Practice question

CAGE exploits the unique 5′ cap structure of RNA polymerase II transcripts. In eukaryotes, a 7-methylguanosine is added co-transcriptionally to the first nucleotide. CAGE employs cap-trapping, where biotinylated cap is selected after cDNA synthesis, ensuring enrichment of full-length 5′ ends. Sequencing of these capped ends yields tags precisely marking transcription initiation sites and promoter boundaries. SAGE uses internal NlaIII sites, poly(A) profiling selects 3′ ends, and microarrays rely on hybridization without cap specificity, so only CAGE intrinsically depends on cap recognition for genome-wide promoter mapping.