Bio

Yingying is a postdoctoral researcher at Kay Lab. She completed her PhD at Peking Union Medical College in China in 2024, under the supervision of Prof. De-Pei Liu. Her research focused on gene editing and ssDNA-protein interactions. During her PhD, she developed an innovative strategy to enhance HDR efficiency of ssDNA donors by incorporating HDR-boosting modules. In 2025, she joined Kay Lab, where her current work involves improving exogenous gene expression delivered by AAV through engineering the AAV genome.

Stanford Advisors

  • Mark Kay, Postdoctoral Faculty Sponsor

Contact

  • Academic
    yyjin@stanford.edu
    University - Scholar Department: Pediatrics Position: Postdoctoral Scholar

Additional Info

All Publications

  • Optimizing homology-directed repair for gene editing: the potential of single-stranded DNA donors. Trends in genetics : TIG Jin, Y. Y., Zhang, P., Liu, D. P. 2025

    Abstract

    CRISPR (clustered regularly interspaced short palindromic repeat) system-based precise genome editing remarkably impacts both scientific investigation and therapeutic practices. Among various techniques, DNA donor-mediated homology-directed repair (HDR) represents a promising method for precise gene editing. Although efficiency constraints have previously limited HDR, recent advancements have significantly enhanced its effectiveness. Therefore, it is essential to highlight the progress made in this field and to reassess the potential of the HDR approach. In this review, we explore the fundamental principles of HDR-dependent gene editing and evaluate current strategies to enhance HDR efficiency, with particular emphasis on single-stranded DNA (ssDNA) donor-mediated HDR. Finally, we discuss the prospects of high-efficiency ssDNA donor-mediated precise gene editing in laboratory research and clinical therapies.

    View details for DOI 10.1016/j.tig.2025.04.014

    View details for PubMedID 40436684

  • Enhancing homology-directed repair efficiency with HDR-boosting modular ssDNA donor. Nature communications Jin, Y. Y., Zhang, P., Liu, L. L., Zhao, X., Hu, X. Q., Liu, S. Z., Li, Z. K., Liu, Q., Wang, J. Q., Hao, D. L., Zhang, Z. Q., Chen, H. Z., Liu, D. P. 2024; 15 (1): 6843

    Abstract

    Despite the potential of small molecules and recombinant proteins to enhance the efficiency of homology-directed repair (HDR), single-stranded DNA (ssDNA) donors, as currently designed and chemically modified, remain suboptimal for precise gene editing. Here, we screen the biased ssDNA binding sequences of DNA repair-related proteins and engineer RAD51-preferred sequences into HDR-boosting modules for ssDNA donors. Donors with these modules exhibit an augmented affinity for RAD51, thereby enhancing HDR efficiency across various genomic loci and cell types when cooperated with Cas9, nCas9, and Cas12a. By combining with an inhibitor of non-homologous end joining (NHEJ) or the HDRobust strategy, these modular ssDNA donors achieve up to 90.03% (median 74.81%) HDR efficiency. The HDR-boosting modules targeting an endogenous protein enable a chemical modification-free strategy to improve the efficacy of ssDNA donors for precise gene editing.

    View details for DOI 10.1038/s41467-024-50788-x

    View details for PubMedID 39122671

    View details for PubMedCentralID PMC11315919

  • Schlafen 11 triggers innate immune responses through its ribonuclease activity upon detection of single-stranded DNA SCIENCE IMMUNOLOGY Zhang, P., Hu, X., Li, Z., Liu, Q., Liu, L., Jin, Y., Liu, S., Zhao, X., Wang, J., Hao, D., Chen, H., Liu, D. 2024; 9 (96): eadj5465

    Abstract

    Nucleic acids are major structures detected by the innate immune system. Although intracellular single-stranded DNA (ssDNA) accumulates during pathogen infection or disease, it remains unclear whether and how intracellular ssDNA stimulates the innate immune system. Here, we report that intracellular ssDNA triggers cytokine expression and cell death in a CGT motif-dependent manner. We identified Schlafen 11 (SLFN11) as an ssDNA-activated RNase, which is essential for the innate immune responses induced by intracellular ssDNA and adeno-associated virus infection. We found that SLFN11 directly binds ssDNA containing CGT motifs through its carboxyl-terminal domain, translocates to the cytoplasm upon ssDNA recognition, and triggers innate immune responses through its amino-terminal ribonuclease activity that cleaves transfer RNA (tRNA). Mice deficient in Slfn9, a mouse homolog of SLFN11, exhibited resistance to CGT ssDNA-induced inflammation, acute hepatitis, and septic shock. This study identifies CGT ssDNA and SLFN11/9 as a class of immunostimulatory nucleic acids and pattern recognition receptors, respectively, and conceptually couples DNA immune sensing to controlled RNase activation and tRNA cleavage.

    View details for DOI 10.1126/sciimmunol.adj5465

    View details for Web of Science ID 001285617800001

    View details for PubMedID 38875319

https://orcid.org/0009-0000-6356-5576