Making contact: Linking glucocorticoid receptor binding to the regulation of genes in the endogenous genomic context

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Making contact: Linking glucocorticoid receptor binding to the regulation of genes in the endogenous genomic contextTranscription factors (TFs) play a pivotal role in specifying which genes are expressed in a given cell. TFs can typically bind to tens of thousands of genomic binding sites, yet they seem to regulate a much smaller number of genes. Consequently, it is mostly unclear which TF-bound regions (enhancers) are responsible for the regulation of individual genes. In work preceding this proposal, we have studied the global connection between glucocorticoid receptor (GR) binding and GR-dependent gene regulation. In addition, we studied the contribution of an individual enhancer to gene regulation using genome-editing (CRISPR/Cas9). These studies uncovered that GR binding and regulation are clearly connected, but that only a subset of binding events results in the regulation of genes. Here, we will combine genome-wide and focused studies with individual enhancers and promoters to unravel molecular mechanisms that facilitate “productive” promoter-enhancer interactions resulting in changes in gene expression. For example, we will generate and computationally analyze genome-wide data (NET-seq, Hi-ChIP, STARR-seq, etc) to identify associated candidate features (e.g. sequence motifs and 3D genome organization). In addition, the role of identified features will be studied using genome editing. One approach will be to study the effect of deleting identified sequence motifs on productive enhancer-promoter engagements. Another approach is to determine if we really understand the operating principles of productive GR binding by engineering synthetic genomic enhancers. Together, this will yield insights into the molecular mechanisms that discriminate “productive” promoter-enhancer interactions resulting in gene regulation from “non-productive” engagements.