Systematic and quantitative identification of cellular glycan regulation using correlation index-based responsible gene screening (cires)

Cells manage the expression of their genomic contents to cope with their needs. In multicellular organisms, different cell types result from differential usage of the genome. In addition, cell surface glycans are often cell type specific and the mechanisms regulating glycan expression are controlled by gene expression, just like other cellular phenotypes. Here, a recently developed method for assessing the glycan-related genes that regulate cell surface glycans will be described. This method, called correlation index-based responsible enzyme gene screening (CIRES), uses statistical analysis of quantitative transcriptome data and glycan expression. Not only is this method useful for identifying the genes that positively regulate glycan expression, but CIRES can also systematically identify genes that negatively regulate glycan expression. CIRES involves three steps: (1) obtaining a glycan expression profile in several cell lines and gene expression profiles of glycan-related genes in the same set of cells, (2) correlating glycan and gene expression, and (3) evaluating the correlations in a gene perturbation study. Using this technique, one can determine the genes that quantitatively regulate the expression of cell surface glycans. This method complements conventional loss-of-function experiments, which can identify the exclusiveness of the gene for glycan expression.