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

联系方式：将糖皮质激素受体结合与内源性基因组背景中的基因调控联系起来转录因子（TF）在指定给定细胞中表达哪些基因方面起着关键作用。转录因子通常可以与数万个基因组结合位点结合，但它们似乎调控的基因数量要少得多。因此，目前还不清楚哪些TF结合区域（增强子）负责调节单个基因。在此之前的工作建议，我们已经研究了糖皮质激素受体（GR）的结合和GR依赖的基因调控之间的全局连接。此外，我们研究了单个增强子对使用基因组编辑（CRISPR/Cas9）的基因调控的贡献。这些研究揭示了GR结合和调节是明确相关的，但只有一部分结合事件导致基因的调节。在这里，我们将结合联合收割机全基因组和集中的研究与个人的增强子和启动子，以解开分子机制，促进“生产性”的启动子-增强子相互作用，导致基因表达的变化。例如，我们将生成和计算分析全基因组数据（NET-seq，Hi-ChIP，STARR-seq等），以识别相关的候选特征（例如序列基序和3D基因组组织）。此外，将使用基因组编辑研究已识别特征的作用。一种方法是研究删除鉴定的序列基序对生产性增强子-启动子接合的影响。另一种方法是确定我们是否真正理解通过工程化合成基因组增强子进行生产性GR结合的操作原理。总之，这将产生深入了解的分子机制，区分“生产性”的启动子-增强子相互作用，导致基因调控从“非生产性”的参与。

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.