A rare form of human ACAT1 mRNA, containing the optional long 5 -untranslated region, is produced as a 4.3-kelonucleotide chimeric mRNA through a novel interchromosomal trans-splicing of two discontinuous RNAs transcribed from chromosomes 1 and 7 (Li, B. L., Li, X. L., Duan, Z. J., Lee, O., Lin, S., Ma, Z. M., Chang, C. C., Yang, X. Y., Park, J. P., Mohandas, T. K., Noll, W., Chan, L., and Chang, T. Y. (1999) J. Biol. Chem. 274, 11060 -11071). To investigate its function, we express the chimeric ACAT1 mRNA in Chinese hamster ovary cells and show that it can produce a larger ACAT1 protein, with an apparent molecular mass of 56 kDa on SDS-PAGE, in addition to the normal, 50-kDa ACAT1 protein, which is produced from the ACAT1 mRNAs without the optional long 5 -untranslated repeat. To produce the 56-kDa ACAT1, acat1 sequences located at both chromosomes 7 and 1 are required. The 56-kDa ACAT1 can be recognized by specific antibodies prepared against the predicted additional amino acid sequence located upstream of the N-terminal of the ACAT1 ORF . The translation initiation codon for the 56-kDa protein is GGC, which encodes for glycine, as deduced by mutation analysis and mass spectrometry. Similar to the 50-kDa protein, when expressed alone, the 56-kDa ACAT1 is located in the endoplasmic reticulum and is enzymatically active. The 56-kDa ACAT1 is present in native human cells, including human monocyte-derived macrophages. Our current results show that the function of the chimeric ACAT1 mRNA is to increase the ACAT enzyme diversity by producing a novel isoenzyme. To our knowledge, our result provides the first mammalian example that a trans-spliced mRNA produces a functional protein.Acyl-coenzyme A:cholesterol acyltransferase (ACAT) 1 is an intracellular enzyme that plays important roles in lipid metabolism. It catalyzes the formation of cholesteryl esters, using long-chain fatty acyl coenzyme A and cholesterol as the two substrates. In mammals, two ACAT genes have been identified (reviewed in Refs. 1-4). The first ACAT gene, acat1, was identified by isolating a human cDNA (ACAT cDNA K1) that functionally complements a Chinese hamster ovary cell mutant (clone AC29) lacking endogenous ACAT activity (5). The second ACAT gene, acat2, was identified by homology cloning, based on the nucleotide sequence of ACAT1 cDNA. The ACAT1 and ACAT2 proteins share extensive sequence homology at their C-terminal halves but not at their N-terminals. Both enzymes are integral membrane proteins. Human ACAT1 (hACAT1) contains seven transmembranes (6), whereas hACAT2 contains only two detectable transmembranes (7). A conserved histidine (His-460 in hACAT1 and His-432 in hACAT2), located within a long stretch of hydrophobic residues, may serve as an active site for ACAT catalysis (7,8). Human ACAT1 message and protein are present in many tissues and various cell types examined, including adrenal, kidney, hepatocytes, Kupffer cells, intestinal enterocytes, fibroblasts, macrophages, and neurons in the brain (5, 9 -12). In contrast, abundant ACA...