Recent and Selected Publications

  1. Karwacki-Neisius, V+., Jang, A., Cukuroglu, E., Tai, A., Jiao, A., Predes, D., Yoon, J., Brookes, E., Chen, J., Iberg, A., Halbritter, F., Õunap, K., Gecz, J., Schlaeger, TM., Ho Sui, S., Göke, J., He, X., Lehtinen, MK., Pomeroy, SL., Shi, Y+. WNT signalling control by KDM5C during development affects cognition. Nature, 2024. +Co-correspondence.

  2. 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. Epub 2022 Feb 25. *Equal contributions; +Co-correspondence. PDF

  3. Liu, Y., Debo, B., Li, MF, Shi, ZN, Sheng, WQ+., and Shi, Y+. LSD1 inhibition sustains T cell invigoration with a durable response to PD-1 blockade. Nature Commun., 2021 Nov 24; 12(6831). +Co-correspondence. PDF

  4. 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):109-967. *Equal contributions; +Co-correspondence. PDF

  5. 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+., and Shen, HJ+. METTL3 regulates heterochromatin in mouse embryonic stem cells. Nature, 2021 Mar; 591(7849):317-321, Epub 2021 Jan 27. +Co-correspondence. PDF

  6. 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 Mar;11(8):1970-1981. *Equal contribution. PDF

  7. Chen, H*., Liu, Q*., Yu, D., Natchiar, K., Zhou, C., Hsu, CH., Hsu, PH., Zhang, X., Klaholz, B., Gregory, RI., Cheng, XD, and Shi, Y. METTL5, an 18S rRNA-specific m6A methyltransferase, regulates the integrated stress response. bioRxiv 2020.04.27.064162. *Equal contribution. PDF

  8. 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 Jan 8; 30(6):544-547. PDF

  9. 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, 2019; 36(5):528-544. +Co-correspondence. PDF

  10. 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. Epub 2019 Jul 3. *Equal contribution. PDF

  11. Sheng, W.Q.*, LaFleur, M.W.*, Nguyen, T.H., Chen, S.J., Chakravarthy, A., Conway, J.R., Li, Y., Chen, ., Yang, H., Hsu, P-H., Van Allen, E.M., Freeman, G.J., De Carvalho, D.D., He, H.H.H., Sharpe, A.H.+, and Y. Shi+. LSD1 ablation in tumor cells simulates anti-tumor immunity and enables checkpoint blockade. Cell, 2018 Jul 26; 174(3):549-563, Online publication 06/21/2018. *Equal contribution; +Co-correspondence. PDF

  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., and Shi, Y. m6A RNA methylation regulates the UV-induced DNA damage response. Nature, 2017 Mar 23; Vol 543:573-576. *Equal contribution. PDF

  13. Li HJ*, Liefke R*, Jiang JY, Tian W, Deng PJ, Zhang WD, He Q, Patel DJ, Shi Y, Wang ZX. Polycomb-like proteins link the PRC2 complex to CpG islands. Nature, 2017 Sep 14; 549(7671):287-291. * Equal contributions. Bold indicates members of the Shi lab.

  14. Liefke R, Karwacki-Neisius V, Shi Y. EPOP interacts with Elongin BC and Usp7 to modulate the chromatin landscape. Mol Cell. 2016 Nov 17; 64(4):659-672. PDF

  15. 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+., and Lan, F+. Suppression of enhancer over-activation by a RACK7-histone demethylase complex. Cell, 2016 Apr 7; Vol 165(2):331-42. *Equal contribution, +Co-correspondence. PDF

  16. 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 contribution, +Co-correspondence. PDF

  17. Greer EL+, Becker B, Latza C, Antebi A, Shi Y+. Mutation of C. elegans demethylase spr-5 extends trans-generational longevity. Cell Res. 2016 Feb; 26(2):229-238. +Co-correspondence. PDF

  18. 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). * Equal contributions, +Co-correspondence. PDF

  19. Murn J+, Zarnack K, Yang YJ, Durak O, Murphy EA, Cheloufi S, Gonzalez DM, Teplova M, Curk T, Zuber J, Patel DJ, Ule J, Luscombe NM, Tsai LH, Christopher A, Shi Y+. Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. Genes & Dev. 2015 Mar 1; 29(5):501-512 (Cover). +Co-corresponding PDF

  20. Laurent B, Ruitu L, Murn J, Hempel K, Ferrao R, Xiang Y, Liu S, Garcia BA, Wu H, Wu F, Steen H, Shi Y. A Specific LSD1/KDM1A isoform regulates neuronal differentiation through H3K9 demethylation. Mol Cell. 2015 Mar 19; 57(6): 957-970. Preview: Shin JH, Ming GL, Song HJ. Molecular toggle switch of histone demethylase LSD1. Mol Cell. 2015 Mar 19; 57(6):949-950. PDF

  21. 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):869-81. *Equal contribution. PDF

  22. 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. PDF

  23. 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. +Co-correspondence. PDF

  24. 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. PDF

  25. 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. *Equal contribution. PDF

  26. Greer EL, Maures TJ, Ucar D, Hauswirth AG, Mancini E, Lim JP, Benayoun BA, Shi Y, Brunet A. Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans. Nature, 2011 Oct 19; 479(7373):365-371. PDF

  27. Iwase S, Xiang B, Ghosh S, Ren T, Lewis PW, Cochrane JC, Allis CD, Picketts DJ, Patel DJ+, Li H+, Shi Y+. ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome. Nat Struct Mol Biol. 2011 Jun 12; 18(7):769-776. +Co-correspondence. PDF

  28. Fang R, Barbera A, Ruternberg M, Lian C, Leonor T, Lan F, Shimizu F, Sui GC, Shi Y, Shi YJG. Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation. Mol Cell. 2010 Jul 30; 39(2):222-233. PDF

  29. Qi, HH*., Sarkissian, M*., Hu, G.Q., Zhao, Z.B., Bhattacharjee, A., Gordon, B., Lim, S., Lan, F., Yaghi, NK., Garcia B., Brizuela, L., Zhao, KJ., Roberts, TM*, and Shi, Y*. Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Nature, 2010 Jul 22; 446:503-07. *Equal contribution, +Co-correspondence. PDF

  30. 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. *Equal contribution. PDF

  31. 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. PDF

  32. 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

  33. Lan, F., Bayliss, PE., Rinn, J., Whetstine JR., Wang JK., Chen, SZ., Iwase, S., Alpatov, R., Issaeva, I., Canaani, E., Roberts, TM., Chang, HY., and Shi, Y. A histone H3 lysine 27 demethylase regulates animal posterior development.  Nature, 2007 Oct 11; 449:689-94. (Mini-review Cell 2007 Vol 131: 29-32). PDF

  34. Lan, F*., Collins, R*., De Cegli, R., Alpatov, R., Horton, J.R., Shi, XB, Gozani, R., Cheng, XD+, and Shi, Y+. Recognition of unmethylated H3K4 links BHC80 to LSD1 mediated gene repression. Nature, 2007 Aug 9; 448:718-23. *Equal contribution, *Co-correspondence. PDF

  35. 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. (Perspective by Calame K and Atchison M. YY1 helps to bring loose ends together. Genes & Dev. 2007 May 15; 21(10):1145-1152). PDF

  36. 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

  37. Iwase, S, Lan, F., Bayliss, P., de la Torre-Ubieta, L., Qi, H., Huarte, M., Whetstine, JR.,Bonni, A., Roberts, T., and Shi, Y. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases.  Cell, 2007 Mar 23; 128:1077-88. PDF

  38. 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. PDF

  39. Whetstine, JR., Nottke, A., Lan, F., Huarte, M., Smolikov, S., Chen, Z., Spooner, E., Li, E., Zhang, G., Colaiacovo, M., and Shi, Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell, 2006 May 5; 125:467-481. [Commented in Research Highlight, Nat. Rev. Mol. Cell. Biol. June, 2006]. PDF

  40. 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). PDF

  41. Shi, Y.J., Lan, F., Matson, C., Mulligan, P., Whetstine, J.R., Cole, P.A., Casero, R.A. and Shi, Y. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell, 2004 Dec 29; Vol 119:941-953. [Mini-review in Cell 119:903-906, findings highlighted in Science 306:2171 (2004), Nature 433:29 (2005), Nature Reviews Mol. Cell Biol. (2005), Faculty of 1000 All Time Top 10 in Biology, one of the 25 Landmark publications of 40 years of Cell. PDF

  42. 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

  43. Shi, Y. J., Sawada, J-I., Sui, G.C., Affar, E.B., Whetstine, J., Lan, F., Ogawa, H., Luke, M., P-S., Nakatani, Y., and Shi, Y. Coordinated histone modifications mediated by a CtBP co-repressor complex. Nature, 2003 Apr 17; 422:735-8. PDF

  44. Gay F, Calvo D, Lo MC, Ceron J, Maduro M, Lin RL, Shi Y. Acetylation regulates subcellular localization of the Wnt signaling nuclear effector POP-1. Genes & Dev. 2003 Mar 15; 17(6):717-22. PDF

  45. Sui, G.C., Soohoo, C, Affar, E.B., Shi, Y.J., Forrester, W., and Shi, Y. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells.  Proc. Natl. Acad. Sci. USA.  2002 Apr 16; 99:5515-20. PDF

  46. 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. *Co-correspondence. PDF

  47. Lee JS, Galvin KM, See RH, Eckner R, Livingston D, Moran E, Shi Y.  Relief of YY1 transcriptional repression by adenovirus E1A is mediated by E1A-associated protein p300. Genes & Dev.1995 May 15; 9(10):1188-1198. PDF

 

Selected Review Articles

  1. Sendinc, E., Shi, Y. (2023). RNA m6A methylation across the transcriptome. Mol Cell. Vol 83(3): 428-41. PDF

  2. Jambhekar, A., Dhall, and Shi, Y. (2019). Roles and regulation of histone methylation in animal development. Nat Rev Mol Cell Biol. Vol 20(10):625-641. PDF

  3. Murn, J., and Shi, Y. (2017). The winding path of protein methylation research: milestones and new frontiers. Nat Rev Mol Cell Biol. Vol 18(8):517-527. PDF

  4. Jambhekar, A., Anastas, JN., and Shi, Y. (2017). Histone lysine demethylase inhibitors. Cold Spring Harb Perspect Med. Vol 7(1). PDF

  5. Brookes, E. and Shi, Y. (2014). Disparate epigenetic mechanisms of human disease, Ann Rev Genet. Vol 48:237-68. PDF

  6. Badeaux AI, Shi Y. (2013). Emerging roles for chromatin as a signal integration and storage platform. Nature Rev Mol Cell Biol. Vol 14(4): 211-24. PDF

  7. Greer EL, Shi Y. (2012). Dynamic regulation of histone methylation in health, disease, and inheritance. Nat Rev Genet. Vol 13(5):343-357. PDF

  8. Mosammaparast N, Shi Y. (2010). Reversal of histone methylation: Biochemical and molecular mechanisms of histone demethylases. Annu Rev Biochem. Vol 79:155-79. PDF

  9. Lan F, Shi Y. (2009). Epigenetic regulation: methylation of histones and non-histone proteins. Sci China C Life Sci. Vol 52(4):311-22. PDF

  10. Nottke AC, Colaiacovo M, Shi Y. (2009). Developmental roles for the histone lysine demethylases. Development. Vol 136(6):879-89. PDF

  11. Shi Y. (2007). Histone demethylases: emerging roles in development, physiology and disease. Nat Rev Genet. Vol 8(11):829-33. PDF

  12. Shi Y*, Whetstine J. (2007). Dynamic regulation of histone lysine methylation by demethylases. Mol Cell. Vol 25(1):1-14. *Correspondence. PDF

  13. Shi YJ, Shi Y. (2004). Metabolic enzymes in transcription-a direct link between metabolism and regulated gene expression? Trends in Genetics. Vol 20:445-52. PDF

  14. Shi Y. (2003). Mammalian RNAi for the masses. Trends in Genetics. Vol 19(1):9-12 (#1 downloaded article among all of Elsevier publications in 2003). PDF

  15. Shi Y, Lee JS, Galvin KM. (1997). Everything you have ever wanted to know about Yin Yang 1…. Biochim Biophys Acta. 1332(2): F49-66. PDF