(480h) Multi-Layered Gene Control in Space and Time

During development, identical cells differentiate into neurons, muscles, skins, etc., depending on the unique combination of genes that each cell type expresses. Mis-regulation of a gene often leads to serious defects. For example, ectopic expression of the eyeless gene in leg progenitor tissues results in the formation of extra eyes on the legs of a fruit fly, or disrupted enhancer-promoter interactions of the lactase gene lead to various degrees of lactose intolerance. While the importance of proper gene control is well acknowledged, complex and dynamic nature of the process makes it very challenging to establish a general “rule” of gene regulation. With combination of CRISPR/Cas9-mediated genome editing, live imaging, and mathematical modeling, we aspire to control gene expression in space and time, by manipulation the DNA in three length-scales: i) “grammar” in regulatory elements, ii) DNA-DNA interactions, and iii) global 3D genome folding. Through systematic analysis on multiple enhancers driving transcription of the same reporter gene, we demonstrated stochastic nature of transcriptional activity by visualizing transcriptional bursting, where transcriptional activity consists of a series of sequential and stochastic bursts. We also show that distinct transcription factors affect different aspects of transcription to regulate gene expression boundaries. Since the mechanism of gene regulation is conserved across species, insights obtained from our work will be relevant to other gene expression phenomena underlying metabolism and diseases.