Shi Group Selected Publications
1998
1. 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. *Correspondence. PDF
2002
2. 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. PDF
2003
3. Y.J. Shi, J.-I. Sawada, G.C. Sui, E.B. Affar, J. Whetstine, F. Lan, H. Ogawa, M. Luke, Y. Nakatani, and Shi, Y. Coordinated histone modifications mediated by a CtBP co-repressor complex. Nature 422:735-8. PDF
2004
4. Y.J. Shi, F. Lan, C. Matson, P. Mulligan, J.R. Whetstine, P.A. Cole, R.A. Casero, and Shi, Y. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119:941-953. (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 milestone papers of 40 years of Cell). PDF
5. 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. PDF
2005
6. Shi YJ, Matson C, Lan F, Iwase S, Baba T, Shi Y. Regulation of LSD1 histone demethylase activity by its associated factors. Mol Cell. 19:857-864 (Minireview in Cell 2005; 122:654-658). PDF
2006
7. J.R Whetstine, A. Nottke, F. Lan, M. Huarte, S. Smolikov, Z. Chen, E. Spooner, E. Li, G. Zhang, M. Colaiacovo, and Shi, Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125:467-481. (Commented in Research Highlight, Nat Rev Mol Cell Biol. 2006 Jun). PDF
8. 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 125:691-702. PDF
2007
9. S. Iwase, F. Lan, P. Bayliss, L. de la Torre-Ubieta, H. Qi, M. Huarte, J.R. Whetstine, A. Bonni, T. Roberts, and Shi, Y. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 trimethyl demethylases. Cell 128:1077-88. PDF
10. F. Lan*, R. Collins*, R. De Cegli, R. Alpatov, J.R. Horton, X.B. Shi, R. Gozani, X.D. Cheng+, and Shi, Y+. Recognition of unmethylated H3K4 links BHC80 to LSD1 mediated gene repression. Nature 448:718-723. *Equal contributions, +Co-correspondence. PDF
11. F. Lan, P.E. Bayliss, J. Rinn, J.R. Whetstine, J.K. Wang, S.Z. Chen, S. Iwase, T.M. Roberts, H.Y. Chang, and Shi, Y. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature 449:689-94. (Minireview: Cell. 2007; 131: 29-32). PDF
12. 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. A two-way street: LSD1 regulates chromatin boundary formation in S. pombe and Drosophila. Mol Cell. 2007 Apr 27; 26(2):160-162). PDF
2008
13. Qi HH, Ongusaha PP, Myllyharju J, Chen DM, Pakkanen O, Shi YJ, Lee SW, Peng JM, Shi Y. Prolyl 4-hydroxylation regulates Argonaute 2 stability. Nature. 2008 Sep 18; 455(7211):421-424. PMCID: PMC2661850. PDF
14. 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). PDF
2009
15. Chen SZ, Whetstine J, Ghosh S, Hanover JA, Shi Y. The conserved NAD(H)-dependent corepressor CTBP-1 regulates Caenorhabditis elegans life span. Proc Natl Acad Sci USA. 2009 Feb 3; 106(5):1496-1501. PMCID: PMC2635826. PDF
2010
16. H.H. Qi*, M. Sarkissian*, G.Q. Hu, Z. Wang, A. Bhattacharjee, D.B. Gordon, M Gonzales, F. Lan, P.P. Ongushaha, M. Huarte, N.K. Yaghi, S. Lim, B. Garcia, L. Brizuela, K.J. Zhao, T.M. Roberts+, and Shi, Y+. Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Nature 466:503-7. *Equal contributions, +Co-correspondence. PDF
17. 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. Nat Struct Mol Biol. 2010 Jan; 17(1):38-43. PMCID: PMC2849977. *Equal Contributions. PDF
2011
18. 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. PMCID: PMC4691841. *Equal contributions. PDF
19. Dango S*, Mosammaparast N*, Sowa ME, Xiong LJ, Wu F, Park K, Rubin M, Gygi SP, Harper JW, Shi Y. DNA unwinding by ASCC3 helicase is coupled to ALKBH3-dependent DNA alkylation repair and cancer cell proliferation. Mol Cell. 2011 Nov 4; 44(3):373-384. PMCID: PMC3258846. *Equal contributions. PDF
2012
20. Chen S, Ma J, Wu F, Xiong LJ, Villen J, Gygi SP, Liu XS, Shi Y. The histone H3 Lys 27 demethylase JMJD3 regulates gene expression by impacting transcription elongation. Genes & Dev. 2012 Jun 15; 26(12):1364-1375. PMCID: PMC3387663. PDF
2013
21. Mosammaparast N+, Kim H, Laurent B, Dango S, Luo Y, Sowa M, Lim HJ, Majid M, Gygi S, Harper W, Yankner B, Shi Y+. The histone demethylase LSD1/KDM1A promotes the DNA damage response. J. Cell. Biol. 2013 Nov 11; 203(3): 457-470. PMCID: PMC3824007. +Co-correspondence. PDF
2014
22. R. Alpatov*, B.J. Lesch*, M. Nakamoto-Kinoshita, A. Blanco, S.Z. Chen, A. Stuetzer, K. Armachi, M.D. Simon, A. Muzaffar, J. Murn, S. Prisic, T.G. Kutateladze, C.R. Vakoc, R.E. Kingston, W. Fischle, S.T. Warren, D.C. Page, and Shi Y. A chromatin-dependent role of the fragile X mental retardation protein FMRP in the DNA damage response. Cell 157:869-81. *Equal contributions. PDF
23. Guo R*, Zheng LJ*, Park JW, Xu WQ, Chen H, Qiu JS, Lv RT, Wang ZT, Yang PY, Wu FZ, Shi XB, Fu XD, Shi GYJ, Xing Y+, Lan F+, Shi Y+. BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processing. Mol Cell. 2014 Oct 23; 56(2):298-310. PMCID: PMC4363072. *Equal contributions, +Co-correspondence. PDF
24. 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. PDF
2015
25. Greer EL* +, Blanco MA*, Gu L, Sendinc E, Liu JZ, Aristizábal-Corrales D, Hsu CH, Aravind L, He C, Shi Y +. DNA methylation on N6-adenine in C. elegans. Cell. 2015 May 7; 161(4): 868-878 (Cover). PMCID: PMC4427530. (Minireview: Cell. 2015; 161:710-13). *Equal contributions, +Co-correspondence. PDF
2016
26. 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 165:331-342. PMCID: PMC4826479. *Equal contributions, +Co-correspondence. PDF
27. 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. PMCID: PMC4749408. *Equal contributions, +Co-correspondence. PDF
2017
28. Y. Xiang*, B. Laurent*, CH. Hsu*, S. Nachtergaele, Z. Lu, W. Sheng, C. Xu, H. Chen, J. Ouyang, S. Wang, D. Ling, PH. Hsu, L. Zou, A. Jambhekar, C. He, and Shi, Y. RNA m6A methylation regulates the ultraviolet-induced DNA damage response. Nature 543:573-576. *Equal contributions. PDF
2018
29. Sheng W*, LaFleur MW*, Nguyen TH, Chen S, Chakravarthy A, Conway JR, Li Y, Chen H, Yang H, Hsu PH, Van Allen EM, Freeman GJ, De Carvalho DD, He HH, Sharpe AH+, and Shi Y+. LSD1 ablation stimulates anti-tumor immunity and enables checkpoint blockade. Cell 174:549-563.e19. *Equal contributions; +Co-correspondence. PDF
30. Wen J*, Lv RT*, Ma HH*, Shen HJ, He CX, Wang JH, Jiao FF, Lui H, Yang PY, Tan L, Lan F, Shi YJG+, He C+, Shi Y+, Diao JB+. Zc3h13 regulates nuclear RNA m6A methylation and mouse embryonic stem cell self-renewal. Mol Cell. 2018 March 15; 69(6):1028-1038. PMCID: PMC5858226. *Equal contributions, +Co-correspondence. PDF
2019
31. 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+., and Shi, Y+. Re-programming chromatin with a bifunctional LSD1/HDAC inhibitor induces therapeutic differentiation in DIPG. Cancer Cell, 36: 528-544. +Co-correspondence. PDF
32. 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. PDF
33. 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. PDF
2020
34. 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/s41422-019-0270-4. [Epub ahead of print]. PDF
2021
35. Liu Y, Debo B, Li M, Shi Z, Sheng W+, and Shi Y+. LSD1 inhibition sustains T cell invigoration with a durable response to PD-1 blockade. Nat Commun.12:6831. +Co-correspondence. PDF
36. Sheng, WQ*., Liu, Y*., Chakraborty, D., Debo, B., and Shi, Y. Simultaneous inhibition of LSD1 and TGF-b enables eradication of poorly immunogenic tumors with anti-PD-1 treatment. Cancer Discovery 2021 Aug; 11:1970-1981. PDF
37. 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, 591:317-321 +Co-correspondence. PDF
38. Zee, B.M., Poels, K.E., Yao, C.H., Jacobus, W.D., Senior, E., Endress, J.E., Jambhekar, A., Lovitch, S.B., Ma, J.X., Dhall, A., Harris, I.S., Blanco, A., Skykes, D.B., Haigis, M.C., Michor, F., Licht, J.D., and Shi, Y. Combined epigenetic and metabolic treatments overcome differentiation blockade in AML. iScience 24(6):102651. doi: 10.1016/j.isci.2021.102651. PDF
39. 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+., and 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. PDF
2022
40. 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+., and 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. PDF
41. 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. PDF
2023
42. Zhang, GH., Jian, PS., Wang, YY, Qiu, FQ., An, J., Zheng, YP., Tang, W., Zhou, JY., Neculai, D., Shi, Y+. and Sheng, WQ+. CPT1A induction promotes MAVs stabilization and activation through palmitoylation to potentiate the antitumor immune effect of epigenetic perturbations. Mol Cell Dec 7;83(23):4370-4385.e9. +Co-correspondence. PDF
2024
43. 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 and Shi, Y+. Wnt signaling control by KDM5C during development impacts cognition. Nature 2024, 627(8004):594-603. +Co-correspondence. PDF
44. Jiao, AL+., Sendinc E., Zee, B., Wallner, F, and Shi Y+. An E2 ubiquitin conjugating enzyme links di-ubiquitinated H2B to H3K27M oncohistone function. Proc. Natl. Acad. Sci. USA 2024, Nov 26;121(48):e2416614121. doi: 10.1073/pnas.2416614121. +Co-correspondence. PDF
2025
45. Hosseini, A*., Dhall, A*., Ikonen, N., Sikora, N., Sylvain, N., Shen, YQ., Jurgensen Amaral, ML., Jiao, A., Wallner, F., Sergeev, P., Lim, YH., Yang, YQ., Vick, B., Kawabata, KC., Melnick, A., Vyas, P., Ren, B., Jeremias, I., Psaila, B., Heckman, CA+., Blanco, A+., and Shi, Y+. Perturbing LSD1 and Wnt pathway rewires transcription to synergistically induce AML differentiation. Nature, 2025. 642(8067): 508-518. Apr 16. doi: 10.1038/s41586-025-08915-1. Online ahead of print. *Equal contributions; +Co-correspondence. PDF
2026
46. Jiao, A.L., Maghrouni A., Velazquez, AG., Annett, A., Manokaran, C., Wen, TY., Grassl, N., Chan, J., Nguyen, S., Tayeh, BB., Le Dily, F., Kleinman, CL., Di Croce, L+., Jabado, N+., and Shi, Y+. H3K27M co-opts ASCL1 to maintain progenitor states and drive gliomagenesis. Nat. Commun. (2026). In press. +Co-correspondence.