Screening and Validation of Dinucleotide Repeats in Intron 1 of the Human EGFR Gene and its Paralog in the HER2 Gene

Abstract

Overexpression or dysfunction of EGFR and other ErbBs is known to be involved in many human cancers. The first intron of several genes, including ErbBs, has an important regulatory function in transcription. In intron 1 of the EGFR gene, simple CA repeats (CA-SSR) have been found to be associated with the level of transcriptional modulation of the EGFR both in vitro and in vivo. The aim of this work was to screen for conserved dinucleotide repeats located in introns of the human ErbB genes. Pairwise BLAST was used to identify paralogs to intron 1 of EGFR in the HER2 gene. Dinucleotide tandem repeats were searched in intron sequences using the Tandem Repeat Software to restrict detection of dinucleotide microsatellites containing at least 10 repeats. With multiple alignment, short conserved DNA sequences should also be detected, revealing the presence of potential regulatory elements near CA repeats. We found that the nearest homolog to intron 1 in the EGFR gene is intron 4 of the HER2 gene. The experimental validation of four predicted short tandem repeats (STRs) (three dinucleotide repeats in intron 1 of the EGFR and one in intron 4 of the HER2 gene) by genotyping of about 100 controls showed that these STRs are polymorphic. In a case-control study to test the association of the four new polymorphic STRs with breast cancer, a significant allelic association was found for all STRs (P < 0.001). These results suggest that the role of transcriptional regulation of CA repeats in intron 1 of the EGFR gene might be conserved in other ErbB genes.