Rai, K., Jafri, I.F., Chidester, S., James, S.R., Karpf, A.R., Cairns, B.R., and Jones, D.A. (2010) Dnmt3 and G9a cooperate for tissue-specific development in zebrafish. The Journal of biological chemistry. 285(6):4110-4121.
Although DNA methylation is critical for proper embryonic and tissue-specific development, how different DNA methyltransferases affect tissue-specific development and their targets remain unknown. We address this issue in zebrafish through antisense-based morpholino knockdown of Dnmt3 and Dnmt1. Our data reveal that Dnmt3 is required for proper neurogenesis and its absence results in profound defects in brain and retina. Interestingly, other organs such as intestine remain unaffected suggesting tissue-specific requirements of Dnmt3. Further, comparison of Dnmt1 knockdown phenotypes with those of Dnmt3 suggested that these two families have distinct functions. Consistent with this idea, Dnmt1 failed to complement Dnmt3 deficiency and Dnmt3 failed to complement Dnmt1 deficiency. Downstream of Dnmt3 we identify a neurogenesis regulator, Lef1, as a Dnmt3-specific target gene that is demethylated and upregulated in Dnmt3 morphants. Knockdown of Lef1 rescued neurogenesis defects resulting from Dnmt3 absence. Mechanistically, we show cooperation between Dnmt3 and an H3K9 methyltransferase G9a in regulating lef1. Further, like Dnmt1-Suv39h1 co-operativity, Dnmt3 and G9a seemed to function together for tissue-specific development. G9a knock down, but not Suv39h1 loss, phenocopied Dnmt3 morphants and G9a overexpression provided a striking rescue of Dnmt3 morphant phenotypes, whereas Suv39h1 overexpression failed supporting notion of specific DNMT-HMT networks. Consistent with this model, H3K9me3 levels on Lef1 promoter were reduced in both Dnmt3 and G9a morphants and its knockdown rescued neurogenesis defects in G9a morphants. We propose a model wherein specific DNMT-HMT networks are utilized to silence critical regulators of cell fating in a tissue-specific manner.