Identification of a syndecan 4 pseudogene

Abstract

The syndecan family of heparan sulfate proteoglycans participates in cellular activation through interactions with growth factors, extracellular matrix, and other molecules. The family consists of four proteins that share sequence homology within their cytosolic domains. Here we report that a 5.8 kb region of human chromosome 22q12.2 contains multiple segments that share greater than 80% sequence homology to the syndecan 4 transcript, including homology to 443 nucleotides of the syndecan 4 coding region. Three pieces of evidence indicate that the chromosome 22 sequences are a syndecan 4 pseudogene. First, single nucleotide gaps need to be inserted into the chromosome 22 sequence in order to maintain maximal alignment to the syndecan 4 coding sequence, and this introduces stop codons into a deduced amino acid sequence. Second, the total length of chromosome 22 containing the homologous sequences is compressed when compared to the genomic organization of the complementary syndecan 4 sequences. Third, the 5.8 kb chromosome 22 sequence contains multiple Alu and other repetitive sequences, and this is a property of pseudogenes. Both RT-PCR and RNase protection assays indicated that the syndecan 4 pseudogene is transcribed in human umbilical vein endothelial cells.