Yunbeen Bae

All Publications

• Programmable promoter editing for precise control of transgene expression NATURE BIOTECHNOLOGY Kabaria, S. R., Bae, Y., Ehmann, M. E., Lende-Dorn, B. A., Beitz, A. M., Peterman, E. L., Love, K. S., Ploessl, D. S., Galloway, K. E. 2025

  Abstract

  Subtle changes in gene expression direct cells to distinct cellular states. Identifying and controlling dose-dependent transgenes require tools for precisely titrating expression. Here, we develop a highly modular, extensible framework called DIAL for building editable promoters that allow for fine-scale, heritable changes in transgene expression. Using DIAL, we increase expression by recombinase-mediated excision of spacers between the binding sites of a synthetic zinc finger transcription factor and the core promoter. By nesting varying numbers and lengths of spacers, DIAL generates a tunable range of unimodal setpoints from a single promoter. Through small-molecule control of transcription factors and recombinases, DIAL supports temporally defined, user-guided control of transgene expression that is extensible to additional transcription factors. Lentiviral delivery of DIAL generates multiple setpoints in primary cells and induced pluripotent stem cells. As promoter editing generates stable states, DIAL setpoints are heritable, facilitating mapping of transgene levels to phenotype and fate in direct conversion to induced motor neurons. The DIAL framework opens opportunities for tailoring transgene expression and improving the predictability and performance of gene circuits across diverse applications.

  View details for DOI 10.1038/s41587-025-02854-y

  View details for Web of Science ID 001591944100001

  View details for PubMedID 41083901

  View details for PubMedCentralID 3913367

• Chemogenetic tuning reveals optimal MAPK signaling for cell-fate programming. Cell reports Lende-Dorn, B. A., Atkinson, J. C., Bae, Y., Galloway, K. E. 2025; 44 (9): 116226

  Abstract

  Cell states evolve through the combined activity of signaling pathways and gene networks. While transcription factors can direct cell fate, these factors rely on a receptive cell state. How signaling levels contribute to the emergence of receptive cell states remains poorly defined. Using a well-defined model of direct conversion, we examined how levels of the mitogen-activated protein kinase (MAPK)-activating oncogene HRASG12V influence direct conversion of primary fibroblasts to induced motor neurons. The rates of direct conversion respond biphasically to increasing HRASG12V levels. An optimal "Goldilocks" level of MAPK signaling efficiently drives cell-fate programming, whereas high levels of HRASG12V induce senescence. Through chemogenetic tuning, we set the optimal MAPK activity for high rates of conversion in the absence of HRAS mutants. In addition to proliferation, MAPK signaling influences conversion by regulating Ngn2 activity. Our results highlight the need to tune therapeutic interventions within a non-monotonic landscape that is shaped by genetics and levels of gene expression.

  View details for DOI 10.1016/j.celrep.2025.116226

  View details for PubMedID 40913769