Characterization of Allelic and Nucleotide Variation Between the RAGE Gene on Chromosome 6 and a Homologous Pseudogene Sequence to Its 5′ Regulatory Region on Chromosome 3

• Published in: Diabetes (New York, N.Y.) Vol. 50; no. 12; pp. 2646 - 2651
• Main Authors: Hudson, Barry I., Stickland, Max H., Grant, Peter J., Futers, T. Simon
• Format: Journal Article
• Language: English
• Published: New York American Diabetes Association 01-12-2001
• ISSN: 0012-1797; 1939-327X
• DOI: 10.2337/diabetes.50.12.2646

Characterization of Allelic and Nucleotide Variation Between the RAGE Gene on Chromosome 6 and a Homologous Pseudogene Sequence
to Its 5′ Regulatory Region on Chromosome 3
Implications for Polymorphic Studies in Diabetes
Barry I. Hudson ,
Max H. Stickland ,
Peter J. Grant and
T. Simon Futers
Academic Unit of Molecular Vascular Medicine, University of Leeds, Leeds General Infirmary, Leeds, U.K.
Abstract
Activation of the receptor for advanced glycation end products (RAGE) appears to be a key mechanism in the pathogenesis of
diabetic vascular disease, making RAGE a candidate gene for investigation. RAGE is located in the major histocompatibility
complex locus on chromosome 6, which contains a multitude of overlapping and duplicated genes involved predominantly in inflammatory
and immune responses. The RAGE 5′ flanking region from −505 in a 5′ direction overlaps with PBX2, a gene that has a pseudogene
copy on chromosome 3, making any studies of polymorphisms in this duplicated region potentially fraught with error. In this
study we have addressed these issues by confirming RAGE as a predominantly single-copy gene and PBX2 to have two gene copies
in the haploid human genome. We have characterized the gene:pseudogene differences between RAGE/PBX2 on chromosome 6 and Ψ PBX2 on chromosome 3, which include a change from C to A at position −1139 RAGE/+2298 PBX2, previously reported as a polymorphism.
Single chromosome–specific DNA amplification of the duplicated region has clarified five polymorphisms to be on chromosome
3 and one (at −1202 RAGE/+2234 PBX2) to be on chromosome 6. In conclusion, this study provides essential data for the study
of RAGE and its genetics.
Footnotes
Address correspondence and reprint requests to Dr Barry I. Hudson, Academic Unit of Molecular Vascular Medicine, Research
School of Medicine, G Floor, Martin Wing, Leeds General Infirmary, Leeds, LS1 3EX, U.K. E-mail: b.hudson{at}leeds.ac.uk .
Received for publication 1 August 2001 and accepted in revised form 1 October 2001. Posted on the World Wide Web at http://www.diabetes.org/diabetes_rapids/ on 9 November 2001.
AGE, advanced glycation end product; DHPLC, denaturing high-performance liquid chromatography; FXIII, Factor XIII; MHC, major
histocompatibility complex; PCR, polymerase chain reaction; RAGE, receptor for AGEs; RFLP, restriction fragment–length polymorphism;
SSCP, single-strand conformation polymorphism; UTR, untranslated region.