The ESET (also called SETDB1) protein contains an N-terminal tudor domain that 
mediates protein-protein interactions and a C-terminal SET domain that catalyzes 
methylation of histone H3 at lysine 9. We report here that ESET protein is 
transiently upregulated in prehypertrophic chondrocytes in newborn mice. To 
investigate the in vivo effects of ESET on chondrocyte differentiation, we 
generated conditional knockout mice to specifically eliminate the catalytic SET 
domain of ESET protein only in mesenchymal cells. Such deletion of the ESET gene 
caused acceleration of chondrocyte hypertrophy in both embryos and young 
animals, depleting chondrocytes that are otherwise available to form epiphyseal 
plates for endochondral bone growth. ESET-deficient mice are thus characterized 
by defective long bone growth and trabecular bone formation. To understand the 
underlying mechanism for ESET regulation of chondrocytes, we carried out 
co-expression experiments and found that ESET associates with histone 
deacetylase 4 to bind and inhibit the activity of Runx2, a hypertrophy-promoting 
transcription factor. Repression of Runx2-mediated gene transactivation by ESET 
is dependent on its H3-K9 methyltransferase activity as well as its associated 
histone deacetylase activity. In addition, knockout of ESET is associated with 
repression of Indian hedgehog gene in pre- and early hypertrophic chondrocytes. 
Together, these results provide clear evidence that ESET controls hypertrophic 
differentiation of growth plate chondrocytes and endochondral ossification 
during embryogenesis and postnatal development.