Periodic Reporting for period 3 - Enhancer ID (Identification and functional characterization of mammalian enhancers and transcriptional co-factors during cellular signaling and cell fate transitions)
Reporting period: 2018-09-01 to 2020-02-29
Our project 'Enhancer ID' undertakes a functional genomics approach in mammalian cells with three specific objectives: First, we aim to identify and functionally characterize transcriptional enhancers in selected human and mouse cells using the recently developed quantitative enhancer activity assay STARR-seq. Second, we will determine enhancer activity changes quantitatively in the presence and absence of cellular signaling cues. Third, we will systematically dissect the functional relationship of enhancers and transcriptional co-factors using small molecule inhibitors and recently developed CRISPR/Cas9-based technologies.
This proposal addresses fundamental questions in enhancer biology and complement the genome-wide profiling of gene expression and chromatin states (e.g. by ENCODE). We will gain insights into the genomic organization of active enhancers and reveal chromatin or sequence features associated with dynamic activity changes. I also expect that we will be able to define co-factor requirements for enhancer function and reveal if different types of enhancers exist, an important advance towards the understanding of gene regulation in mammals.
Our main results from this period are a new and improved STARR-seq protocol and optimized parameters and protocols for screening under signaling conditions. The pilot experiments using cofactor inhibition further revealed the existence of enhancers with different cofactor dependencies, which we will now follow up.
The systematic characterization of the cofactor-requirements of different enhancers should not only be important for our basic understanding of transcriptional regulation but might also inform novel therapeutic strategies that are based on the inhibition of different transcriptional cofactors.