Direct Cap Analysis of Gene Expression (direct CAGE) is an high-throughput method which enables genome-wide profiling of transcription start sites (TSS) at single-base resolution, allowing precise mapping of promoter and enhancer initiation events, as well as quantitative measurement of gene expression across different cell types and differentiation states (Delobel, D et al.,2025).
This method is based on the selection of 5′ ends of capped RNAs, (‘cap-trap’, Carninci et al.1996). CAGE tags are mapped to the reference genome to identify TSS and their related promoter regions. The number of CAGE tags mapped at specific locations in the genome provides quantification on promoter activities on a genome-wide scale.
This protocol can be used for the detection of differential gene expression between different cell types (tissue specific expression), different stages of cell differentiation (regulation of cell differentiation), determination of promoter and enhancer usage.