2024

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.

Wang, YY*., Zhou, C*., Bou-Tayeh, B., Lisle, R., Kriaucionis, S., and Shi, Y. UXS1 regulates UDP-GlcA levels to support growth of UGDH-high cancer cells. BioRxiv 2024.02.08.579288; doi: https://doi.org/10.1101/2024.02.08.579288, *Equal contributions.

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. Epub 2024 Nov 19. +Co-correspondence.

2023

Mu, MD., Li, XZ., Dong, L., Zhao, P., Zhang, L., Tan, L., Wu, FZ., Shi, YJG., Xu, WQ+, Shi, Y+., and Shen, HJ+. METTL14 regulates chromatin bivalent domains in mouse embryonic stem cells. Cell Rep. 2023, Jun 13;42(6):112650. +Co-correspondence.

Ng, J., Marneth, AE., Griffth, Younger, D., Ghanta, S., Jiao, A., Willis, G., Han, JW., Imani, J., Hancock, B., Keegan, JW., Fuo, F., Shi, Y., Mullally, A., Perrella, MA., Lederer, JA. Mesenchymal Stromal Cells Facilitate Neutrophil Trained Immunity. Journal of Trained Immunity. 2023, 15(1):765-781.

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. 2023. Dec 7;83(23):4370-4385.e9. +Co-correspondence.

2022

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.

Chu, ZW*, Gu, L*., Hu, YG., Zhang, XY, Li, M., Chen,JJ., Teng, D., Huang, M., Shen, C-H., Cai, L. Yoshida, T., Qi, YF., Niu, ZX., Feng, A., Geng, SM., Frederick, D., Specht, E., Piris, A., Sullivan, R., Flaherty, K., Boland, G., Georgopoulos, G., Liu, D., Shi, Y., and Zheng, B. STAG2 regulates interferon signaling in melanoma via enhancer loop reprogramming. Nat Commun. 2022, Apr 6;13(1):1859. doi: 10.1038/s41467-022-29541-9. Bolded authors: members of my lab. *Equal contributions.

Panditharatna, E., Marques, J., Trissal, M., Wang, TJ., Liu, I., Jiang, L., Groves, A., Dharia, N., Li, DY., Hoffman, S., Kugener, G., Shaw, M., Mire, H., Hack, O., Dempster, J., Lareau, C., Dai, LL., Sigua, L., Quezada, M., Stanton, A-C., Wyatt, M., Kalani, Z., Goodale, A., Vazquez, F., Piccioni, F., Doench, J., Root, D., Anastas, J., Jones, K., Conway, AS., Stopka, S., Regan, M., Liang, Y., Seo, H-S., Song,KJ., Bashyal, P., Jerome, W., Mathewson, N., Dhe-Paganon, S., Suvà, M., Carcaboso, A., Lavarino, C., Mora, J., Nguyen, Q-D., Ligon, K., Shi, Y., Agnihotri, S., Agar, NYR., Stegmaier, K., Stiles, C., Monje, M., Golub, T., Qi, J.,  and Filbin, M. BAF complex maintains glioma stem cells in pediatric H3K27M-glioma. Cancer Discov. 2022, Oct 28:CD-21-1491.

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.

Chen, Z., Huang, H., Wang, YY, Sendinc, E., and Shi, Y. Selective regulation of Tuft cell-like small cell lung cancer by novel transcriptional co-activators C11orf53 and COLCA2. Cell Discov. 2022, Oct 18;8(1):112.

2021

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 Discov. 2021. Aug;11(8):1970-1981. doi: 10.1158/2159-8290.CD-20-0017. Online ahead of print.*Equal contributions.

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 doi: 10.1038/s41586-021-03210-1. Epub 2021 Jan 27. PMID: 33505026. +Co-correspondence.

Stielow, B., Zhou, Y., Cao, Y. Simon, C., Pogoda, HM., Jiang, J., Reri, Y., Phanor, SK., Rohner, I., Nist, A., Stiewe, T., Hammerschmidt, M., Shi, Y., Bulyk, ML., Wang, Z., and Liefke, R. The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands. Sci Adv. 2021. 7(20):eabf2229. doi: 10.1126/sciadv.abf2229

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. 2021. May 25;24(6):102651. doi: 10.1016/j.isci.2021.102651. eCollection 2021 Jun 25. PMID: 34151238

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.

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(1):6831. doi: 10.1038/s41467-021-27179-7. +Co-correspondence.

2020

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].

Li, WJ*., Karwacki-Neisius, V*, Ma, C., Tan, L., Shi, Y., Wu, FZ., and Shi, YJG. Nono deficiency compromises TET1 chromatin association and impedes neuronal differentiation of mouse embryonic stem cells. Nucl. Acids Res. 2020 pii: gkaa213. doi: 10.1093/nar/gkaa213. [Epub ahead of print, PMID: 32286661. *Equal contributions. Bolded co-first author: member of my lab.

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; doi: https://doi.org/10.1101/2020.04.27.064162. *Equal contributions.

Chen, H*., Shi, ZN*., Guo, JJ*., Chang, KJ., Chen, QQ., Yao, CH., Haigis, MC., and Shi, Y. The human mitochondrial 12S rRNA m4C methyltransferase METTL15 is required for mitochondrial function. J Biol. Chem. 2020 Jun 19;295(25):8505-8513. doi: 10.1074/jbc.RA119.012127. Epub 2020 May 5. *Equal contributions.

Gu, L*., Wang, LF*., Chen, H*., Hong JX*., Shen, ZF., Dhall, A., Lao, TT., Liu, CZ., Wang, Z., Xu, YF., Tang, HW, Chakraborty, D., Chen, JK., Liu, ZH., Rogulja, D., Perrimon, N., Wu, H., and Shi, Y. CG14906 (mettl4) mediates m6A methylation of U2 snRNA in Drosophila. Cell Discovery. 2020 6:44. *Equal contributions.

Sendinc, E., Valle-Garcia, D., Jiao, A. and Shi Y. Analysis of m6A RNA methylation in C. elegans. Cell Discovery. 2020 6:47.

Cui, J., Liu, Q., Sendinc, E., Shi, Y., and Gregory, R. Nucleotide resolution profiling of m3C RNA modification by HAC-seq. Nucl. Acids Res. 2020. Dec 11: gkaa1186. doi: 10.1093/nar/gkaa1186. Online ahead of print. PMID: 33313824

2019

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.

Chen, H., Yu, D., Fang, R., Rabidou, K., Wu, D., Hu, D., Jia, P., Zhao, Z., Wu Z., Peng J., Shi, Y., Shi YG. TET2 stabilization by 14-3-3 binding to the phosphorylated Serine 99 is deregulated by mutations in cancer. Cell Res. 2019, 29(3): 248-250.

Byrum AK, Carvajal-Maldonado D, Mudge MC, Valle-Garcia D, Majid MC, Patel R, Sowa ME, Gygi SP, Harper JW, Shi Y, Vindigni A, Mosammaparast N. Mitotic regulators TPX2 and Aurora A protect DNA forks during replication stress by counteracting 53BP1 function. The Journal of Cell Biology. 2019 Feb 4; 218(2):422-432. PMCID: PMC6363440 [Available on 2019-08-04]

Zhang J, Lee YR, Dang F, Gan W, Menon AV, Katon JM, Hsu CH, Asara JM, Tibarewal P, Leslie NR, Shi Y, Pandolfi PP, Wei W. PTEN Methylation by NSD2 Controls Cellular Sensitivity to DNA Damage. Cancer Discov. 2019 Jun 19; Epub ahead of print. PMID: 31217297

Guo J, Dai X, Laurent B, Zheng N, Gan W, Zhang J, Guo A, Yuan M, Liu P, Asara JM, Toker A, Shi Y, Pandolfi PP, Wei W. AKT methylation by SETDB1 promotes AKT kinase activity and oncogenic functions. Nat Cell Biol. 2019 Feb; 21(2):226-237.

O’Brown ZK, Boulias K, Wang J, Wang SY, O’Brown NM, Hao Z, Shibuya H, Fady PE, Shi Y, He C, Megason SG, Liu T, Greer EL. Sources of artifact in measures of 6mA and 4mC abundance in eukaryotic genomic DNA. BMC Genomics. 2019 Jun 3; 20(1):445. doi: 10.1186/s1286-019-5754-6. PMID 31159718. PMCID: PMC6547475

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.

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.

Wang, J., Wang, L., Diao, J., Shi, YG, Shi Y+, Ma, H+., and Shen H+. Binding to m6A RNA promotes YTHDF2-mediated phase separation. Protein Cell. 2019 Oct 22. doi: 10.1007/s13238-019-00660-2. [Epub ahead of print]. +Co-correspondence.

2018

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.

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.

Wu D*, Hu D*, Chen H*, Shi GM*, Fetahu IS, Wu FZ, Rabidou K, Fang R, Tan L, Xu SY, Arguta C, Zhang L, Mao F, Yan GQ, Chen JJ, Dong ZR, Lv RT, Xu YF, Wang M, Ye Y, Zhang SK, Duqette D, Geng SM, Yin C, Lian CG, Murphy GF, Adler GK, Garg R, Lynch L, Yang PY, Li YM, Lan F, Fan J, Shi Y, Shi YJG. Glucose-regulated phosphorylation of TET2 by AMPK reveals a pathway linking diabetes to cancer. Nature. 2018 Jul; 559(7715):637-641. Epub 2018 Jul 18. *Equal contributions.

Spadafora, R., Lu, JJ, Khetain, R., Zhang, C., Iberg, A., Li, H., Shi, Y., and Lerou, PH. Lung-resident mesenchymal stromal cells reveal transcriptional dynamics of lung development in preterm infants. AJRCCM. 2018 Vol 198 (7): 961-64.

Zhao B, Xu W, Rong B, Chen G, Ye X, Dai R, Li W, Chen J, Cai J, Song L, Luo ZQ, Zeng R, Shi Y, Han JJ, Lan F. H3K14me3 genomic distributions and its regulation by KDM4 family demethylases. Cell Res. 2018 Nov; 28(11):1118-1120. PMCID: PMC6218439. Epub 2018 Oct 18.

2017

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. PMCID: PMC593728. Epub 2017 Sep 6. *Equal contributions.

Tan L, Ke ZH, Tombline G, Tian X, Lv R, Ablaeva J, Gilbert M, Bhanu NV, Yuan ZF, Garcia BA, Shi YG, Shi Y, Seluanov A, Gorbunova V. Naked mole rat cells have a stable epigenome that resists iPSC reprogramming. Stem Cell Rep. 2017 Nov 14; 9(5):1721-1734. PMCID: PMC5831052. Epub 2017 Oct 26.

Xiang Y*, Laurent B*, Hsu CH*, Nachtergaele S, Lu Z, Sheng W, Xu C, Chen H, Ouyang J, Wang S, Ling D, Hsu PH, Zou L, Jambhekar A, He C, Shi Y. RNA m6A methylation regulates the ultraviolet-induced DNA damage response. Nature. 2017 Mar 23; 543(7646):573-576. PMCID: PMC5490984 *Equal contributions.

Iberg-Badeaux A, Collombet S, Laurent B, van Oevelen C, Chin KK, Thieffry D, Graf T+, Shi Y+. A Transcription Factor Pulse Can Prime Chromatin for Heritable Transcriptional Memory. Mol. Cell Biol. 2017 Feb 1; 37(4) pii: e00372-16. PMCID: PMC5288571. +Co-correspondence.

Scandaglia M, Medrano-Fernandez A, Lopez-Atalaya J, Lopez-Cascales M, del Blaco B, Lipinski M, Olivares R, Iwase S, Shi Y, Barco A. Loss of Kdm5c causes spurious transcription and prevents the fine-tuning of activity-regulated enhancers in neurons. Cell Rep. 2017 Oct 3; 21(1): 47-59. PMCID: PMC5679733

2016

Murn J*, Teplova M*, Zarnack K, Shi Y+, Patel DJ+. Recognition of distinct RNA motifs by the clustered CCCH zinc fingers of neuronal protein Unkempt. Nat. Struct. Mol. Biol. 2016 Jan; 23(1):16-23. PMCID: PMC4703518   *Equal contributions, +Co-correspondence.

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. PMCID: PMC4746603 +Co-correspondence.

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.

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. PMCID: PMC4826479 *Co-first, +Co-correspondence.

Kong L, Tan L, Lv R, Shi Z, Xiong L, Wu F, Rabidou K, Smith M, He C, Zhang L, Qian Y, Ma D, Lan F, Shi Y+, Shi YG+. A primary role of TET proteins in establishment and maintenance of de novo bivalency at CpG islands. Nucl. Acids Res. 2016 Oct 14; 44(18):8682-8692. Epub 2016 Jun 10. PMCID: PMC5062965. +Co-correspondence.

Ma C, Karwacki-Neisius V, Tang HR, Li WJ, Shi ZN, Tan L, Xu WQ, Wang ZT, Kong LC, Lv RT, Fan Z, Zhou WH, Yang PY, Wu FZ, Diao JB, Shi YJG, Lan F+, Shi Y+. Nono, a bivalent domain factor, regulates Erk signaling and mouse embryonic stem cell pluripotency. Cell Rep. 2016 Oct 18;17(4):997-1007. PMCID: PMC5086807. +Co-correspondence.