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Glycobiology Advance Access published online on October 19, 2005
Glycobiology, doi:10.1093/glycob/cwj048
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© The Author 2005. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Received July 15, 2005
Revised September 15, 2005
Accepted October 11, 2005

Article

A Focused Microarray Approach to Functional Glycomics: Transcriptional Regulation of the Glycome

Elena M. Comelli 1, Steven R. Head 2, Tim Gilmartin 3, Thomas Whisenant 3, Stuart M. Haslam 4, Simon J. North 4, Nyet-Kui Wong 4, Takashi Kudo 5, Hisashi Narimatsu 5, Jeffrey D. Esko 6, Kurt Drickamer 4, Anne Dell 4, and James C. Paulson 7*

1 Department of Molecular Biology and Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, 92037, USA; These two authors contributed equally to this work; Present address: Nestlé Research Centre, Lausanne, Switzerland
2 DNA microarray core facility, The Scripps Research Institute, La Jolla, California, 92037, USA; These two authors contributed equally to this work
3 DNA microarray core facility, The Scripps Research Institute, La Jolla, California, 92037, USA
4 Imperial College, London, UK
5 AIST, Tsukuba, 305-8568, Japan
6 University of California San Diego, La Jolla, 92037, California, USA.
7 Department of Molecular Biology and Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, 92037, USA.

* To whom correspondence should be addressed.
James C. Paulson, E-mail: jpaulson{at}scripps.edu


  Abstract

Glycosylation is the most common post-translational modification of proteins, yet genes relevant to the synthesis of glycan structure and function are incompletely represented and poorly annotated on the commercially available arrays. To fill the need for expression analysis of such genes we employed the Affymetrix technology to develop a focused and highly annotated glycogene-chip representing human and murine glycogenes, including glycosyltranferases, nucleotide sugar transporters, glycosidases, proteoglycans and glycan-binding proteins. In this report the array has been used to generate glycogene expression profiles of nine murine tissues. Global analysis with a hierarchical clustering algorithm, reveals that expression profiles in immune tissues (thymus, spleen, lymph node and bone marrow) are more closely related, relative to those of non-immune tissues (kidney, liver, brain and testes). Of the biosynthetic enzymes, those responsible for synthesis of the core regions of N-and O-linked oligosaccharides are ubiquitously expressed, while glycosyltransferase that elaborate terminal structures are expressed in a highly tissue-specific manner, accounting for tissue and ultimately cell type-specific glycosylation. Comparison of gene expression profiles with MALDI-TOF profiling of N-linked oligosaccharides suggested that the {alpha}1-3 fucosyltransferase IX, Fut9, is the enzyme responsible for terminal fucosylation in kidney and brain, a finding validated by analysis of Fut9 knockout mice. Two families of glycan-binding proteins, C-type lectins and siglecs, are predominately expressed in the immune tissues, consistent with their emerging functions in both innate and acquired immunity. The glycogene chip reported in this study is available to the scientific community through the Consortium for Functional Glycomics (http://www.functionalglycomics.org).

Keywords: Glycogenes/Glycomics/Glycosyltransferase/Lectin/Glycosylation/Glycome/Microarray/Kidney/Fut9.
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