Which method maps transcription start sites genome-wide?

• A. 5' RACE
• B. RNA-Seq
• C. CAGE (Cap Analysis of Gene Expression)
• D. ChIP-Seq

Answer: (C)

Mapping transcription start sites across the genome relies on capturing the 5' ends of capped RNAs. CAGE does exactly this by selecting RNAs with a 5' cap, extracting short tags from their beginnings, and sequencing those tags. Each tag points to where transcription starts in the genome, so clustering many tags reveals the precise transcription start sites and how promoter activity is used across genes. This genome-wide, base-precision view isn’t provided by standard RNA-Seq, which samples reads throughout transcripts and often doesn’t pinpoint the exact start site. It also isn’t what 5' RACE does, since 5' RACE targets the start of a single known transcript rather than surveying the whole genome. ChIP-Seq maps protein binding or histone marks associated with promoters, giving promoter locations but not the exact start coordinates of transcription.