Histone lysine methylation, as one of the most important factors in transcriptional regulation, is associated with a various physiological conditions. Using a bioinformatics search, we identified and subsequently cloned mouse SET domain containing 3 (SETD3) with SET (Su(var)3-9, Enhancer-of-zeste and Trithorax) and Rubis-subs-bind domains. SETD3 is a novel histone H3K4 and H3K36 methyltransferase with transcriptional activation activity. SETD3 is expressed abundantly in muscular tissues and, when overexpressed, activates transcription of muscle-related genes, myogenin, muscle creatine kinase (MCK), and myogenic factor 6 (Myf6), thereby inducing muscle cell differentiation. Conversely, knockdown of SETD3 by shRNA significantly retards muscle cell differentiation. In this study, SETD3 was recruited to the myogenin gene promoter along with MyoD where it activated transcription. Together, these data indicate that SETD3 is a H3K4/K36 methyltransferase and plays an important role in the transcriptional regulation of muscle cell differentiation.The conformational structure or molecular charge of the histone core complex can be modified via methylation of the lysine/arginine residue in the histone tail, which affects gene expression and heterochromatin formation (1). Arginine methylation is mediated by PRDM family proteins, which are characterized by the presence of a PR (PRD1-BF1 and RIZ homology) domain at their N terminus, whereas lysine is methylated by histone methyltransferase (HMTase), 4 which commonly harbors the SET (Su(var)3-9, Enhancer-of-zeste and Trithorax) domain (2). By forming complexes with a broad variety of transcription factors, HMTases perform an important role in the regulation of gene expression, stem cell renewal, reproductive organ maturation, and tumorigenesis in mammals (2-5).Additionally, HMTases have been confirmed as crucial to myofibril organization (6), intestinal and pancreatic differentiation (7), and neurogenesis (8) in zebrafish.Muscle differentiation requires sequences of harmonized steps after the commitment of mesodermal progenitor cells to the muscular lineage (9). Under the regulation of diverse modifiers, myoblasts fuse with other neighboring myoblasts to generate multinucleated myotubes (10). During differentiation, the cell cycle is withdrawn and muscle-specific transcription factors activated. Mesodermal precursor cells with muscular lineages are differentiated into skeletal muscle or smooth muscle via the interplay of muscle-specific factors, including MyoD, myogenin, myogenic factor 5 (Myf5), muscle regulatory factor 4 (MRF4), and myocyte enhancer factor-2 (MEF2) (10).Histone modification enzymes have been implicated in muscle cell differentiation through the regulation of musclespecific gene expression (11,12). Chromatin modification enzymes such as histone acetyltransferases, deacetylases (HDACs), and chromatin remodeling factors have recently been reported to regulate MyoD activity during muscle differentiation. For example, the histone acetyltransferases p300 and p300/C...