Correlation index-based responsible-enzyme gene screening (CIRES), a novel DNA microarray-based method for enzyme gene involved in glycan biosynthesis.
BACKGROUND
Glycan biosynthesis occurs though a multi-step process that requires a variety of enzymes ranging from glycosyltransferases to those involved in cytosolic sugar metabolism. In many cases, glycan biosynthesis follows a glycan-specific, linear pathway. As glycosyltransferases are generally regulated at the level of transcription, assessing the overall transcriptional profile for glycan biosynthesis genes seems warranted. However, a systematic approach for assessing the correlation between glycan expression and glycan-related gene expression has not been reported previously.


METHODS
To facilitate genetic analysis of glycan biosynthesis, we sought to correlate the expression of genes involved in cell-surface glycan formation with the expression of the glycans, as detected by glycan-recognizing probes. We performed cross-sample comparisons of gene expression profiles using a newly developed, glycan-focused cDNA microarray. Cell-surface glycan expression profiles were obtained using flow cytometry of cells stained with plant lectins. Pearson's correlation coefficients were calculated for these profiles and were used to identify enzyme genes correlated with glycan biosynthesis.


CONCLUSIONS
This method, designated correlation index-based responsible-enzyme gene screening (CIRES), successfully identified genes already known to be involved in the biosynthesis of certain glycans. Our evaluation of CIRES indicates that it is useful for identifying genes involved in the biosynthesis of glycan chains that can be probed with lectins using flow cytometry.
Yamamoto
Harumi
H
Laboratory of Membrane Biochemistry and Biophysics, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan.
Takematsu
Hiromu
H
Fujinawa
Reiko
R
Naito
Yuko
Y
Okuno
Yasushi
Y
Tsujimoto
Gozoh
G
Suzuki
Akemi
A
Kozutsumi
Yasunori
Y
D018076:DNA, Complementary / Q000235:genetics; D005434:Flow Cytometry; D020869:Gene Expression Profiling; D005820:Genetic Testing / Q000379:methods*; D016695:Glycosyltransferases / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D011134:Polysaccharides / Q000096:biosynthesis*
D018076:DNA, Complementary; D011134:Polysaccharides; D016695:Glycosyltransferases