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for AMPK phosphorylation has been associated with decreased carnitine palmitoyltransferase II, the enzyme that is responsible for the import of long-chain fatty acyl-CoAs into the mitochondria for fatty acid synthesis. Conversely, AMPK phosphorylation was increased in FTO−/− cells and has been associated with increased fatty acid synthesis [[@B79-biomolecules-05-02690],[@B80-biomolecules-05-02690]]. These conflicting findings suggest that although the *FTO* gene has a similar function in the two different tissues, FTO has different functions in the two tissues. It is possible that FTO may be an important determinant of the fate of the methyl group transferred by the methyltransferase through substrate specficity and/or through its own enzymatic activity (see [Figure 1](#biomolecules-05-02690-f001){ref-type=”fig”}). The ability of FTO to recognize both a short and a long chain 5mC substrate allows for the possibility of a cofactor-dependent activity. In addition, the methyl group transferred from the SAM to the nucleophile is oxidized to *S*-adenosyl homocysteine, which is a potent inhibitor of Methyltransferase-3 (MT3), an essential cofactor of the methyltransferase [[@B64-biomolecules-05-02690],[@B81-biomolecules-05-02690]]. In a recent study the importance of the enzymatic activity of FTO in a single replication cycle was demonstrated [[@B82-biomolecules-05-02690]]. In this study the authors provided evidence that in the T-cell receptor (TCR) gene-deficient *FTO*^Δ/ΔT^ mice the number of 5-mC positions at the Vβ promoter was reduced by 70% compared to the
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