A polymerase chain reaction-based method for isolation of gene-specific sequences from the interferon-alpha gene cluster

Isolation of human promoter regions by Alu repeat consensus-based polymerase chain reaction

Knowledge of the promoter structure is critical for an understanding of the regulation of genes. We demonstrate by analysis of 405 human genes that human promoter regions are flanked by upstream Alu repeat elements, typically at a distance of 0.5-5 kb from their protein-coding areas. We identified common Alu repeat consensus sequences (ARC) among the different members of the Alu subfamilies that can be used as universal anchor sites for polymerase chain reaction (PCR) amplification. Utilizing ARC-specific primers and oligonucleotides specific for the 5' end of a selected target gene, we show that sequences spanning unknown human gene promoter regions can be directly amplified by PCR from genomic DNA. This novel technique, termed ARC-PCR, allowed us to characterize the proximal promoters of the human LTA4 hydrolase and SPARC genes, each within 1 day.

Detection of human interferon-alpha-encoding gene expression

We have devised a sensitive method based on the polymerase chain reaction (PCR) to detect expression of human interferon-alpha-encoding genes (IFN-A) in general, and specifically, expression of the IFN-A2 or IFN-A4 genes. The utility of the PCR approach was assessed by analysis of cloned IFN-A genes, as well as genomic DNA and mRNA isolated from peripheral blood mononuclear cells. We demonstrate the specific amplification of sequences encoding IFN subtypes IFN-alpha-2 and IFN-alpha-4 from as little as 0.1 pg of IFN-A mRNA. The PCR technique has potential clinical application for the detection of IFN-A expression and, thus, identification of the IFN-alpha subtypes produced, particularly in small biopsy samples or otherwise, where only low numbers of cells are available.