies are the 
first to systematically analyze the interactome of HP1 paralogs and provide the 
basic clues as to the molecular mechanism by which HP1 might control cellular 
processes.
BIOLOGICAL SIGNIFICANCE: Most eukaryotes have at least three HP1 homologs with 
similar domain structures but with differential roles in heterochromatin and 
euchromatin. However, little is known about the overall interactome of the three 
Drosophila HP1 homologs, HP1a, HP1b, and HP1c. The present study compared 
interacting proteins of three HP1 homologs in Drosophila. To better understand 
the underlying mechanisms for gene regulation of HP1, a double-affinity 
purification and MudPIT mass spectrometry were employed to identify differential 
proteins as well as common binding proteins of HP1. Therefore, this study 
provides not only the comparative proteomic analysis but also molecular 
mechanism underlying the HP1 homolog-specific function.