Practice question

CAGE, or Cap Analysis of Gene Expression, specifically captures the 7-methylguanosine cap at the 5′ end of eukaryotic mRNAs. By trapping capped RNAs, synthesizing cDNA, and sequencing a short 20–27 nucleotide tag from the extreme 5′ terminus, it maps transcription start sites at single-base resolution. This enables promoter identification, alternative promoter usage, and core promoter architecture analysis. RNA-seq suffers from 5′ end underrepresentation and SAGE samples internal tags, while northern blotting lacks nucleotide precision, making CAGE uniquely suited for TSS mapping.