Genome 3D organization as a determinant of cell-fate decisions

Eunice Kennedy Shriver National Institute Of Child Health & Human Development

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Abstract

Studying gene regulation is crucial for understanding how disruptions in developmental gene expression lead to birth defects, enabling earlier diagnosis and potential intervention strategies. Our long-term scientific goal is to decipher how, within a crowded nucleus, regulatory elements known as enhancers are specifically guided to their target genes. Some enhancers can activate genes across large distances while bypassing potential off-target genes. This demonstrates a remarkable degree of specificity for their targets, in contrast to other enhancers that are largely promiscuous and activate a wide variety of promoters. How such specificity is achieved for distal enhancers has remained extremely unclear. DNA loops formed by the protein CTCF provide a simple and testable model to explain how genome-folding mechanisms can influence enhancer–promoter specificity. CTCF loops have been proposed to help recruit distal enhancers to initiate transcription. These loops also restrict enhancer–promoter interactions, and several boundary deletions have been shown to expose promoters to neighboring enhancers, resulting in ectopic expression and developmental phenotypes. However, our previous work has shown that disruption of some chromatin domains has a negligible effect on gene regulation and animal development. Because loops are constantly remodeled and their anchors remain in close proximity only transiently, it is unclear how they molecularly insulate enhancers. These observations highlight our incomplete understanding of the physiological impact of CTCF loops on gene regulation. This past year, we finalized a study in which we hypothesized that CTCF loops containing multiple genes important for mammalian development may play a particularly important role in ensuring healthy pregnancies. This hypothesis turned out to be correct. When we disrupted a loop containing three genes from the FGF family of growth factors, we demonstrated that very small DNA variants—as short as a single CTCF motif—can have a dramatically severe impact on healthy development. Specifically, we showed that disruption of a CTCF motif between the FGF and Ano1 genes results in encephalocele, a human birth defect that affects approximately 1 in 10,000 births. Importantly, we have generated an in vivo model of this disease, which we are now using to test therapies that may improve this severe birth defect.