ABSTRACT
Most human protein-coding genes are regulated by multiple, distinct promoters, suggesting that the choice of promoter is as important as its level of transcriptional activity. While the role of promoters as driver elements in cancer has been recognized, the contribution of alternative promoters to regulation of the cancer transcriptome remains largely unexplored. Here we show that active promoters can be identified using RNA-Seq data, enabling the analysis of promoter activity in more than 1,000 cancer samples with matched whole genome sequencing data. We find that alternative promoters are a major contributor to tissue-specific regulation of isoform expression and that alternative promoters are frequently deregulated in cancer, affecting known cancer-genes and novel candidates. Noncoding passenger mutations are enriched at promoters of genes with lower regulatory complexity, whereas noncoding driver mutations occur at genes with multiple promoters, often affecting the promoter that shows the highest level of activity. Together our study demonstrates that the landscape of active promoters shapes the cancer transcriptome, opening many opportunities to further explore the interplay of regulatory mechanism and noncoding somatic mutations with transcriptional aberrations in cancer.
