Enhancers are DNA switches that regulate the expression of genes in cells. Human cells have about 20,000 genes and more than 200,000 enhancers. Alterations in enhancer activity is increasingly linked to cancer development. Clear cell renal cell carcinoma (ccRCC) is the prototypical enhancer-driven cancer. Enhancers can be located within or outside genes and can regulate multiple genes simultaneously. However, pairing enhancers with their target genes is extremely challenging. This is because enhancers can regulate genes that are located hundreds of kilobase pairs away and can often skip the nearest genes. Understanding the enhancer-gene connectivity can explain how gene transcription gets dy...

Read More

Enhancers are DNA switches that regulate the expression of genes in cells. Human cells have about 20,000 genes and more than 200,000 enhancers. Alterations in enhancer activity is increasingly linked to cancer development. Clear cell renal cell carcinoma (ccRCC) is the prototypical enhancer-driven cancer. Enhancers can be located within or outside genes and can regulate multiple genes simultaneously. However, pairing enhancers with their target genes is extremely challenging. This is because enhancers can regulate genes that are located hundreds of kilobase pairs away and can often skip the nearest genes. Understanding the enhancer-gene connectivity can explain how gene transcription gets dysregulated in ccRCC. Such studies can also set the stage for enhancer-targeting approaches for cancer treatment. We propose to develop new technologies to understand enhancer-gene interactions. Long-read sequencing was selected as the method of the year by the journal Nature Methods in 2022. However prior studies have not been successful in using long-read sequencing to define the enhancer hubs. The presence of bulky protein adducts in the DNA interferes with long-read sequencing. We propose to solve this problem by developing the Chromatin Interaction Analysis by Sequencing (ChIA-Seq) technology. With this approach, we seek to unleash the power of long-read sequencing in combination with our innovative method to map multivalent chromatin interactions associated with RNA Polymerase II in patient tumors. Our method will be optimized by analyzing human specimens (rather than cell lines and xenografts), making it truly high impact and high risk. Successful completion of the proposed study will enhance our understanding of transcriptional regulation in ccRCC from a one-dimensional to a multi-dimensional level. Overall, our studies will impact several aspects of clinical disease management ranging from prevention, early diagnosis and therapeutic targeting.

Read Less