Glycan structures covalently attached to proteins and lipids play numerous roles in mammalian cells, including protein folding, targeting, recognition, and adhesion at the molecular or cellular level. Regulating the abundance of glycan structures on cellular glycoproteins and glycolipids is a complex process that depends on numerous factors. Most models for glycan regulation hypothesize that transcriptional control of the enzymes involved in glycan synthesis, modification, and catabolism determines glycan abundance and diversity. However, few broad-based studies have examined correlations between glycan structures and transcripts encoding the relevant biosynthetic and catabolic enzymes. Low transcript abundance for many glycan-related genes has hampered broad-based transcript profiling for comparison with glycan structural data. In an effort to facilitate comparison with glycan structural data and to identify the molecular basis of alterations in glycan structures, we have developed a medium-throughput quantitative real time reverse transcriptase-PCR platform for the analysis of transcripts encoding glycan-related enzymes and proteins in mouse tissues and cells. The method employs a comprehensive list of >700 genes, including enzymes involved in sugar-nucleotide biosynthesis, transporters, glycan extension, modification, recognition, catabolism, and numerous glycosylated core proteins. Comparison with parallel microarray analyses indicates a significantly greater sensitivity and dynamic range for our quantitative real time reverse transcriptase-PCR approach, particularly for the numerous low abundance glycan-related enzymes. Mapping of the genes and transcript levels to their respective biosynthetic pathway steps allowed a comparison with glycan structural data and provides support for a model where many, but not all, changes in glycan abundance result from alterations in transcript expression of corresponding biosynthetic enzymes.Carbohydrate structures attached to glycoproteins, glycolipids, and proteoglycans have been shown to play key roles in a variety of biological recognition events (1). Although there are many examples of the contribution of N-glycans to the bioactivity, folding, localization, and immunogenicity of the attached polypeptide, the functional roles of individual oligosaccharide structures on a given glycoprotein are difficult to predict (1-5). At the cellular level, N-linked, O-linked, and glycolipid glycan structures have been shown to contribute to several essential aspects of biological recognition, including cell adhesion during development, immune surveillance, inflammatory reactions, hormone action, viral infection, arthritis, and metastasis of oncogenically transformed cells (6 -9). Most of our understanding of the roles of cellular glycosylation in physiology and pathology comes from a combination of glycan structural analysis on specific glycoproteins, cell surfaces, or total tissue extracts in combination with years of study on the biochemistry and enzymology of glycan biosynthetic...