Looping Enhancers and Promoters give Specificity

Objetivo

The next frontier in genomics is to understand and predict how the non-coding genome, including distal regulatory elements (enhancers), regulate precise patterns of gene expression. This is crucial to our understanding of development, evolution and disease, with huge clinical relevance to decode the vast majority of disease associated variants. Although many variants impact enhancers, it remains a major challenge to identify their target gene. This is largely because genes have many enhancers, often spanning great distances with many genes in between. How enhancers recognise the correct gene, ignoring others, remains one of the greatest mysteries in genome regulation. The factors involved and sequence-level determinants of enhancer-promoter (E-P) specificity remain elusive.

Here, we will combine systematic genetics, high-resolution genomics, and deep learning to perform the first large-scale functional dissection of the trans-factors and cis-regulatory features required for E-P looping and specificity in an in vivo context, using Drosophila embryogenesis. Drosophila has a track record of identifying conserved regulators of E-P communication from flies to man, including the discovery of Ldb1 and cohesin, and offers unmatched resources for this task: (a) genome-wide lines enabling tissue-specific knockdown of every gene; (b) efficient P-element transposon hopping, to force loops and sense enhancers to assess E-P specificity; (c) a near-complete map of regulatory elements for all embryonic stages. This proposal has three complementary Aims, to: 1) Identify new genes and cis-regulatory features functionally required for E-P looping; 2) Dissect, model, and predict sequence rules underlying E-P specificity & 3) Determine functional E-P pairs at scale by combining promoter engineering and mobilised enhancer sensors. Together, these approaches will provide unprecedented insights into regulatory specificity, transforming our understanding and decoding of genome regulation