Functional genetic screens for structural regulatory DNA elements driving tumor progression and drug resistance

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The human genome carries genetic information in two distinct forms: Transcribed coding and non-coding genes as well as non-transcribed regulatory DNA elements (rDEs). rDEs control the magnitude and pattern of expression of genes and are indispensable for organismal development. In line with this, increasing evidence indicates that variation of rDEs is key to tumor pathogenesis, suggesting that rDEs play crucial roles in cell identity in health and disease.rDEs can be subdivided into transcriptional rDEs (t-rDEs) that recruit transcription factors to enhancers, thereby affecting gene expression, and structural rDEs (s-rDEs) that maintain chromatin 3D structure, a feature essential for regulation of genes by t-rDEs. While large-scale functional genetic screens greatly advanced our knowledge in studying mammalian genes, such tools to analyze rDEs were lacking. In the last few years, spectacular advance in genome editing technologies by the CRISPR/Cas system has not only expanded the available screening toolbox to examine genes, but also opened up novel possibilities for studying rDEs. Recently, the Agami group has developed a CRISPR strategy to target t-rDEs and has shown its scalability and effectivity in identifying potential oncogenic and tumor-suppressive t-rDEs. In the proposed project, we will exploit this experience for targeting s-rDEs, and setup functional genetic screens to identify key players in cell proliferation and survival, cancer progression and resistance to therapy. Moreover, we will investigate underlying molecular mechanisms. Thereby, our results will provide the functional knowledge necessary to better understand the role of s-rDEs in controlling the 3D chromatin structure in cancer and its implication for cancer progression and drug resistance.