Isabel Esain Garcia

CRISPR genome editing is revolutionising the world of treatment possibilities for genetic diseases, however safe and precise editing remains an open challenge. Each cell of our body has the same genetic code (DNA), however how the information in each cell is accessed and regulated is different based on an additional layer of information, the epigenome. This layer is built by chemical modifications which decorate the DNA and dysregulation of those epigenetic patterns lead to changes in the 3D shape of DNA which allows it to be recognised differently by cellular machinery often leading to genetic disease and cancer. My PhD research is based on the idea that DNA secondary structure stores information in the human genome, acting like an epigenetic feature with a critical role in gene expression, particularly in cancer genes. My main aim is to target and engineer DNA structure to control cancer genes. In this study, I investigated by genetically editing human cells the role of DNA structure as regulatory element of the MYC oncogene, one of the most critical genes that control how cancer cells divide. Using gene-editing CRISPR technologies, genome profiling analytical techniques, next-generation sequencing (NGS) and biophysical assays, I demonstrate the critical role of DNA structure in driving cancer gene expression. Changes in DNA structure are accompanied by the loss of binding of essential proteins that regulate gene expression, such as transcription factors, histone modifiers and nucleosome remodellers. Remarkably, when we replace a specific DNA structure with an unrelated sequence that folds into a similar 3D shape, we can recover the same gene expression and protein binding. Overall, we now have a greater understanding of oncogene regulation where DNA secondary structure takes a leading role that we can target in our path towards precision genome engineering.