Stem cell, mRNA processing, virus-host interactions
2012: American Cancer Society Research Scholar Award
2019-2022: UCI Chancellor's Fellow
mRNA Processing Regulation in Cell Fate Decisions and virus-host interactions
We are broadly interested in post-transcriptional gene regulation and its role in stem cell biology and in virus-host interactions. Our current focus is on the mRNA 3' end processing. The 3' ends of most eukaryotic mRNAs are formed by an endonucleolytic cleavage and the subsequent addition of a string of adenosines. Interestingly, the transcripts of ~70% of genes in all eukaryotes have alternative 3' ends that are formed by cleavage/polyadenylation at different sites, a phenomenon called mRNA alternative polyadenylation (APA). APA not only expands the proteomic and functional diversity, but also plays important roles in gene regulation. Deregulation of mRNA 3' processing and APA have been implicated in a wide spectrum of human diseases. However, it remains poorly understood how poly(A) sites are recognized and how their recognition is regulated. Our goal is to decipher the rules that govern poly(A) site choice, or the “polyadenylation code”, by using a combination of biochemical, genomic, and genetic approaches. Our studies aim to provide novel insights into the basic mechanisms of post-transcriptional gene regulation as well as its role in many physiological and pathological processes..
1. mRNA APA regulation in stem cells and cancer.
We have developed a high throughput sequencing-based method called PAS-seq for quantitatively RNA polyadenylation profiling at the transcriptome level. Using this method, we detected extensive changes in the global APA profile during stem cell differentiation to neurons that, in most cases, lead to 3' UTR lengthening (Shepard et al., RNA 2011). We have identified the protein Fip1 as a critical regulator of the global APA profile and we have demonstrated that Fip1-mediated APA regulation is essential for embryonic stem cell self-renewal and for somatic reprogramming (Lackford et al., EMBO J 2014). Recently we have identified the mRNA 3' processing factor CFIm25/Nudt21 as a key "roadblock" gene that prevent somatic reprogramming and CFIm25/Nudt21 does so through regulating poly(A) site choice. These studies revealed an unexpected role for post-transcriptional gene regulation in cell fate determination (Brumbaugh et al, Cell 2018). Given the similarities between stem cells and cancer cells, we are also investigating whether and how APA regulation may contribute to cancer development.
2. Characterization of the mRNA 3' processing machinery.
Previously we have purified the human mRNA 3' processing complex in its active and intact form (Shi et al., Mol Cell 2009). Surprisingly, this complex consists of more than 85 proteins, including the core 3' processing factors and many peripheral factors that may couple mRNA 3' end formation to other cellular processes. Currently we are carrying out proteomic, structural and functional analyses to understand the inner workings of this amazing molecular machine. We have re-defined the mechanism for poly(A) signal (AAUAAA) recognition (Chan et al, Genes & Dev 2014; Sun et al, 2018). We have mapped the RNA interactions for some of the core mRNA 3' processing factors (Yao et al., PNAS 2012; Yao et al., RNA 2013) and our results revealed a surprising diversity in the mechanisms for poly(A) site recognition in mammalian cells.
3. mRNA 3' processing regulation in virus-host interactions.
Given their limited genome capacities, viruses often suppress host gene expression and hijack the host cell factors for expressing viral genes. mRNA 3' processing machinery is targeted by a number of viruses, including influenza and herpes simplex viruses. We are investigating how viruses target mRNA 3' processing and the functional significance of this inhibition on viral replication.
1. Shi, Y., Reddy, B. & Manley, JL. (2006) PP1/PP2A phosphatases are required for the second step of pre-mRNA splicing and target specific snRNP proteins. Mol Cell. 23(6): 819-29.
2. Shi, Y. & Manley, JL. (2007) A complex signaling pathway in response to heat shock regulates SRp38 phosphorylation and pre-mRNA splicing. Mol Cell. 28(1): 79-90.
3. Shi, Y., Giammartino, DD., Sharkeshik, A., Taylor, D., Rice, W, Yates, JR, 3rd, Frank, J. & Manley, JL. (2009) Molecular architecture of the human pre-mRNA 3’ processing complex. Mol Cell. 33(3): 365-76.
4. Shi, Y., Chan, S., & Martinez-Santibañez, G. (2009) An up-close look at the pre-mRNA 3’ processing complex. RNA Biol. 6(5):522-5.
5. Shepard, PJ., Choi, E., Lu, J., Flanagan, LA., Hertel, KJ., & Shi, Y. (2011) Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA. 17(4) 761-772.
6. Chan, S., Choi, E., & Shi, Y. (2011) Pre-mRNA 3’-end processing complex assembly and function. Wiley Interdisciplinary Reviews: RNA. 2: 321-35
7. Shi, Y. (2012) Alternative polyadenylation: new insights from global analyses. RNA 18: 2105-2117. (Invited review)
8. Yao, C., Biesinger, J., Wan, J., Weng, L., Busch, A., Xing, Y., Xie, X., & Shi, Y. (2012) Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation. Proc Natl Acad Sci U S A. 109 (46): 18773-8.
9. Giammartino, DD., Shi, Y., & Manley, JL. (2013) PARP1 Represses PAP and Inhibits Polyadenylation during Heat Shock. Molecular Cell 49: 1-11.
10. Yao, C., Choi, E., Weng, L., Xie, X., Wan, J., Xing, Y., Moresco, JJ., Tu, PG., Yates, JR, 3rd. & Shi, Y. (2013) Overlapping and distinct functions of CstF64 and CstF64t in mammalian mRNA 3' processing. RNA 19: 1-10.
11. Wang, L., Miao, Y., Zheng, X., Lackford, B., Zhou, B., Han, L., Yao, C., Ward, J., Burkholder, A., Fargo, DC., Shi, Y., Williams, CJ., & Hu, G. The THO complex regulates pluripotency gene mRNA export to control embryonic stem cell self-renewal and somatic cell reprogramming. Cell Stem Cell 13: 676-690.
12. Lackford, B., Yao, C., Charles, GM., Weng, L., Zheng, X., Choi, EA., Xie, X., Wan, J., Xing, Y., Freudenberg, JM., Yang, P., Jothi, R., Hu, G* & Shi, Y.* (2014) Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal. EMBO J. 33: 878-889. (*Co-corresponding author)
- Featured on the cover.
13. Chan, SL., Huppertz, I., Yao, C., Weng, L., Moresco, JJ., Yates, JR. 3rd, Ule, J., Manley, JL. & Shi, Y. (2014) CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3’ processing. Genes & Dev. 28: 2370-2380.
- Featured on the cover.
14. Shi, Y. (2015) Two decades of RNA as I see it. RNA 21: 733-734.
15. Shi, Y. & Manley, JL. (2015) The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site. Genes & Dev. 29: 889-897.
16. Zou D, McSweeney C, Sebastian A, Reynolds DJ, Dong F, Zhou Y, Deng D, Wang Y, Liu L, Zhu J, Zou J, Shi Y, Albert I & Mao Y. (2015) A critical role of RBM8a in proliferation and differentiation of embryonic neural progenitors. Neural Dev. 10(1):18
17. Weng L, Li Y, Xie X & Shi Y (2016) Poly(A) code analyses reveal key determinants for tissue-specific mRNA alternative polyadenylation. RNA 22:1-9.
18. Movassat M, Crabb TL, Busch A Yao C, Reynolds DJ, Shi Y, Hertel KJ. (2016) Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns. RNA Biol 13(7): 646-655.
19. Huang C, Shi J, Guo Y,Huang W, Huang S, Ming S, Wu X, Zhang R, Ding J, Zhao W, Jia J, Huang X, Xiang P, Shi Y*, Yao C* (2017) A snoRNA modulates mRNA 3’ end processing and the expression of a subset of mRNAs. Nucleic Acids Research
- Designated as a “breakthrough article” by the journal
20. Zhu Y, Wang X, Forouzmand E, Jeong J, Feng Q, Sowd G, Engelman A, Xie X, Hertel KJ & Shi Y (2018) Molecular mechanisms for CFIm-mediated regulation of mRNA alternative polyadenylation. Mol Cell 69(1):62-74.
21. Brumbaugh J., Stefano BD, Wang X, Borkent M, Forouzmand .E, Clowers KJ, Schwarz BA, Kalocsay M, Elledge S, Gygi SP, Hu G, Shi Y*, Hochedlinger K*. (2018) Nudt21 controls cell fate by connecting alternative polyadenylation to chromatin signaling. Cell 172, 106–120.
* co-corresponding authors
22. Sun Y, Zhang Y, Hamilton K, Manley JL, Shi Y, Walz T & Tong L (2018) Molecular basis for the recognition of the human AAUAAA polyadenylation signal. Proc Natl Acad Sci U S A. 115(7): 1419-1428.
23. Chang JW, Zhang W, Yeh HS, Park M, Yao C, Shi Y, Kuang R & Yong J (2018) An integrative model for alternative polyadenylation, IntMAP, delineates mTOR-modulated endoplasmic reticulum stress response. Nucleic Acids Research 46(12):5996-6008.
24. Wang X, Hennig T, Whisnant AW, Erhard F, Friedel CC, Forouzmand E, Hu W, Erber L, Chen Y, Sandri-Goldin R*, Dölken L* & Shi Y* (2020) Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27. Nature Communications 11:293 (*: co-corresponding authors)
25. Zhang Y, Sun Y, Shi Y, Walz T & Tong L (2020) Structural insights into the human pre-mRNA 3'-end processing machinery. Mol Cell 77(4): 800-809.
1. National Institute of Health (NIH R01GM090056):
Characterization of the mammalian mRNA 3’ processing complex.
2. National Institute of Health (NIH R01 GM28441):
Herpes simplex virus-mediated regulation of the host gene expression.
3. R01 MH122556 (co-PI) Translational control in neurogenesis and behavior by a schizophrenia factor.
The RNA Society
Cellular and Molecular Biosciences
Stem Cell Biology
Institute of Genomics and Bioinformatics
Center for Complex Biological Systems