Enhancers cause a high level of transcription and activation of chromatin 
structure at target genes. Hyperacetylation of histones H3 and H4, a mark of 
active chromatin, is established broadly across target loci by enhancers that 
function over long distances. In the present study, we studied the role of an 
enhancer in methylation of various lysine residues on H3 by comparing a model 
gene locus having an active enhancer with one in which the enhancer has been 
inactivated within the context of minichromosomes. The intact enhancer affected 
histone methylation at K4, K9 and K36 in distinct ways depending on the 
methylation level and the location in the locus. All three lysine residues were 
highly tri-methylated in the coding region of the gene linked to the active 
enhancer but not the inactive enhancer. However di-methylation of K9 and K36 was 
not affected by the enhancer. The enhancer region itself was marked by 
mono-methylation at K4 and K9, distinguishing it from the methyl marks in the 
gene coding region. These results indicate that an enhancer has roles in 
establishing active histone methylation patterns linked with gene transcription 
rather than removing methylation linked with gene inactivation.