Shi Lab

Shi Lab

Publications

  • Jeong J, Hertel KJ, Shi Y. (2025) RNA-binding proteins: it’s better to play in a band. Genes Dev. 2025 Feb 12.
  • Sievert EP, Franke MC, Thomas KB, Yoon Y, Shi Y*, Sciammas R*. (2025) Distinct plasmablast developmental intermediates produce graded expression of IgM secretory transcripts. Cell Rep. 44(2):115283. (*: co-corresponding authors) (PDF)
  • Guo Z, Huang J, Lu ZJ, Shi Y, David CJ, Chen M. (2025) Targeting TUT1 Depletes Tri-snRNP Pools to Suppress Splicing and Inhibit Pancreatic Cancer Cell Survival. Cancer Res. 2025 Jan 24. doi: 10.1158/0008-5472.CAN-24-2563.
  • Yoon Y, Bournique E, Soles LV, Yin H, Chu HF, Yin C, Zhuang Y, Liu X, Liu L, Jeong J, Yu C, Valdez M, Tian L, Huang L, Shi X, Seelig G, Ding F, Tong L, Buisson R, Shi Y*. (2025) RBBP6 anchors pre-mRNA 3′ end processing to nuclear speckles for efficient gene expression.Mol Cell. 2025 Jan 8:S1097-2765(24)01033-5. (PDF)
  • Fleur AL, Shi Y*, and Seelig G*. (2024) Decoding biology with massively parallel reporter assays and machine learning. Genes Dev (*co-corresponding authors) (PDF)
  • Torre D, Fstkchyan YS, Ho JSY, Cheon Y, Patel RS, Degrace EJ, Mzoughi S, Schwarz M, Mohammed K, Seo JS, Romero-Bueno R, Demircioglu D, Hasson D, Tang W, Mahajani SU, Campisi L, Zheng S, Song WS, Wang YC, Shah H, Francoeur N, Soto J, Salfati Z, Weirauch MT, Warburton P, Beaumont K, Smith ML, Mulder L, Villalta SA, Kessenbrock K, Jang C, Lee D, De Rubeis S, Cobos I, Tam O, Hammell MG, Seldin M, Shi Y, Basu U, Sebastiano V, Byun M, Sebra R, Rosenberg BR, Benner C, Guccione E, Marazzi I. (2023) Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentation. Mol Cell 83(23)4255-4271.
  • 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* (2023) The anticancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3′ processing machinery. Nature Structural and Molecular Biology 30: 1947–1957. *: co-corresponding authors. (PDF)

  • Yoon Y and Shi Y (2022) Human pre-mRNA 3’ processing: reconstituting is believing. Genes & Dev 36(3-4):106-107. (PDF)
  • Chan D,  Feng C, England WE, Wyman D, Flynn RA, Wang X, Shi Y, Mortazavi A & Spitale RC (2021) Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing. Nucleic Acids Research 49(20):11868-11882.
  • 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. (2021) Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation. PLoS Genetics. 17(3):e1009263. (PDF)
  • Soles LV and Shi Y (2021) Crosstalk Between mRNA 3′-End Processing and Epigenetics. Frontiers in Genetics. 12:637705.
  • Yoon Y and Shi Y (2021) PAS-seq 2: a fast and sensitive method for global profiling of polyadenylated RNAs. Methods in Enzymology 655:25-35.
  • Habowski AN, Flesher JL, Bates JM, Tsai CF, Martin K, Zhao R, Ganesan AK, Edwards RA, Shi T, Wiley HS, Shi Y, Hertel KJ, Waterman ML. (2020) Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt. Commun Biol. 3(1):453.
  • 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  (PDF)
  • 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 (PDF) (*: co-corresponding authors)
  • 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.
  • 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. (PDF)
  • 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) (PDF)

  • 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. (PDF)

  • 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 45(15):8647-8660. (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. 28: 2370–2380. (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)