In Metazoans, transcription of most genes is driven through the use of multiple alternative promoters. Although the precise spatio-temporal regulation of alternative promoters is important for proper gene expression, the mechanism that mediates their differential utilization remains unclear. Here, we investigate how the two alternative promoters (P1, P2) that drive MYC expression are regulated. We find that P1 and P2 can be differentially regulated across cell-types, and that their selective usage is largely mediated by distal regulatory sequences. Moreover, we show that in the colon carcinoma cell line HCT-116, Wnt-responsive enhancers preferentially upregulate transcription from the P1 promoter using both transgenic reporter assays and in the context of the endogenous Myc locus upon Wnt induction. In addition, multiple enhancer deletions using CRISPR/Cas9 corroborate the regulatory specificity of P1. Finally, we show that preferential activation between Wnt-responsive enhancers and the P1 promoter is influenced by distinct core promoter elements present in the two MYC promoters. Taken together, our results provide new insights into how enhancers can specifically target alternative promoters and suggest that formation of these selective interactions could allow more diverse combinatorial regulation of transcription initiation.
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