Publications

  • Journal Articles
  • Zhu Y, Wang X, Forouzmand E, Jeong J, Feng Q, Sowd G, Engelman A, Xie X, Hertel KJ & Shi Y (2017) Molecular mechanisms for CFIm-mediated regulation of mRNA alternative polyadenylation. Mol Cell (in press)
  • Sun Y, Zhang Y, Hamilton K, Manley JL, Shi Y, Walz T & Tong L (2017) Molecular basis for the recognition of the human AAUAAA polyadenylation signal. Proc Natl Acad Sci U S A. (in press)
  • 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*. Nudt21 controls cell fate by connecting alternative polyadenylation to chromatin signaling. Cell (In press) (* co-corresponding authors)
  • 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 (PDF) (*co-corresponding authors)
    • Designated as a “breakthrough article” by the journal
  • 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.
  • 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. (PDF)
  • 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.
  • Shi, Y. & Manley, JL. (2015) The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site. Genes & Dev. 29: 889-897. (PDF)
  • Shi, Y. (2015) Two decades of RNA as I see it. RNA 21: 733-734.
  • 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. 2823702380. (PDF)
    • Featured on the cover.
  • 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) (PDF)
    • Featured on the cover.
  • Yao, C. and Shi, Y. (2014) Global and Quantitative Profiling of Polyadenylated RNAs Using PAS-seq. Methods Mol Biol. 1125:179-185.
  • Yao, C., Weng, L., & Shi, Y. (2014) Global protein-RNA interaction mapping at single nucleotide resolution by iCLIP-seq. Methods Mol Biol. 1126:399-410.
  • 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. (2013) 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.
  • 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: 1781-1790. (PDF)
  • Giammartino, DD., Shi, Y., & Manley, JL. (2013) PARP1 Represses PAP and Inhibits Polyadenylation during Heat Shock. Molecular Cell  49 (1): 7-17.
  • Shi, Y. (2012) Alternative polyadenylation: new insights from global anlyses. RNA 18: 2105-2117. (PDF)
  • 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): 18773-18778. (PDF)
  • Chan, S., Choi, E., & Shi, Y. (2011) Pre-mRNA 3’-end processing complex assembly and function. Wiley Interdisciplinary Reviews: RNA. 2: 321-335. (PDF)
  • 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. (PDF)
  • Shi, Y., Chan, S., & Martinez-Santibañez, G. (2009) An up-close look at the pre-mRNA 3’ processing complex. RNA Biol. 6(5):522-525. (PDF)
  • 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. Molecular Cell. 33(3): 365-376. (PDF)
    • Highlighted in Nature Chemical Biology 5 (4): 205  (PDF)

 

 

 

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