Shi Laboratory

Selected Publications


Yu Y*, Tencer A*, Xuan H*, Kutateladze TG, Shi X. 2021. ZZEF1 is a histone reader and transcriptional coregulator of Krüppel-like factors. J Mol Biol 433(2):166722.

Ren X, Zhou Y, Xue Z, Hao N, Li Y, Guo X, Wang D, Shi X, Li H. 2021. Histone benzoylation serves as an epigenetic mark for DPF and YEATS family proteins. Nucleic Acids Res 49(1):114–126.


Wen H, Shi X. 2020. H3.3S31 phosphorylation: linking transcription elongation to stimulation responses. Signal Transduct Target Ther 5(1):176.

Shen X, Wang R, Kim MJ, Hu Q, Hsu CC, Yao J, Klages-Mundt N, Tian Y, Lynn E, Brewer TF, Zhang Y, Arun B, Gan B, Andreeff M, Takeda S, Chen J, Park JI, Shi X, Chang CJ, Jung SY, Qin J, Li L. 2020. A surge of DNA damage links transcriptional reprogramming and hematopoietic deficit in Fanconi anemia. Mol Cell 80(6):1013–1024.

Zhang Y, Guo Y, Gough SM, Zhang J, Vann KR, Li K, Cai L, Shi X, Aplan PD, Wang GG, Kutateladze TG. 2020. Mechanistic insights into chromatin targeting by leukemic NUP98-PHF23 fusion. Nat Commun 11(1):3339.

Liu J, Xue Z, Vann KR, Shi X, Kutateladze TG. 2020. Protocol for biochemical analysis and structure determination of the ZZ domain of the E3 ubiquitin ligase HERC2. STAR Protoc 1(3):100155.

Liu J*, Xue Z*, Zhang Y, Vann KR, Shi X*, Kutateladze TG*. 2020. Structural insight into binding of the ZZ domain of HERC2 to histone H3 and SUMO1. Structure 28(11):1225–1230.

Chen Y, Fang R, Yue C, Chang G, Li P, Guo Q, Wang J, Zhou A, Zhang S, Fuller GN, Shi X, Huang S. 2020. Wnt-induced stabilization of KDM4C is required for Wnt/β-Catenin target gene expression and glioblastoma tumorigenesis. Cancer Res 80(5):1049–1063.


Klein BJ, Jang SM, Lachance C, Mi W, Lyu J, Sakuraba S, Krajewski K, Wang WW, Sidoli S, Liu J, Zhang Y, Wang X, Warfield BM, Kueh AJ, Voss AK, Thomas T, Garcia BA, Liu WR, Strahl BD, Kono H, Li W, Shi X, Côté J, Kutateladze TG. 2019. Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation. Nat Commun 10(1):4724.

He W, Zhang L, Villarreal OD, Fu R, Bedford E, Dou J, Patel AY, Bedford MT, Shi X, Chen T, Bartholomew B, Xu H. 2019. De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens. Nat Commun 10(1):4541.

Gao G, Zhang L, Villarreal OD, He W, Su D, Bedford E, Moh P, Shen J, Shi X, Bedford MT, Xu H. 2019. PRMT1 loss sensitizes cells to PRMT5 inhibition. Nucleic Acids Res.

Zhang Y, Jang Y, Lee JE, Ahn J, Xu L, Holden MR, Cornett EM, Krajewski K, Klein BJ, Wang SP, Dou Y, Roeder RG, Strahl BD, Rothbart SB, Shi X, Ge K, Kutateladze TG. 2019. Selective binding of the PHD6 finger of MLL4 to histone H4K16ac links MLL4 and MOF. Nat Commun 10(1):2314.

Zhang Y*, Mi W*, Xue Y*, Shi X#, Kutateladze TG#. 2019 The ZZ domain as a new epigenetic reader and a degradation signal sensor. Crit Rev Biochem Mol Biol.;54(1):1-10. Review.
*Equal contribution


Mi W*, Zhang Y*, Lyu J*, Wang X, Tong Q, Peng D, Xue Y, Tencer AH, Wen H, Li W, Kutateladze TG*, Shi X*. 2018. The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation. Nat Commun 9(1):3759.

Zhang Y*, Xue Y*, Shi J, Ahn J, Mi W, Ali M, Wang X, Klein BJ, Wen H, Li W, Shi X*, Kutateladze TG*. 2018. The ZZ domain of p300 mediates specificity of the adjacent HAT domain for histone H3.
Nat Struct Mol Biol 25(9):841-849.

Zhu S, Zhao D, Yan L, Jiang W, Kim JS, Gu B, Liu Q, Wang R, Xia B, Zhao JC, Song G, Mi W, Wang RF, Shi X, Lam HM, Dong X, Yu J, Chen K, Cao Q. 2018. BMI1 regulates androgen receptor in prostate cancer independently of the polycomb repressive complex 1. Nat Commun 9(1):500.

Shi L*, Shi J*, X S, Li W, Wen H. 2018. Histone H3.3 G34 mutations alter histone H3K36 and H3K27 methylation in cis. J Mol Biolpii:S0022-2836(18)30248-1.

Hsu C*, Shi J*, Yuan C*, Zhao D*, Jiang S, Lyu J, Wang X, Li H, Wen H, Li W*, Shi X*. 2018. Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition in non-small cell lung cancerGenes Dev 32(1):58–69.

Zhu S, Zhao D, Yan L, Jiang W, Kim JS, Gu B, Liu Q, Wang R, Xia B, Zhao JC, Song G, Mi W, Wang RF, Shi X, Lam HM, Dong X, Yu J, Chen K, Cao Q. 2018. BMI1 regulates androgen receptor in prostate cancer independently of the polycomb repressive complex 1. Nat Commun 9(1):500.

Franco HL, Nagari A, Malladi VS, Li W, Xi Y, Richardson D, Allton KL, Tanaka K, Li J, Murakami S, Keyomarsi K, Bedford MT, Shi X, Li W, Barton MC, Dent SYR, Kraus WL. 2018. Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis. Genome Res 28(2):159–170.

Xi Y*, Shi J*, Li W*, Tanaka K*, Allton KL*, Richardson D, Li J, Franco HL, Nagari A, Malladi VS, Coletta LD, Simper MS, Keyomarsi K, Shen J, Bedford MT, Shi X, Barton MC, Lee Kraus W, Li W, Dent SYR. 2018. Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes. BMC Genomics 19(1):150.
*Equal contribution


Shi L, Wen H, Shi X. 2017. The histone variant H3.3 in transcriptional regulation and human disease. J Mol Biol 429(13):1934–1945.

Mi W, Guan H, Lyu J, Zhao D, Xi Y, Jiang S, Andrews FH, Wang X, Gagea M, Wen H, Tora L, Dent SYR, Kutateladze TG, Li W*, Li H*, Shi X*. 2017. YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancerNat Commun 8(1):1088.

Klein BJ, Simithy J, Wang X, Ahn J, Andrews FH, Zhang Y, Côté J, Shi X, Garcia BA, Kutateladze TG. 2017. Recognition of histone H3K14 acylation by MORFStructure 25(4):650–654.e2.

Wan L*, Wen H*, Li Y*, Lyu J, Xi Y, Hoshii T, Joseph J, Wang X, Loh Y, Souza AL, Bradner JE, Shen L, Li W, Li H, Allis CD*, Armstrong SA*, Shi X*. 2017. ENL links histone acetylation to oncogenic gene expression in AMLNature 543(7644):265–269.


Schibler A, Koutelou E, Tomida J, Wilson-Pham M, Wang L, Lu Y, Cabrera AP, Chosed RJ, Li W, Li B, Shi X, Wood RD, Dent SY. 2016. Histone H3K4 methylation regulates deactivation of the spindle assembly checkpoint through direct binding of Mad2Genes Dev 30(10):1187–1197.

Zhao D, Guan H, Zhao S, Mi W, Wen H, Li Y, Zhao Y, Allis CD, Shi X*, Li H*. (2016) YEATS2 is a selective histone crotonylation readerCell Res 26(5):629–632.

Andrews FH*, Shinsky SA*, Shanle EK, Bridgers JB, Gest A, Tsun IK, Krajewski K, Shi X, Strahl BD*, Kutateladze TG*. 2016. The Taf14 YEATS domain is a reader of histone crotonylationNature Chem Biol 12(6):396–398.

Li Y*, Sabari BR*, Panchenko T, Wen H, Zhao D, Guan H, Wan L, Huang H, Tang Z, Zhao Y, Roeder RG, Shi X, Allis CD*, Li H*. 2016. Molecular coupling of histone crotonylation and active transcription by AF9 YEATS domainMol Cell 62(2):181–193.

Zhang X, Peng D, Xi Y, Yuan C, Sagum CA, Klein BJ, Tanaka K, Wen H, Kutateladze TG, Li W, Bedford MT, Shi X. 2016. G9a-mediated methylation of ERα links the PHF20/MOF histone acetyltransferase complex to hormonal gene expressionNature Commun 7:10810.

Klein BJ*, Wang X*, Cui G, Yuan C, Botuyan MV, Lin K, Lu Y, Wang X, Zhao Y, Bruns CJ, Mer G, Shi X*, Kutateladze TG*. 2016. PHF20 readers link methylation of histone H3K4 and p53 with H4K16 acetylationCell Rep 17(4):1158–1170.

Shi L, Wen H, Shi X. 2016. The histone variant H3.3 in transcriptional regulation and human diseaseJ Mol Biol 429(13):1934–1945.

Li N, Li Y, Lv J, Zheng X, Wen H, Shen H, Zhu G, Chen TY, Dhar SS, Kan PY, Wang Z, Shiekhattar R, Shi X, Lan F, Chen K, Li W, Li H, Lee MG. 2016. ZMYND8 reads the dual histone mark H3K4me1-H3K14ac to antagonize the expression of metastasis-linked genesMol Cell 63(3):470–484.


Chen K, Chen Z, Wu D, Zhang L, Lin X, Su J, Rodriguez B, Xi Y, Xia Z, Chen X, Shi X, Wang Q, Li W. 2015. Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genesNature Genet 47(10):1149–1157.

Zhang X, Huang Y, Shi X. 2015. Emerging roles of lysine methylation on non-histone proteinsCell Mol Life Sci 72(22):4257–4272.


Li Y*, Wen H*, Xi Y, Tanaka K, Wang H, Peng D, Ren Y, Jin Q, Dent SR, Li W*, Li H*, Shi X*. 2014. AF9 YEATS domain links histone acetylation to DOT1L-mediated H3K79 methylationCell 159(3):558–571.

Guo R*, Zheng L*, Park JW, Lv R, Chen H, Jiao F, Xu W, Mu S, Wen H, Qiu J, Wang Z, Yang P, Wu F, Hui J, Fu X, Shi X*, Shi YG*, Xing Y*, Lan F*, Shi Y*. 2014. BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processingMol Cell 56(2):298–310.

Wen H, Li Y, Li H, Shi X. 2014. ZMYND11: An H3.3-specific reader of H3K36me3Cell Cycle 13(14):2153–2154.

Wen H*, Li Y*, Xi Y*, Jiang S, Stratton S, Peng D, Tanaka K, Ren Y, Xia Z, Wu J, Li B, Barton MC, Li W*, Li H*, Shi X*. 2014. ZMYND11 links histone H3.3 K36 trimethylation to transcription elongation and tumor suppressionNature 508(7495):263–268.

Jiang Y, Trescott L, Holcomb J, Zhang X, Brunzelle J, Sirinupong N, Shi X, Yang Z. 2014. Structural insights into estrogen receptor a methylation by histone methyltransferase SMYD2, a cellular event implicated in estrogen signaling regulationJ Mol Biol 426(20):3413–3425.

Klein BJ*, Piao L*, Xi Y, Rincon-Arano H, Rothbart SB, Peng D, Wen H, Larson C, Zheng X, Cortazar M, Peña PV, Mangan A, Bentley DL, Strahl BD, Groudine M, Li W, Shi X*, Kutateladze T*. 2014. KDM5B demethylase binds to its histone target and the product through distinct modulesCell Reports 6(2):325–335.


Wang J, Leung JW, Gong Z, Feng L, Shi X, Chen J. 2013. PHF6 regulates cell cycle progression by suppressing ribosomal RNA synthesisJ Biol Chem 288(5):3174–3183.

Zhang H, Ma ZY, Zeng L, Tanaka K, Zhang CJ, Ma J, Bai G, Wang P, Zhang SW, Liu ZW, Cai T, Tang K, Liu R, Shi X, He XJ, Zhu JK. 2013. DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IVProc Natl Acad Sci U S A 110(20):8290–8295.

Zhang X, Tanaka K, Yan J, Li J, Peng D, Jiang Y, Yang Z, Barton MC, Wen H, Shi X. 2013. Regulation of estrogen receptor α by histone methyltransferase SMYD2-mediated protein methylationProc Natl Acad Sci U S A 110(43):17284–17289.


Qian W, Miki D, Zhang H, Liu Y, Zhang X, Tang K, Kan Y, La H, Li X, Li S, Zhu X, Shi X, Zhang K, Pontes O, Chen X, Liu R, Gong Z, Zhu JK. 2012. A histone acetyltransferase regulates active DNA demethylation in ArabidopsisScience 336(6087):1445–1448.

Brien GL, Gambero G, O’Connell DJ, Jerman E, Turner SA, Egan CM, Dunne EJ, Jurgens MC, Wynne K, Piao L, Lohan AJ, Ferguson N, Shi X, Sinha KM, Loftus BJ, Cagney G, Bracken AP. 2012. Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiationNat Struct Mol Biol 19(12):1273–1281.

Dhar SS, Lee SH, Kan PY, Voigt P, Ma L, Shi X, Reinberg D, Lee MG. 2012. Trans-tail regulation of MLL4-catalyzed H3K4 methylation by H4R3 symmetric dimethylation is mediated by a tandem PHD of MLL4Genes Dev 26(24):2749–2762.


Levy D, Kuo AJ, Chang Y, Schaefer U, Kitson C, Cheung P, Espejo A, Zee BM, Liu CL, Tangsombatvisit S, Tennen RI, Kuo AY, Tanjing S, Cheung R, Chua KF, Utz PJ, Shi X, Prinjha RK, Lee K, Garcia BA, Bedford MT, Tarakhovsky A, Cheng X, Gozani O. 2011. Lysine methylation of the NF-kB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-kB signalingNat Immunol 12(1):29–36.

Kuo AJ, Cheung P, Chen K, Zee BM, Kioi M, Lauring J, Xi Y, Park BH, Shi X, Garcia BA, Li W, Gozani O. 2011. NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programmingMol Cell 44(4):609–620.


Wen H, Li J, Song T, Lu M, Kan PY, Lee MG, Sha B, Shi X. 2010. Recognition of histone H3K4 trimethylation by the PHD finger of PHF2 modulates histone demethylationJ Biol Chem 285(13):9322.

Kleine-Kohlbrecher D, Christensen J, Vandamme J, Abarrategui I, Bak M, Tommerup N, Shi X, Gozani O, Rappsilber J, Salcini AE, Helin K. 2010. A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardationMol Cell 38(2):1–14.

West LE, Roy S, Lachmi-Weiner K, Hayashi R, Shi X, Appella E, Kutateladze TG, Gozani O. 2010. The MBT repeats of L3MBTL1 link SET8-mediated p53 methylation at lysine 382 to target gene repressionJ Biol Chem 285(48):37725–37732.

Tsai WW, Wang Z, Yiu TT, Akdemir KC, Xia W, Winter S, Tsai CY, Shi X, Schwarzer D, Plunkett W, Aronow B, Gozani O, Fischle W, Hung MC, Patel DJ, Barton MC. 2010. TRIM24 links a non-canonical histone signature to breast cancerNature 468(7326):927–932.

Selected publications before 2009

Shi X, Kachirskaia I, Yamaguchi H, West LE, Wen H, Wang EW, Dutta S, Appella E, Gozani O. 2007. Modulation of p53 function by SET8-mediated methylation at lysine 382Mol Cell 27(4):636–46.

Shi X*, Kachirskaia I*, Walter KL, Kuo JH, Lake A, Davrazou F, Chan SM, Martin DG, Fingerman IM, Briggs SD, Howe L, Utz PJ, Kutateladze TG, Lugovskoy AA, Bedford MT, Gozani O. 2007. Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36. J Biol Chem 282(4):2450–2455.

Shi X, Hong T, Walter KL, Ewalt M, Michishita E, Hung T, Carney D, Peña P, Lan F, Kaadige MR, Lacoste N, Cayrou C, Davrazou F, Saha A, Cairns BR, Ayer DE, Kutateladze TG, Shi Y, Côté J, Chua KF, Gozani O. 2006. ING2 PHD domain links histone H3 lysine 4 methylation to active gene repressionNature 442(7098):96–99.

Peña PV, Davrazou F, Shi X, Walter KL, Verkhusha VV, Gozani O, Zhao R, Kutateladze TG. 2006. Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2Nature 442(7098):100–103.

Shi X, Rao NN, Kornberg A. 2004. Inorganic polyphosphate in Bacillus cereus: motility, biofilm formation, and sporulationProc Natl Acad Sci U S A 101(49):17061–17065.