Cis-Regulatory Role of Alternative Promoters in Cancer

Alternative promoters are increasingly recognized as critical regulators in cancer, enabling the expression of isoforms with distinct functions, often supporting oncogenic activity. Beyond initiating transcription, promoters have been shown to serve as cis-regulatory elements, enhancing or compensating for the expression of neighboring genes. 3D genomics assays show that alternative promoters of the same gene interact with each other at the chromatin level. However, it is unknown whether this chromatin interaction plays a functional cis-regulatory role in the transcriptional expression of the host gene. Our analysis of TCGA and ENCODE data shows that minor alternative promoters exhibit enhancer-like histone modification signatures and cancer-specific chromatin accessibility. Preliminary studies further reveal that minor alternative promoters of oncogenes, such as EGFR, interact with the major alternative promoter, and show both enhancer and compensation activity in a cancer-type specific manner, indicating their cis-regulatory potential. However, the prevalence and mechanism of cis-regulatory alternative promoters in cancer remains largely unexplored. Our hypothesis is that minor alternative promoters serve as cis-regulatory elements that can enhance or compensate for major promoters, representing a common mechanism to ensure robust expression of cancer-related genes. Aim 1 will assess the enhancer role of minor alternative promoters for cancer-related genes. Focusing on genes that harbor enhancer-like minor promoters, we will use CRISPR interference (CRISPRi) and CRISPR activation to manipulate minor promoter activity and assess the impact on major isoform expression. We will also evaluate the role of cancer-type specific transcriptional master regulators in governing this enhancer activity and further determine the functional relevance of this enhancer activity on cancer cell fitness. Aim 2 will evaluate the compensatory role of minor promoters by repressing the major promoter with CRISPRi and assessing minor isoform expression. We will use HiChIP assays to assess whether shifts in enhancer interactions contribute mechanistically to the compensation. Currently the field lacks understanding in how alternative promoters function as cis-regulatory elements, limiting our ability to comprehend how cancer cells exploit alternative promoters to promote oncogenic activity in cancer cells. These studies will define a mechanism by which alternative promoters regulate oncogenic gene expression through enhancer-like and compensatory functions. Our findings will generate a resource of cancer-type specific genes with alternative promoters that exhibit cis-regulatory functions, offering potential targets for cancer therapy and providing a new approach to modulate oncogene expression in cancer cells. Project Number: 1F31CA310722-01 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Emily Wilson | Institution: UTAH STATE HIGHER EDUCATION SYSTEM--UNIVERSITY OF UTAH, SALT LAKE CITY, UT | Award Amount: $40,908 | Activity Code: F31 | Study Section: Special Emphasis Panel[ZRG1 F09A-R (20)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11318708