G13 and G12 belong to the same subfamily of heterotrimeric G proteins. The major physiological difference between them is revealed by knockout mice. Mice with null mutant of G13 alpha subunit (Gα13) are embryonic lethal, while those with null mutant alpha subunit of G12 (Gα12) are alive. This difference suggests that G13 and G12 may differently regulate gene transcription during embryonic development. Muscle enhance factor 2C (MEF2C) is an important transcription factor during angiogenesis. Here we characterized MEF2-dependent gene transcription by constitutively activated Gα13 (Gα13Q226L) and Gα12 (Gα12Q229L). We found that Gα13Q226L was more potent than Gα12Q229L to stimulate MEF2-dependent gene transcription in NIH 3T3 cells and only Gα13Q226L was able to stimulate MEF2-dependent gene transcription in HUVEC cells. Repression of MEF2C-mediated gene transcription by HDAC4 and HDAC5 was abolished by Gα13Q226L but not by Gα12Q229L. In addition, Gα13Q226L but not Gα12Q229L was able to induce the translocation of histone deacetylase 5 (HDAC5) from nucleus to cytoplasm. Gα13Q226L stimulated MEF2-dependent gene transcription was inhibited by dominant negative mutant of calcium/calmodulin-dependent kinase IV (CaMKIV). Furthermore, Gα13Q226L but not Gα12Q229L was able to increase Ca2+ /CaM-independent CaMKIV actvity. Our studies indicate the different regulation of CaMKIV activity may result in the different functions of G13 and G12 in MEF2-dependent gene transcription.