Glycogene Expression and Glycan Processing Pathways

Our Resource has compiled from several sources a list of glycogenes involved in the biosynthesis of glycans that are found on human and mouse glycoproteins and glycolipids. 


Kelley Morement, Senior Investigator

Alison Nairn, Senior Investigator

Melina Galizzi Research Professional


The overall objective for this project is focused on developing technologies to probe the regulation of glycan structures by examining transcript abundance of the enzymatic machinery involved in the synthesis, modification, and degradation of glycans in animal systems and correlating these changes with alterations in glycan structural abundance. Cell surface carbohydrates play significant roles in cell-cell and cell-substratum adhesion, cell migration, cellular uptake of glycosylated products, and numerous other critical functions. Despite decades of studies on the analysis of glycan structures and the enzymology of glycan biosynthetic and degradative enzymes, very little is known about the global regulation of glycan synthesis and degradation.
The goals of this Resource have been to create strategies for glycan analysis and transcript quantitation using ES cell differentiation as a model biological system. We developed technologies for transcript profiling, first using a qRT-PCR transcriptome analysis platform and more recently by a parallel application of RNA-Seq approaches. The technologies were used to study gene regulation in pluripotent and differentiated ES cell populations and collaborative studies in other organism systems for correlation with glycan structural analyses. Strategies were also developed to correlate the two related but disparate data sets to reveal where gene expression and corresponding glycan structures predict transcriptional or post-transcriptional control of glycan diversity.

Human Stem Cell Differentiation Pathways used for Transcriptome Analysis by qRT-PCR or RNA-Seq

Cell pellets for pluripotent human ES (ES)

Cell pellets for pluripotent human ES (ES),  a cardiac progenitor cell line (WT1), smooth muscle (SM) and a hepatic cell line (Liver) and neural crest (NC) were characterized and provided by the Dalton lab.

qRT-PCR Analysis of ES and Differentiated Cell Lines for Gene Transcripts Involved in N-linked Glycan Trimming and Branching

qRT-PCR graphic

A cartoon representation for processing steps involving N-glycan trimming and branching in the endoplasmic reticulum and Golgi complex, including a key for glycan structural components in the pathway, is shown in the upper panel. Linkages are shown for each step of the biosynthetic pathway and the numbers in the blue ovals designate the pathway steps in the upper panel that link to the transcript abundance data in the corresponding numbered step in the lower panel (plotted as a histogram on a log10 scale). Relative transcript abundances for transcripts from ES, Smooth Muscle (SM), Cardiac Precursor (WT1), Liver (LIV) and Neural Crest (NC) are presented as a clustered set of histograms above the corresponding pathway step number (blue numbered oval) and gene names. Multiple genes for a given pathway step are listed in cases where multiple distinct subunits contribute to catalysis or where several genes within a common family encode enzymes capable of creating the specified linkage. The center panel represents fold change in transcript abundance relative to undifferentiated ES.

Detailed information is available: