ABSTRACT
This chapter describes some of the major biological lessons learned by applying Cap Analysis of Gene Expression (CAGE) to the human and mouse genomes. It discusses these finding to text-book views on core promoters and transcription initiation, and shows that the data opens many doors for both experimental and computational analysis of core promoters and their mechanisms. The chapter summarizes the lessons learned from CAGE so far, and highlights some examples of studies that were motivated from these findings. When comparing well-annotated promoters with multiple transcriptional starting sites (TSS), these generally agree well with the CAGE data — differences are often due to that the CAGE tag sampling is much deeper than that of the original experiments. A byproduct of the investigation of exonic TSSs was the finding that some protein-coding genes have a higher aggregation of TSSs in the last 20% portion of its last exon — usually in the 3’ UTR.
