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Exploring enhancers’ Achilles Heel

Final Report Summary - ENHREG (Exploring enhancers’ Achilles Heel)

More than 95% of the human genome is not used for coding of proteins; named also the “dark matter” of the genome. It has become increasingly clear in recent years that this non-protein-coding DNA is in fact a crucial determinat in the regulation of genes. In these regions are approximately half a million 'enhancer' elements. Enhancers are genomic regions that contain a unique set of epigenetic composition of histone marks and harbor specific binding sites for transcription factors. Enhancers function by activating target genes through DNA looping across large genomic distances. We showed that enhancers produce RNA (termed enhancerRNA) that is required for efficient expression of target genes.
Interestingly, recent studies indicated that dysfunctional enhancers contribute to disease progression. For example, cancer-predisposing single-nucleotide polymorphisms, large-scale genomic rearrangements, and somatic mutations, were shown to affect enhancer activity and cause cancer. However, to further study the role of eRNAs we lack unbiased methods to systematically interrogate the functions of enhancers. Towards this goal, we recently published a proof-of-concept paper demonstrating the possibility to perform enhancer screens using the CRISPR-Cas9 genome editing technology. We showed that both positive selection and drop out types of screens could be used, as well as a tiling approach to uncover novel functional elements within enhancers.
Our established procedures for identifying functional enhancers allowing us to perform functional genetic screens and assess the role of enhancers as oncogenes and tumor suppressor regions. Moreover, this technology will be used to identify crucial elements of eRNAs in their endogenous location, experiments that were impossible to efficiently perform before the emergence of the CRISPR-Cas9 technology. In the last two years we continued to establish the approach, and improve it. As of now, our approach is widely used by researchers in the field of transcription regulation.
Lastly, we also opened a new field of gene regulation. This was based on our expertise in the fields of transcription and translation. We found mRNA modifications to link the two processes, a new phenomenon that helps understand the tight control of gene regulation in times of stress or during cancer progression.