Cell Fusion and Gene Expression in the C. elegans Epidermis

Cell–cell fusion, a fundamental biological process that is critical for multicellular organism development, has essential roles in conception, placentation, myogenesis, the immune response, and tissue regeneration. Despite the ubiquity of cell–cell fusion, the molecular mechanisms governing gene expression and nuclear function in multinucleate cells remain largely unknown. This research proposal uses the C. elegans epidermal syncytium as a powerful in vivo system to uncover fundamental mechanisms of multinucleate cell formation and function. This innovative, multidisciplinary approach combines single-nucleus genomics, advanced microscopy, and genome engineering to investigate three key scientific aims. First, this work will explore how cell fusion facilitates epidermal specification by examining transcriptional regulation and focusing on the ELT-3 transcription factor and its downstream genes. By tracking target gene expression and ELT-3 localization, the study will determine how cytoplasmic sharing during fusion drives developmental progression. The second aim will investigate fusion's role in synchronizing oscillatory gene control and extracellular matrix organization. Through longitudinal RNA sequencing paired with confocal light and transmission electron microscopy, I will track cuticle gene expression patterns and structural changes in fusion-defective mutants. This approach will reveal how cell fusion coordinates developmental timing and gene regulation across different developmental stages. The third aim will comprehensively examine nuclear heterogeneity within the syncytium. Using single-nucleus RNA sequencing and single-molecule FISH, I will map individual nuclear transcriptomes and connect them to developmental lineages to explore whether nuclei maintain distinct identities or converge to a shared fate. This study will offer unprecedented insights into the transcriptional consequences of cell fusion, in part through innovative technical approaches—including conditional fusion mutants and single-nucleus sequencing. This research will provide a comprehensive understanding of how cytoplasmic sharing and nuclear interactions drive cellular differentiation and tissue development. My findings will have broad implications across biology, illuminating mechanisms underlying developmental processes in syncytial tissues and providing a basis for understanding the implications of fusion defects in human health and disease. Project Number: 1K99GM163004-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of General Medical Sciences (NIGMS) | Principal Investigator: Owen Funk | Institution: UNIVERSITY OF WYOMING, LARAMIE, WY | Award Amount: $123,687 | Activity Code: K99 | Study Section: Special Emphasis Panel[ZRG1 CDB-Z (80)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11282482