We previously cloned heparan sulfate 6-O-sulfotransferase (HS6ST) (Habuchi, H., Kobayashi, M., and Kimata, K. (1998) J. Biol. Chem. 273, 9208 -9213). In this study, we report the cloning and characterization of three mouse isoforms of HS6ST, a mouse homologue to the original human HS6ST (HS6ST-1) and two novel HS6STs (HS6ST-2 and HS6ST-3). The cDNAs have been obtained from mouse brain cDNA library by cross-hybridization with human HS6ST cDNA. The three cDNAs contained single open reading frames that predicted type II transmembrane proteins composed of 401, 506, and 470 amino acid residues, respectively. Amino acid sequence of HS6ST-1 was 51 and 57% identical to those of HS6ST-2 and HS6ST-3, respectively. HS6ST-2 and HS6ST-3 had the 50% identity. Overexpression of each isoform in COS-7 cells resulted in about 10-fold increase of HS6ST activity. The three isoforms purified with anti-FLAG antibody affinity column transferred sulfate to heparan sulfate and heparin but not to other glycosaminoglycans. Each isoform showed different specificity toward the isomeric hexuronic acid adjacent to the targeted N-sulfoglucosamine; HS6ST-1 appeared to prefer the iduronosyl N-sulfoglucosamine while HS6ST-2 had a different preference, depending upon the substrate concentrations, and HS6ST-3 acted on either substrate. Northern analysis showed that the expression of each message in various tissues was characteristic to the respective isoform. HS6ST-1 was expressed strongly in liver, and HS6ST-2 was expressed mainly in brain and spleen. In contrast, HS6ST-3 was expressed rather ubiquitously. These results suggest that the expression of these isoforms may be regulated in tissue-specific manners and that each isoform may be involved in the synthesis of heparan sulfates with tissue-specific structures and functions.Heparan sulfate proteoglycans (HSPGs) 1 are ubiquitously present on cell surface and in extracellular matrix including basement membrane and have divergent structures and functions (1-3). The heparan sulfate (HS) chains in HSPGs are known to interact with a variety of proteins such as heparinbinding growth factors, extracellular matrix components, protease inhibitors, protease, and lipoprotein lipase (4 -8). These interactions are implicated not only in various dynamic cellular behaviors including cell proliferation, differentiation, adhesion, migration, and morphology during development (9 -16), but also in various physiological phenomena such as inflammation (17), blood coagulation (18 -20), and tumor cell invasion and malignancy (21-23). Moreover, the pathogens such as bacteria, parasites, and viruses are known to infect host cells through the interactions between the cell surface HS on host cell and the coat proteins or cell surface proteins of pathogens (24,25).Recently, genetic screens and analyses are suggesting not only in Drosophila but also in mammals that these interactions also play pivotal roles in embryonic development. For example, the sugarless mutant (10 -12), which is deficient in UDP-glucose dehydrogenas...