The histone methyltransferase enhancer of zeste homolog 2 (Ezh2) mediates 
trimethylation of lysine 27 in histone 3, which acts as a repressive epigenetic 
mark. Ezh2 is essential for maintaining pluripotency of stem cells, but 
information on its role in differentiated cells is sparse. Whole-genome mRNA 
expression arrays identified 964 genes that were regulated by >2-fold 72 hours 
after small interfering RNA-mediated silencing of Ezh2 in human umbilical vein 
endothelial cells. Among them, genes associated with the gene ontology terms 
cell communication and cell adhesion were significantly overrepresented, 
suggesting a functional role for Ezh2 in the regulation of angiogenesis. Indeed, 
adhesion, migration, and tube formation assays revealed significantly altered 
angiogenic properties of human umbilical vein endothelial cells after silencing 
of Ezh2. To identify direct target genes of Ezh2, we performed chromatin 
immunoprecipitation experiments followed by whole-genome promoter arrays 
(chromatin immunoprecipitation-on-chip) and identified 5585 genes associated 
with trimethylation of lysine 27 in histone 3. Comparative analysis with our 
mRNA expression data identified 276 genes that met our criteria for putative 
Ezh2 target genes, upregulation by >2-fold after Ezh2 silencing and association 
with trimethylation of lysine 27 in histone 3. Notably, we observed a striking 
overrepresentation of genes involved in wingless-type mouse mammary tumor virus 
integration site (WNT) signaling pathways. Epigenetic regulation of several of 
these genes by Ezh2 was specifically confirmed by polymerase chain reaction 
analysis of DNA enrichment after chromatin immunoprecipitation using an antibody 
specific for trimethylation of lysine 27 in histone 3. Combining mRNA expression 
arrays and chromatin immunoprecipitation-on-chip analysis, we identified 276 
Ezh2 target genes in endothelial cells. Ezh2-dependent repression of genes 
involved in cell adhesion and communication contributes to the regulation of 
angiogenesis.