ABSTRACT

This chapter discusses the rapid improvements in the analytical capability of Cap Analysis of Gene Expression (CAGE) and explains the principles underlying the technology and associated details of data analysis and applications. CAGE, originally developed by our group, is used to perform a genome-wide survey of promoters. In CAGE, the 5’-CAP of messengerribonucleic acids (mRNA) is obtained using this full-length complementarydeoxyribonucleic acids (cDNA) selection method, or Cap Trapper. From the 5’ end of mRNA, which is a product of transcription, 20-base pair are collected as tags using Type IIS restriction enzymes and the tag sequence is determined by sequencing. In the international project called Functional Annotation of Mammalian cDNA, more than 230,000 mouse promoters were identified by CAGE, and on average that represents approximately 5 promoters for each gene, and therefore the same number of transcription start sites. CAGE was developed to determine the position of the genome from which RNAs are transcribed.