ISOLATION OF HUMAN PROMOTER REGIONS BY ALU REPEAT CONSENSUS-BASED POLYMERASE-CHAIN-REACTION

Knowledge of the promoter structure is critical for an understanding o f the regulation of genes. We demonstrate by analysis of 405 human gen es that human promoter regions are flanked by upstream Alu repeat elem ents, typically at a distance of 0.5-5 kb from their protein-coding ar eas. We identified common Alu repeat consensus sequences (ARC) among t he different members of the Alu subfamilies that can be used as univer sal anchor sites for polymerase chain reaction (PCR) amplification. Ut ilizing 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 gen omic DNA. This novel technique, termed ARC-PCR, allowed us to characte rize the proximal promoters of the human LTA(4) hydrolase and SPARC ge nes, each within 1 day. (C) 1998 Academic Press.