Yongsheng Shi
Biography
Yongsheng Shi, Ph.D., is Dean's Professor and Director of the UCI Center for RNA Science and Therapeutics in the Department of Microbiology and Molecular Genetics at the University of California, Irvine. His research focuses on RNA processing and degradation, particularly the mechanisms of mRNA 3' end processing and alternative polyadenylation, and their roles in stem cell biology, cancer, and viral infection. Shi received his Ph.D. in Biology from Syracuse University in 2002 and completed postdoctoral training with Dr. James L. Manley at Columbia University before joining the UCI faculty in 2008.
Shi has made contributions to understanding how cells regulate mRNA 3' processing through protein-RNA interactions and how these mechanisms control gene expression in development and disease. His laboratory developed PAS-seq, a method for global profiling of polyadenylated RNAs, and has used genome-wide approaches to map protein-RNA interactions that determine polyadenylation site selection. His work has revealed how mRNA processing factors regulate stem cell self-renewal and differentiation, how viruses manipulate host RNA processing machinery, and how cells use nuclear RNA degradation pathways for transcriptome surveillance. Recent work from his laboratory identified a nuclear degradation code that governs RNA quality control in eukaryotic cells.
Shi has served as a regular member of NIH study sections and the American Cancer Society RNA Mechanisms Study Section. He has been an editorial board member for Gene Expression and Genes and Development, and co-organized the Cold Spring Harbor Laboratories RNA Processing meeting from 2021 to 2025. Shi is a member of The RNA Society and has organized multiple RNA symposia, including the SoCal RNA Symposium and the UCI RNA symposium.
Return to topEducation
- Ph.D. in Biology, Syracuse University, 2002
- B.S. in Biochemistry and Molecular Biology, Nankai University, 1996
Distinctions
- Ruth L. Kirschstein National Research Award, National Institutes of Health, 2004-2006
- Dean's Professor, University of California, Irvine, 2025
- American Cancer Society Research Scholar Award, 2012
- Chancellor's Fellow, University of California, Irvine, 2019-2021
Areas of Expertise
- RNA Processing and Regulation
- Alternative Polyadenylation Mechanisms
- Stem Cell Self-Renewal
- Pre-mRNA 3' End Formation
- Nuclear RNA Degradation Pathways
- Viral Infection Host Interactions
- Transcriptome Surveillance Mechanisms
Recent Publications
- Tian L., Liu L., Yoon Y., Soles L.V., Valdez M., Jeong J., Yu C., Huang L., Shi Y., “LENG8 mediates RNA nuclear retention and degradation in eukaryotes” (opens in new tab), Molecular Cell, 2026.
- Yoon Y, Bournique E, Soles LV, Yin H, Chu HF, Zhuang Y, Liu X, Liu L, Yu C, Valdez M, Tian L, Huang L, Shi X, Ding F, Tong L, Buisson R, Shi Y, “RBBP6 anchors pre-mRNA 3' end processing to nuclear speckles” (opens in new tab), Molecular Cell, vol. 85, no. 3, pp. 555-570, 2025.
- Soles LV, Liu L, Zou X, Yoon Y, Li S, Tian L, Valdez MC, Yu A, Yin H, Li W, Ding F, Seelig G, Li L, Shi Y, “A nuclear degradation code for eukaryotic transcriptome surveillance” (opens in new tab), Molecular Cell, vol. 85, no. 8, pp. 1575-1588, 2025.
- Jeong J., Hertel K.J., Shi Y., “RNA-binding proteins: it’s better to play in a band” (opens in new tab), Genes and Development, vol. 39, pp. 301-303, 2025.
- Fleur AL, Shi Y, Seelig G, “Decoding biology with massively parallel reporter assays and machine learning” (opens in new tab), Genes and Development, vol. 38, pp. 823-842, 2024.
- Liu L, Yu AM, Wang X, Soles LV, Teng X, Chen Y, Yoon Y, Sarkan KSK, Valdez MC, Linder J, England W, Spitale RC, Yu Z, Marazzi I, Qiao F, Li W, Seelig G, Shi Y, “Hidden sequence specificity of mRNA 3' processing revealed by the anti-cancer compound JTE-607”, Nature Structural and Molecular Biology, vol. 30, no. 12, pp. 1947-1957, 2023.
- Liu L., Yu A.M., Wang X., Soles L.V., Teng X., Chen Y., Yoon Y., Sarkan K.S.K., Valdez M.C., Linder J., England W., Spitale R., Yu Z., Marazzi I., Qiao F., Li W., Seelig G., Shi Y., “The anticancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3′ processing machinery” (opens in new tab), Nature Structural and Molecular Biology, vol. 30, pp. 1947-1957, 2023.
- Yoon Y, Shi Y, “Human pre-mRNA 3' processing: reconstitution is believing” (opens in new tab), Genes and Development, vol. 36, no. 3-4, pp. 106-107, 2022.
- Soles LV, Shi Y, “Crosstalk Between mRNA 3′-End Processing and Epigenetics” (opens in new tab), Frontiers in Genetics, vol. 12, pp. 637705, 2021.
- Wang X, Liu L, Whisnant AW, Hennig T, Djakovic L, Haque N, Bach C, Sandri-Goldin RM, Erhard F, Friedel CC, Dölken L, Shi Y, “Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation” (opens in new tab), Plos Genetics, vol. 17, no. 3, pp. e1009263, 2021.
- Yoon Y, Shi Y, “PAS-seq2: a fast and sensitive method for global profiling of polyadenylated RNAs” (opens in new tab), Methods in Enzymology, vol. 655, pp. 25-35, 2021.
Most Cited Publications
- Shi, Y., Giammartino, DD., Sharkeshik, A., Taylor, D., Rice, W, Yates, JR, 3rd, Frank, J., Manley, JL., “Molecular architecture of the human pre-mRNA 3' processing complex” (opens in new tab), Molecular Cell, vol. 33, no. 3, pp. 365-76, 2009.
- Shepard, PJ., Choi, E., Lu, J., Flanagan, LA., Hertel, KJ., Shi, Y., “Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq” (opens in new tab), RNA., vol. 17, no. 4, pp. 761-772, 2011.
- Shi, Y., Manley, JL., “The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site” (opens in new tab), Genes and Development, vol. 29, pp. 889-897, 2015.
- Chan, SL., Huppertz, I., Yao, C., Weng, L., Moresco, JJ., Yates, JR. 3rd, Ule, J., Manley, JL., Shi, Y., “CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3' processing” (opens in new tab), Genes and Development, vol. 28, pp. 2370-2380, 2014.
- Shi, Y., “Alternative polyadenylation: new insights from global analyses” (opens in new tab), RNA, vol. 18, no. 12, pp. 2105-2117, 2012.
- Yao, C., Biesinger, J., Wan, J., Weng, L., Busch, A., Xing, Y., Xie, X., Shi, Y., “Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation” (opens in new tab), Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 46, pp. 18773-8, 2012.
- Zhu Y, Wang X, Forouzmand E, Jeong J, Feng Q, Sowd G, Engelman A, Xie X, Hertel KJ, Shi Y, “Molecular mechanisms for CFIm-mediated regulation of mRNA alternative polyadenylation” (opens in new tab), Molecular Cell, vol. 69, no. 1, pp. 62-74, 2018.
- Shi, Y., Yokoyama, S., “Molecular analysis of the evolutionary significance of ultraviolet vision in vertebrates” (opens in new tab), Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 14, pp. 8308-13, 2003.
- Lackford, B., Yao, C., Charles, G., Weng, L., Zheng, X., Choi, E., Xie, X., Wan, J., Xing, Y., Freudenberg, J., Yang, P., Jothi, R., Hu, G., Shi, Y., “Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal” (opens in new tab), EMBO Journal, vol. 33, no. 8, pp. 878-889, 2014.
Contact Information
Website: https://faculty.sites.uci.edu/shi/
Email: yongshes@uci.edu
Phone: (949) 824-0358
Address: B251 Med Sci I
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Last updated on 4/6/2026.