Shi Group Selected Publications

 

  1. Karwacki-Neisius, V+., Jang, A., Cukuroglu, E., Tai, Al. Jiao, A., Yoon, J., Brookes, E., Chen, JK, Iberg, A., Halbriter, F, Ounap, K., Gecz, J., Schlaeger, TM., Sui, SH., Goke, J., Lehtinen, MK., Pomeroy, SL Shi, Y+. Wnt signaling control by KDM5C during development impacts cognition. Nature, 2024; 627(8004):594-603. +Co-correspondence.

  2. Zhang, GH., Jian, PS., Wang, YY, Qiu, FQ., An, J., Zheng, YP., Tang, W., Zhou, JY., Neculai, D., Shi, Y+. Sheng, WQ+. CPT1A induction promotes MAVs stabilization and activation through palmitoylation to potentiate the antitumor immune effect of epigenetic perturbations. Mol. Cell, 2023 Dec; 7;83(23):4370-4385.e9. +Co-correspondence.

  3. Luo, Q*., Mo, JZ*., Chen, H*., Hu, ZT., Wang, BH., Wu, JB., Liang, ZY., Xie, WH., Du, KX., Peng, ML., Li, YP., Li, TY., Zhang, YY., Shi, XY., Shen, WH., Shi, Y+., Dong, AW+., Wang, HL+., Ma, JB+. Structural insights into molecular mechanism for N6-adenosine methylation by MT-A70 family methyltransferase METTL4. Nat. Commun., 2022 Sep; 26;13(1):5636. *Equal contributions; +Co-correspondence.

  4. Xu, WQ*., He, CX*., Kaye, EG., Li, JH*., Mu, MD., Nelson, GM., Dong, L., Wang, JH., Wu, FZ, Shi, YJG., Adelman, K+., Lan, F+., Shi, Y+., Shen, HJ+. Dynamic control of chromatin associated m6A methylation regulates nascent RNA synthesis. Mol. Cell, 2022 Mar; 17;82(6):1156-1168.e7. doi: 10.1016/j.molcel.2022.02.006. Epub 2022 Feb 25. *Equal contributions; +Co-correspondence.

  5. Blanco, AM*, +., Skyes, DB*., Gu, L*., Wu, MJ., Petroni, R., Karnik, R., Wawer, M., Rico, J., Li, HT., Jacobus, WD., Jambhekar, A., Cheloufi, S., Meissner, A., Hochedlinger, K., Scadden, DT+., Shi, Y+.  Chromatin state barriers enforce an irreversible mammalian cell fate decision. Cell Rep., 2021 Nov; 9;37(6):109967. doi: 10.1016/j.celrep.2021.109967. *Equal contributions; +Co-correspondence.

  6. Xu, WQ., Li, JH., He, CX., Wen, J., Ma, HH., Rong, BW., Dian, JB., Wang, LY., Wang, JH., Wu, FZ., Tan, L., Shi, YG., Shi, Y+., Shen, HJ+. METTL3 regulates heterochromatin in mouse embryonic stem cells. Nature, 2021 Mar; 591(7849):317-321 doi: 10.1038/s41586-02103210-1. Epub 2021 Jan 27. PMID: 33505026. +Co-correspondence.

  7. Chen, H., Gu, L., Orellana, EA., Wang, Y., Guo, J., Liu, Q., Wang, L., Shen, Z., Wu, H., Gregory, RI., Xing, Y., Shi, Y. METTL4 is an snRNA m6Am methyltransferase that Regulates RNA splicing. Cell Res., 2020; 30(6):544-547. Jan 8. doi: 10.1038/s41422-019-02704. [Epub ahead of print].

  8. Anastas, JN., Zee, BM., Kalin, JH., Kim, MH., Guo, R., Alexandrescu, S., Blanco, MA., Giera, S., Gillespie, SM., Das, J., Wu, MH., Nocco, S., Bonal, D.M., Suva, M.L., Bernstein, BE., Alani, R., Golub, TR., Cole, PA., Filbin, MG+., Shi, Y+. Re-programming chromatin with a bifunctional LSD1/HDAC inhibitor induces therapeutic differentiation in DIPG. Cancer Cell, 2019; 36(5): 528-544.  +Co-correspondence.

  9. Sendinc, E*, Valle-Garcia, D*., Dhall, A., Chen, H., Henriques, T., Navarrete-Perea, J., Sheng, WQ., Gygi, SP., Adelman, K., Shi, Y. PCIF1 catalyzes m6Am methylation to regulate gene expression. Mol. Cell., 2019; 5(3):620-630.e9. doi: 10.1016/j.molcel.2019.05.030. Epub 2019 Jul 3. PMID: 31279659. *Equal contributions.

  10. Ma HH*, Wang XY*, Cai JB*, Dai Q, Lv RT, Chen K, Lu ZK, Chen H, Shi YJG, Lan F, Fan J, Pan T, Shi Y+, He C+.  N6-methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat. Chem. Biol., 2019 Jan; 15(1):88-94. Epub 2018 Dec 10. *Equal contributions, +Co-correspondence.

  11. Sheng WQ*, LaFleur MW*, Nguyen TH, Chen SJ, Chakravarthy A, Conway JR, Li Y, Chen H, Yang H, Hsu PH, Van Allen EM, Freeman GJ, De Carvalho DD, He HH, Sharpe AH+, Shi Y+. LSD1 ablation simulates anti-tumor immunity and enables checkpoint blockade. Cell, 2018 Jul 26; 174(3):549-63. PMCID: PMC6063761, *Equal contributions; +Co-correspondence.

  12. Xiang, Y*., Laurent, B*., Hsu, C-H*., Nachtergaele, S., Lu, ZK., Xu, CY., Sheng, WQ., Jian, OY., Wang, SQ., Ling, D., Hsu, P-H., Zou, L., Jambhekar, A., He, C., Shi, Y. m6A RNA methylation regulates the UV-induced DNA damage response. Nature, 2017; 543:573-576. *Equal contributions.

  13. Shen HJ*, Xu WQ*, Guo R, Rong BW, Gu L, Wang ZT, He CX, Zheng LJ, Hu X, Shao ZM, Yang PY, Wu FZ, Shi YJG, Shi Y+, Lan F+. Suppression of enhancer overactivation by a RACK7-histone demethylase complex. Cell, 2016 Apr 7; 165(2):331-342. *Equal Contributions, +Co-Correspondence.

  14. Iwase S*, +, Brookes E*, Agarwal S*, Badeaux AI, Ito H, Tomassy GS, Kasza T, Vallianatos C, Lin G, Thompson A, Gu L, Kwan KY, Chen CF, Sarto MA, Egan B, Xu J+, Shi Y+. A mouse model of X-linked intellectual disability associated with impaired removal of histone methylation. Cell Rep., 2016 Feb 9; 14(5):1000-1009. *Equal contributions, +Co-correspondence

  15. Greer EL, Beese-Sims S, Brookes E, Spadafora R, Zhu Y, Rothbart SB, Aristizabal-Corrales D, Chen SZ, Badeaux AI, Qin QY, Wang W, Strahl BD, Colaiacovo MP, Shi Y. A histone methylation network regulates transgenerational epigenetic memory in C. elegans. Cell Rep., 2014 Apr 10; 7(1):113-126. PMCID: PMC4012616.

  16. Alpatov R*, Lesch BJ*, Nakamoto-Kinoshita M, Blanco A, Chen S, Stützer A, Armache KJ, Simon MD, Xu C, Ali M, Murn J, Prisic S, Kutateladze TG, Vakoc CR, Min J, Kingston RE, Fischle W, Warren ST, Page DC and Shi Y. A chromatin-dependent role of the fragile x mental retardation protein FMRP in the DNA damage response. Cell, 2014 May 8;157(4):869-881 PMCID: PMC4038154. *Equal contributions.

  17. Rajakumara E*, Wang Z*, Ma H, Hu L, Chen H, Lin Y, Guo R, Wu F, Li H, Lan F, Shi YG, Xu Y, Patel DJ, Shi Y. PHD finger recognition of unmodified histone H3R2 links UHRF1 to regulation of euchromatic gene expression. Mol. Cell, 2011 Jul 22; 43(2):275-284.

  18. Qi HH*, Sarkissian M*, Hu GQ, Wang Z, Bhattacharjee A, Gordon DB, Gonzales M, Lan F, Ongushaha PP, Huarte M, Yaghi NK, Lim S, Garcia B, Brizuela L, Zhao KJ, Roberts TM+, Shi Y+. Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Nature, 2010 Jul 22; 466(7305):503-507. *Equal contributions; +Co-correspondence.

  19. Horton JR*, Upadhyay AK*, Qi HH*, Zhang X, Shi Y, Cheng XD. Enzymatic and structural insights for substrate specificity of a family of Jumonji histone lysine demethylases. NSMB, 2010 Jan; 17(1):38-43. *Equal Contributions.

  20. Mulligan P, Westbrook T, Ottinger M, Macia E, Liu JS, Shi YJ, Barretina J, Howley P, Elledge S, Shi, Y. CDYL bridges REST and histone methyltransferases for gene repression and suppression of cellular transformation. Mol. Cell, 2008 Dec 5; 32(5):718-726 (Featured Article, highlighted by Cell. 2008; 135 Leading Edge pg. 981).

  21. Liu HF, Schmidt-Supprian M, Shi YJ, Hobeika E, Barteneva N, Jumaa H, Pelanda R, Reth M, Skok J, Rajewsky K, Shi, Y. Yin Yang 1 is a critical regulator of B-cell development. Genes & Dev., 2007 May 15; 21(10):1179-1189. PMCID: PMC1865490. (Perspective: Calame K, Atchison M. Genes & Dev. 2007 May 15; 21(10):1145-1152).

  22. Lan F*, Collins R*, De Cegli R, Alpatov R, Horton JR, Shi XB, Gozani O, Cheng XD+, Shi Y+. Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1 mediated gene repression. Nature, 2007 Aug 9; 448(7154):718-722. *Equal contributions; +Co-correspondence.

  23. Lan F, Zaratiegui M, Villen J, Vaughn M, Verdel A, Gygi S, Moazed D, Martienssen R, Shi Y. S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatin gene transcription. Mol. Cell, 2007 Apr 13; 26(1):89-101. (Preview: Chosed R, Dent SY. Mol Cell. 2007 Apr 27; 26(2):160-162).

  24. Iwase S, Lan F, Bayliss P, de la Torre-Ubieta L, Qi HH, Huarte M, Whetstine JR, Bonni A, Roberts T, Shi Y.  The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell, 2007 Mar 23; 128(6):1077-1088.

  25. Lan F, Bayliss PE, Rinn J, Whetstine JR, Wang JK, Chen SZ, Iwase S, Roberts TM, Chang HY, and Shi Y. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature, 2007 Oct 11; 449(7163):689-694. (Minireview: Cell. 2007; 131: 29-32).

  26. Chen Z, Zhang J, Whetstine JR, Hong X, Davrazou F, Kutateladze TG, Simpson M, Mao Q, Pan CH, Dai S, Hagman J, Hansen K, Shi Y, Zhang G. Structural insights into histone Demethylation by JMJD2 family members. Cell, 2006 May 19; 125(4):691-702.

  27. Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, Spooner E, Li E, Zhang G, Colaiacovo M, Shi Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell, 2006 May 5; 125(3):467-481. (Commented in Research Highlight, Nat RevMol Cell Biol. 2006 Jun)

  28. Shi YJ, Matson C, Lan F, Iwase S, Baba T, Shi Y. Regulation of LSD1 histone demethylase activity by its associated factors. Mol. Cell, 2005 Sep 16; 19(6):857-864 (Minireview in Cell 2005; 122:654-658).

  29. Shi YJ, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, Casero RA, Shi Y. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell, 2004 Dec 29; 119(7):941-953. (Minireview in Cell. 119:903-906. Findings highlighted in Science. 2004; 306:2171, Nature. 2005; 433:29, Nature Reviews Mol Cell Biol. 2005; Faculty of 1000 All Time Top 10 in Biology). Selected as one of the 25 landmark publications of 40 years of Cell.

  30. Sui GC, Affar EB, Shi YJ, Wall N, Brignone C, Yin P, Dohonoe M, Calvo D, Grossman S, Shi Y. Yin Yang 1 is a negative regulator of p53. Cell, 2004 Jun 25; 117(7):859-872.

  31. Shi YJ, Sawada JI, Sui GC, Affar EB, Whetstine J, Lan F, Ogawa H, Luke MP, Nakatani Y, Shi Y. Coordinated histone modifications mediated by a CtBP co-repressor complex. Nature, 2003 Apr 17; 422(6933):735-738.

  32. Sui GC, Soohoo C, Affar EB, Shi YJ, Forrester W, Shi Y. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc. Natl. Acad. Sci. USA., 2002 Apr 16; 99(8):5515-5520. PMCID: PMC122801.

  33. Calvo D, Victor M, Sui GC, Luke MP, Wen GY, Dufourcq P, Maduro M, Rothman J, Shi Y. A POP-1 repressor complex restricts inappropriate cell type-specific gene transcription during Caenorhabditis elegans embryogenesis. EMBO J., 2001 Dec 17; 20(24):7197-7208. PMCID: PMC125335

  34. Shi Y*, Mello C. A CBP/p300 homolog specifies multiple differentiation pathways in caenorhabditis elegans. Genes & Dev., 1998 Apr 1; 12(7):943-955. (Cover Photo). Commented in Trends in Genetics 14:183,1998; Nature Biotechnology 16:405, 1998. *Correspondence.

  35. Shi Y, Seto E, Chang LS, Shenk T. Transcriptional repression by YY1, a human GLI-Kruppel related protein, and relief of repression by adenovirus E1A protein. Cell, 1991 Oct 18; 67(2):377-388.