Genomic Analysis into Transcriptional Regulation of Cell Identity

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Project Summary/Abstract Every single cell in an organism has almost the exact same genomic information, yet cells in the body develop into vastly different cell identities. For example, how does one cell become a liver cell and another cell become a skin cell? This terminal differentiation into distinct cell types is due to correct transcriptional regulation for that cell type. Transcription factors (TFs) are regulatory proteins that bind to specific sequences of DNA, response elements, to turn on or off genes for that cell type. Throughout development, TFs navigate the chromatin landscape of the cell and bind response elements, integrating physiological and gene-specific cues, directing precise gene regulatory networks. Critical to TF action is recognition of the correct response element and subsequent regulation to its appropriate target gene, while not affecting the neighboring genes’ regulation. However, how a TF recognizes the correct response element and target gene is not well understood. Mutations in TFs and their response elements result in a wide array of human diseases, thus understanding these basic mechanisms of transcription factor fidelity is critical to our understanding of human health. Our long-term goal is to characterize the mechanism of TF response element recognition and target gene recognition in dinstinct cell types. C. elegans provides a unique opportunity to study TF regulation due to its compact genome. Intergenic distance in C. elegans is on average 2 Kbp, which allows for easier correlation of response element to target gene due to the reduced genomic complexity while likely requiring efficient mechanism to shield aberrant TF action. In this proposal we use a well-studied nuclear hormone receptor, NHR-25, with two mammalian orthologs, NR5A1/SF-1 and NR5A2/SF-2, to interrogate TF binding and cell-type specific target gene regulation. We will do so through a combination of genomic and genetic techniques, exploiting new genome editing methods, chromatin binding assays, and unique genomic features of C. elegans. These experiments will provide insight into how TFs recognize their response element and target gene while training undergraduate scientists in cutting-edge, genomic techniques.