A major goal in biology is to understand how gene regulatory information is encoded by the human genome and how it defines different gene expression programs and cell types. This is an important goal for both basic science and medical research, as mis-regulation of genes underlies many diseases such as cancer. Enhancers are genomic elements that control transcription, yet despite their importance, only a minority of enhancers are known and functionally characterized. In particular, their activities, activity changes and the underlying DNA sequence features have largely remained elusive. Furthermore, fundamental questions about transcriptional cofactors have remained unanswered even though they regulate enhancer activities and have become attractive therapeutic targets, e.g. for cancer treatment.
Our project 'Enhancer ID' undertook a functional genomics approach to identify transcriptional enhancers using the recently developed quantitative enhancer activity assay STARR-seq. We adapted STARR-seq to mammalian cells, identified enhancers and measured their activities and activity changes. We also determined chromatin and sequence properties of the identified enhancers, particularly the DNA sequence motifs that underly enhancer activity and strength. Finally, we systematically dissected the functional relationship between enhancers and transcriptional cofactors using rapid cofactor depletion with the recently developed auxin-inducible-degron (AID) technology.
This proposal addressed fundamental questions in enhancer biology and complemented the genome-wide profiling of gene expression and chromatin states (e.g. by ENCODE). We gained insights into the genomic organization of enhancers and revealed their chromatin and sequence features. Finally, we defined cofactor requirements for enhancer function and revealed that different types of enhancers exist that differentially depend on different cofactors, an important advance towards the understanding of enhancer biology and gene regulation.
