Heterochromatin protein 1a (HP1a) is a chromatin-associated protein important 
for the formation and maintenance of heterochromatin. In Drosophila, the two 
histone methyltransferases SETDB1 and Su(var)3-9 mediate H3K9 methylation marks 
that initiates the establishment and spreading of HP1a-enriched chromatin. 
Although HP1a is generally regarded as a factor that represses gene 
transcription, several reports have linked HP1a binding to active genes, and in 
some cases, it has been shown to stimulate transcriptional activity. To clarify 
the function of HP1a in transcription regulation and its association with 
Su(var)3-9, SETDB1 and the chromosome 4-specific protein POF, we conducted 
genome-wide expression studies and combined the results with available binding 
data in Drosophila melanogaster. The results suggest that HP1a, SETDB1 and 
Su(var)3-9 repress genes on chromosome 4, where non-ubiquitously expressed genes 
are preferentially targeted, and stimulate genes in pericentromeric regions. 
Further, we showed that on chromosome 4, Su(var)3-9, SETDB1 and HP1a target the 
same genes. In addition, we found that transposons are repressed by HP1a and 
Su(var)3-9 and that the binding level and expression effects of HP1a are 
affected by gene length. Our results indicate that genes have adapted to be 
properly expressed in their local chromatin environment.