MANIPULATING ENHANCER RNA ACTIVITY TO STUDY THEIR ROLES IN GENE REGULATION AND CANCER

Enhancers are essential regulatory elements that precisely control gene transcription during development and disease. Especially in cancer, enhancers modulate tumor gene expression, and in some cases directly drive tumorigenesis. With the recent advances in next-generation sequencing, researchers discovered that active enhancers are pervasively transcribed into RNAs, which are named enhancer RNAs (eRNAs). Studies have suggested that eRNAs have a functional role in the enhancer action mechanism. Studying their roles will provide a new understanding of gene regulation and cancer development. In my MS study, I focused on using novel methods to study eRNA functions. Using a breast-cancer-specific eRNA, I have conducted effective knockdown with both antisense oligos and CRISPR inhibition. I also explored in situ enhancer RNA activation by CRISPR mediated epigenetic activator. For some eRNAs, my data showed that individual knockdown of a single eRNA sometimes causes strong phenotypical changes of cancer cells, providing important novel targets for cancer therapeutics. To further validate and understand the functional role of specific eRNAs, I conducted ChIRP-Seq to identify its potential location in the genome to regulate target genes. Our work by using several novel methods to manipulate eRNAs has provided important knowledge of enhancer functions in gene regulation and cancer development