Xing Zhang

Peer-Reviewed Articles

1. Zhou J, Chen Q, Ren R, Yang J, Liu B, Horton JR, Chang C, Li C, Maksoud L, Yang Y, Rotili D, Jain AK, Zhang X, Blumenthal RM, Chen T, Gao Y, Valente S, Mai A, Cheng X. Quinoline-based compounds can inhibit diverse enzymes that act on DNA. Cell Chem Biol None(None):None, 2024. PMID: 39437789.
2. Hardikar S, Ren R, Ying Z, Zhou J, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, Coletta LD, Shen J, Dan J, Zhang X, Cheng X, Chen T. The ICF syndrome protein CDCA7 harbors a unique DNA binding domain that recognizes a CpG dyad in the context of a non-B DNA. Sci Adv 10(34):eadr0036, 2024. PMID: 39178265.
3. Yang J, Horton JR, Liu B, Corces VG, Blumenthal RM, Zhang X, Cheng X. Structures of CTCF-DNA complexes including all 11 zinc fingers. Nucleic Acids Res 51(16):8447-8462, 2023. PMID: 37439339.
4. Zhou J, Horton JR, Kaur G, Chen Q, Li X, Mendoza F, Wu T, Blumenthal RM, Zhang X, Cheng X. Biochemical and structural characterization of the first-discovered metazoan DNA cytosine-N4 methyltransferase from the bdelloid rotifer Adineta vaga. J Biol Chem 299(8):105017, 2023. e-Pub 2023. PMID: 37414145.
5. Chen Q, Liu B, Zeng Y, Hwang JW, Dai N, Corrêa IR, Estecio MR, Zhang X, Santos MA, Chen T, Cheng X. GSK-3484862 targets DNMT1 for degradation in cells. NAR Cancer 5(2):zcad022, 2023. e-Pub 2023. PMID: 37206360.
6. Zhou J, Deng Y, Iyamu ID, Horton JR, Yu D, Hajian T, Vedadi M, Rotili D, Mai A, Blumenthal RM, Zhang X, Huang R, Cheng X. Comparative Study of Adenosine Analogs as Inhibitors of Protein Arginine Methyltransferases and a Clostridioides difficile-Specific DNA Adenine Methyltransferase. ACS Chem Biol 18(4):734-745, 2023. e-Pub 2023. PMID: 37082867.
7. Horton JR, Zhou J, Chen Q, Zhang X, Bedford MT, Cheng X. A complete methyl-lysine binding aromatic cage constructed by two domains of PHF2. J Biol Chem 299(2):102862, 2023. e-Pub 2022. PMID: 36596360.
8. Ren R, Horton JR, Chen Q, Yang J, Liu B, Huang Y, Blumenthal RM, Zhang X, Cheng X. Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia. J Biol Chem 299(2):102885, 2023. e-Pub 2023. PMID: 36626981.
9. Kaur G, Ren R, Hammel M, Horton JR, Yang J, Cao Y, He C, Lan F, Lan X, Blobel GA, Blumenthal RM, Zhang X, Cheng X. Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410-DNA interaction using small angle X-ray scattering. Nucleic Acids Res 51(4):1674-1686, 2023. PMID: 36660822.
10. Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Hüben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X. Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile-Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence. J Med Chem 66(1):934-950, 2023. e-Pub 2022. PMID: 36581322.
11. Horton JR, Pathuri S, Wong K, Ren R, Rueda L, Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB, Zhang X, King BW, Cheng X. Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors. Structure 30(6):793-802.e5, 2022. e-Pub 2022. PMID: 35395178.
12. Yu D, Zhou J, Chen Q, Wu T, Blumenthal RM, Zhang X, Cheng X. Enzymatic Characterization of In Vitro Activity of RNA Methyltransferase PCIF1 on DNA. Biochemistry 61(11):1005-13. e-Pub 2022. PMID: 35605980.
13. Yang J, Gupta E, Horton JR, Blumenthal RM, Zhang X, Cheng X. Differential ETS1 binding to T:G mismatches within a CpG dinucleotide contributes to C-to-T somatic mutation rate of the IDH2 hotspot at codon Arg140. DNA Repair (Amst) 113:103306. e-Pub 2022. PMID: 35255310.
14. Yu D, Dai N, Wolf EJ, Corrêa IR, Zhou J, Wu T, Blumenthal RM, Zhang X, Cheng X. Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs. J Biol Chem 298(4):101751. e-Pub 2022. PMID: 35189146.
15. Yu D, Horton JR, Yang J, Hajian T, Vedadi M, Sagum CA, Bedford MT, Blumenthal RM, Zhang X, Cheng X. Human MettL3-MettL14 RNA adenine methyltransferase complex is active on double-stranded DNA containing lesions. Nucleic Acids Res 49(20):11629-11642, 2021. PMID: 34086966.
16. Pappalardi MB, Keenan K, Cockerill M, Kellner WA, Stowell A, Sherk C, Wong K, Pathuri S, Briand J, Steidel M, Chapman P, Groy A, Wiseman AK, McHugh CF, Campobasso N, Graves AP, Fairweather E, Werner T, Raoof A, Butlin RJ, Rueda L, Horton JR, Fosbenner DT, Zhang C, Handler JL, Muliaditan M, Mebrahtu M, Jaworski JP, McNulty DE, Burt C, Eberl HC, Taylor AN, Ho T, Merrihew S, Foley SW, Rutkowska A, Li M, Romeril SP, Goldberg K, Zhang X, Kershaw CS, Bantscheff M, Jurewicz AJ, Minthorn E, Grandi P, Patel M, Benowitz AB, Mohammad HP, Gilmartin AG, Prinjha RK, Ogilvie D, Carpenter C, Heerding D, Baylin SB, Jones PA, Cheng X, King BW, Luengo JI, Jordan AM, Waddell I, Kruger RG, McCabe MT. Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia. Nat Cancer 2(10):1002-1017, 2021. e-Pub 2021. PMID: 34790902.
17. Zhou J, Horton JR, Yu D, Ren R, Blumenthal RM, Zhang X, Cheng X. Repurposing epigenetic inhibitors to target the Clostridioides difficile-specific DNA adenine methyltransferase and sporulation regulator CamA. Epigenetics:1-12. e-Pub 2021. PMID: 34523387.
18. Zhou J, Horton JR, Blumenthal RM, Zhang X, Cheng X. Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix. Nat Commun 12(1):3436, 2021. e-Pub 2021. PMID: 34103525.
19. Yang J, Horton JR, Akdemir KC, Li J, Huang Y, Kumar J, Blumenthal RM, Zhang X, Cheng X. Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations. Nucleic Acids Res 49(9):5084-5094, 2021. PMID: 33877329.
20. Yu D, Kaur G, Blumenthal RM, Zhang X, Cheng X. Enzymatic characterization of three human RNA adenosine methyltransferases reveals diverse substrate affinities and reaction optima. J Biol Chem 296:100270, 2021. e-Pub 2021. PMID: 33428944.
21. Zeng Y, Ren R, Kaur G, Hardikar S, Ying Z, Babcock L, Gupta E, Zhang X, Chen T, Cheng X. The inactive Dnmt3b3 isoform preferentially enhances Dnmt3b-mediated DNA methylation. Genes Dev 34(21-22):1546-1558, 2020. e-Pub 2020. PMID: 33004415.
22. Woodcock CB, Horton JR, Zhou J, Bedford MT, Blumenthal RM, Zhang X, Cheng X. Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA. Nucleic Acids Res 48(18):10329-10341, 2020. PMID: 32663306.
23. Dai S, Holt MV, Horton JR, Woodcock CB, Patel A, Zhang X, Young NL, Wilkinson AW, Cheng X. Characterization of SETD3 methyltransferase-mediated protein methionine methylation. J Biol Chem 295(32):10901-10910, 2020. e-Pub 2020. PMID: 32503840.
24. Kumar J, Kaur G, Ren R, Lu Y, Lin K, Li J, Huang Y, Patel A, Barton MC, Macfarlan T, Zhang X, Cheng X. KRAB domain of ZFP568 disrupts TRIM28-mediated abnormal interactions in cancer cells. NAR Cancer 2(2):zcaa007, 2020. e-Pub 2020. PMID: 32743551.
25. Mahgoub M, Paiano J, Bruno M, Wu W, Pathuri S, Zhang X, Ralls S, Cheng X, Nussenzweig A, Macfarlan TS. Dual histone methyl reader ZCWPW1 facilitates repair of meiotic double strand breaks in male mice. Elife 9, 2020. e-Pub 2020. PMID: 32352380.
26. Dai S, Horton JR, Wilkinson AW, Gozani O, Zhang X, Cheng X. An engineered variant of SETD3 methyltransferase alters target specificity from histidine to lysine methylation. J Biol Chem 295(9):2582-2589, 2020. e-Pub 2020. PMID: 31911441.
27. Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A, Wilson GG, Roberts RJ, Cheng X. Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å. Nucleic Acids Res. e-Pub 2019. PMID: 31879785.
28. Horton JR, Woodcock CB, Opot SB, Reich NO, Zhang X, Cheng X. The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site. Nat Commun 10(1):4600, 2019. e-Pub 2019. PMID: 31601797.
29. Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, Zhang X, Chen T, Cheng X. Structural basis of specific DNA binding by the transcription factor ZBTB24. Nucleic Acids Res 47(16):8388-8398, 2019. PMID: 31226215.
30. Yang J, Horton JR, Li J, Huang Y, Zhang X, Blumenthal RM, Cheng X. Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine. Nucleic Acids Res 47(16):8375-8387, 2019. PMID: 31081034.
31. Dai S, Horton JR, Woodcock CB, Wilkinson AW, Zhang X, Gozani O, Cheng X. Structural basis for the target specificity of actin histidine methyltransferase SETD3. Nat Commun 10(1):3541, 2019. e-Pub 2019. PMID: 31388018.
32. Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang Y, Zhang X, Blumenthal RM, Cheng X. Structural basis for effects of CpA modifications on C/EBPβ binding of DNA. Nucleic Acids Res 47(4):1774-1785, 2019. PMID: 30566668.
33. Wilkinson AW, Diep J, Dai S, Liu S, Ooi YS, Song D, Li TM, Horton JR, Zhang X, Liu C, Trivedi DV, Ruppel KM, Vilches-Moure JG, Casey KM, Mak J, Cowan T, Elias JE, Nagamine CM, Spudich JA, Cheng X, Carette JE, Gozani O. SETD3 is an actin histidine methyltransferase that prevents primary dystocia. Nature 565(7739):372-376, 2019. e-Pub 2018. PMID: 30626964.
34. Woodcock CB, Yu D, Zhang X, Cheng X. Human HemK2/KMT9/N6AMT1 is an active protein methyltransferase, but does not act on DNA in vitro, in the presence of Trm112. Cell Discov 5:50, 2019. e-Pub 2019. PMID: 31632689.
35. Woodcock CB, Yu D, Hajian T, Li J, Huang Y, Dai N, Corrêa IR, Wu T, Vedadi M, Zhang X, Cheng X. Human MettL3-MettL14 complex is a sequence-specific DNA adenine methyltransferase active on single-strand and unpaired DNA in vitro. Cell Discov 5:63, 2019. e-Pub 2019. PMID: 31885874.
36. Horton JR, Woodcock CB, Chen Q, Liu X, Zhang X, Shanks J, Rai G, Mott BT, Jansen DJ, Kales SC, Henderson MJ, Cyr M, Pohida K, Hu X, Shah P, Xu X, Jadhav A, Maloney DJ, Hall MD, Simeonov A, Fu H, Vertino PM, Cheng X. Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A. J Med Chem 61(23):10588-10601, 2018. e-Pub 2018. PMID: 30392349.
37. Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X, Cheng X. Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites. Nucleic Acids Res 46(8):3864-3877, 2018. PMID: 29294058.
38. Horton JR, Liu X, Wu L, Zhang K, Shanks J, Zhang X, Rai G, Mott BT, Jansen DJ, Kales SC, Henderson MJ, Pohida K, Fang Y, Hu X, Jadhav A, Maloney DJ, Hall MD, Simeonov A, Fu H, Vertino PM, Yan Q, Cheng X. Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A. J Med Chem 61(7):3193-3208, 2018. e-Pub 2018. PMID: 29537847.
39. Patel A, Yang P, Tinkham M, Pradhan M, Sun MA, Wang Y, Hoang D, Wolf G, Horton JR, Zhang X, Macfarlan T, Cheng X. DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins. Cell 173(1):221-233.e12, 2018. e-Pub 2018. PMID: 29551271.
40. Murray IA, Morgan RD, Luyten Y, Fomenkov A, Corrêa IR, Dai N, Allaw MB, Zhang X, Cheng X, Roberts RJ. The non-specific adenine DNA methyltransferase M.EcoGII. Nucleic Acids Res 46(2):840-848, 2018. PMID: 29228259.
41. Patel A, Zhang X, Blumenthal RM, Cheng X. Structural basis of human PR/SET domain 9 (PRDM9) allele C-specific recognition of its cognate DNA sequence. J Biol Chem 292(39):15994-16002, 2017. e-Pub 2017. PMID: 28801461.
42. Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X. Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA. Mol Cell 66(5):711-720.e3, 2017. e-Pub 2017. PMID: 28529057.
43. Wang D, Hashimoto H, Zhang X, Barwick BG, Lonial S, Boise LH, Vertino PM, Cheng X. MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma. Nucleic Acids Res 45(5):2396-2407, 2017. PMID: 27903915.
44. Hong S, Wang D, Horton JR, Zhang X, Speck SH, Blumenthal RM, Cheng X. Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta. Nucleic Acids Res 45(5):2503-2515, 2017. PMID: 28158710.
45. Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng X. Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications. Nucleic Acids Res 44(21):10165-10176, 2016. e-Pub 2016. PMID: 27596598.
46. Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X. Distinctive Klf4 mutants determine preference for DNA methylation status. Nucleic Acids Res 44(21):10177-10185, 2016. e-Pub 2016. PMID: 27596594.
47. Horton JR, Liu X, Gale M, Wu L, Shanks JR, Zhang X, Webber PJ, Bell JSK, Kales SC, Mott BT, Rai G, Jansen DJ, Henderson MJ, Urban DJ, Hall MD, Simeonov A, Maloney DJ, Johns MA, Fu H, Jadhav A, Vertino PM, Yan Q, Cheng X. Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds. Cell Chem Biol 23(7):769-781, 2016. e-Pub 2016. PMID: 27427228.
48. Horton JR, Engstrom A, Zoeller EL, Liu X, Shanks JR, Zhang X, Johns MA, Vertino PM, Fu H, Cheng X. Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases. J Biol Chem 291(6):2631-46, 2016. e-Pub 2015. PMID: 26645689.
49. Patel A, Horton JR, Wilson GG, Zhang X, Cheng X. Structural basis for human PRDM9 action at recombination hot spots. Genes Dev 30(3):257-65, 2016. PMID: 26833727.
50. Patel A, Hashimoto H, Zhang X, Cheng X. Characterization of How DNA Modifications Affect DNA Binding by C2H2 Zinc Finger Proteins. Methods Enzymol 573:387-401, 2016. e-Pub 2016. PMID: 27372763.
51. Hashimoto H, Pais JE, Dai N, Corrêa IR, Zhang X, Zheng Y, Cheng X. Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA. Nucleic Acids Res 43(22):10713-21, 2015. e-Pub 2015. PMID: 26323320.
52. Horton JR, Zhang X, Blumenthal RM, Cheng X. Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression. Nucleic Acids Res 43(8):4296-308, 2015. e-Pub 2015. PMID: 25845600.
53. Hong S, Hashimoto H, Kow YW, Zhang X, Cheng X. The carboxy-terminal domain of ROS1 is essential for 5-methylcytosine DNA glycosylase activity. J Mol Biol 426(22):3703-3712, 2014. e-Pub 2014. PMID: 25240767.
54. Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X. Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence. Genes Dev 28(20):2304-13, 2014. e-Pub 2014. PMID: 25258363.
55. Horton JR, Wang H, Mabuchi MY, Zhang X, Roberts RJ, Zheng Y, Wilson GG, Cheng X. Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix. Nucleic Acids Res 42(19):12092-101, 2014. e-Pub 2014. PMID: 25262349.
56. Kao TH, Liao HF, Wolf D, Tai KY, Chuang CY, Lee HS, Kuo HC, Hata K, Zhang X, Cheng X, Goff SP, Ooi SK, Bestor TH, Lin SP. Ectopic DNMT3L triggers assembly of a repressive complex for retroviral silencing in somatic cells. J Virol 88(18):10680-95, 2014. e-Pub 2014. PMID: 24991018.
57. Horton JR, Borgaro JG, Griggs RM, Quimby A, Guan S, Zhang X, Wilson GG, Zheng Y, Zhu Z, Cheng X. Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA. Nucleic Acids Res 42(12):7947-59, 2014. e-Pub 2014. PMID: 24895434.
58. Liu Y, Olanrewaju YO, Zheng Y, Hashimoto H, Blumenthal RM, Zhang X, Cheng X. Structural basis for Klf4 recognition of methylated DNA. Nucleic Acids Res 42(8):4859-67, 2014. e-Pub 2014. PMID: 24520114.
59. Horton JR, Nugent RL, Li A, Mabuchi MY, Fomenkov A, Cohen-Karni D, Griggs RM, Zhang X, Wilson GG, Zheng Y, Xu SY, Cheng X. Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI. Sci Rep 4:4246, 2014. e-Pub 2014. PMID: 24604015.
60. Hashimoto H, Pais JE, Zhang X, Saleh L, Fu ZQ, Dai N, Corrêa IR, Zheng Y, Cheng X. Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA. Nature 506(7488):391-5, 2014. e-Pub 2013. PMID: 24390346.
61. Valente S, Liu Y, Schnekenburger M, Zwergel C, Cosconati S, Gros C, Tardugno M, Labella D, Florean C, Minden S, Hashimoto H, Chang Y, Zhang X, Kirsch G, Novellino E, Arimondo PB, Miele E, Ferretti E, Gulino A, Diederich M, Cheng X, Mai A. Selective non-nucleoside inhibitors of human DNA methyltransferases active in cancer including in cancer stem cells. J Med Chem 57(3):701-13, 2014. e-Pub 2014. PMID: 24387159.
62. Liu Y, Olanrewaju YO, Zhang X, Cheng X. DNA recognition of 5-carboxylcytosine by a Zfp57 mutant at an atomic resolution of 0.97 Å. Biochemistry 52(51):9310-7, 2013. e-Pub 2013. PMID: 24236546.
63. Hashimoto H, Zhang X, Cheng X. Activity and crystal structure of human thymine DNA glycosylase mutant N140A with 5-carboxylcytosine DNA at low pH. DNA Repair (Amst) 12(7):535-40, 2013. e-Pub 2013. PMID: 23680598.
64. Hashimoto H, Zhang X, Cheng X. Selective excision of 5-carboxylcytosine by a thymine DNA glycosylase mutant. J Mol Biol 425(6):971-6, 2013. e-Pub 2013. PMID: 23337108.
65. Liu Y, Toh H, Sasaki H, Zhang X, Cheng X. An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence. Genes Dev 26(21):2374-9, 2012. e-Pub 2012. PMID: 23059534.
66. Hashimoto H, Hong S, Bhagwat AS, Zhang X, Cheng X. Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation. Nucleic Acids Res 40(20):10203-14, 2012. e-Pub 2012. PMID: 22962365.
67. Horton JR, Mabuchi MY, Cohen-Karni D, Zhang X, Griggs RM, Samaranayake M, Roberts RJ, Zheng Y, Cheng X. Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease. Nucleic Acids Res 40(19):9763-73, 2012. e-Pub 2012. PMID: 22848107.
68. Hashimoto H, Zhang X, Cheng X. Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation. Nucleic Acids Res 40(17):8276-84, 2012. e-Pub 2012. PMID: 22740654.
69. Hashimoto H, Liu Y, Upadhyay AK, Chang Y, Howerton SB, Vertino PM, Zhang X, Cheng X. Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation. Nucleic Acids Res 40(11):4841-9, 2012. e-Pub 2012. PMID: 22362737.
70. Upadhyay AK, Rotili D, Han JW, Hu R, Chang Y, Labella D, Zhang X, Yoon YS, Mai A, Cheng X. An analog of BIX-01294 selectively inhibits a family of histone H3 lysine 9 Jumonji demethylases. J Mol Biol 416(3):319-27, 2012. e-Pub 2011. PMID: 22227394.
71. Upadhyay AK, Horton JR, Zhang X, Cheng X. Coordinated methyl-lysine erasure: structural and functional linkage of a Jumonji demethylase domain and a reader domain. Curr Opin Struct Biol 21(6):750-60, 2011. e-Pub 2011. PMID: 21872465.
72. Chang Y, Sun L, Kokura K, Horton JR, Fukuda M, Espejo A, Izumi V, Koomen JM, Bedford MT, Zhang X, Shinkai Y, Fang J, Cheng X. MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a. Nat Commun 2:533, 2011. e-Pub 2011. PMID: 22086334.
73. Zhao J, Du Y, Horton JR, Upadhyay AK, Lou B, Bai Y, Zhang X, Du L, Li M, Wang B, Zhang L, Barbieri JT, Khuri FR, Cheng X, Fu H. Discovery and structural characterization of a small molecule 14-3-3 protein-protein interaction inhibitor. Proc Natl Acad Sci U S A 108(39):16212-6, 2011. e-Pub 2011. PMID: 21908710.
74. Chang Y, Levy D, Horton JR, Peng J, Zhang X, Gozani O, Cheng X. Structural basis of SETD6-mediated regulation of the NF-kB network via methyl-lysine signaling. Nucleic Acids Res 39(15):6380-9, 2011. e-Pub 2011. PMID: 21515635.
75. Chang Y, Horton JR, Bedford MT, Zhang X, Cheng X. Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9: potential effect of phosphorylation on methyl-lysine binding. J Mol Biol 408(5):807-14, 2011. e-Pub 2011. PMID: 21419134.
76. Horton JR, Upadhyay AK, Hashimoto H, Zhang X, Cheng X. Structural basis for human PHF2 Jumonji domain interaction with metal ions. J Mol Biol 406(1):1-8, 2011. e-Pub 2010. PMID: 21167174.
77. Chang Y, Ganesh T, Horton JR, Spannhoff A, Liu J, Sun A, Zhang X, Bedford MT, Shinkai Y, Snyder JP, Cheng X. Adding a lysine mimic in the design of potent inhibitors of histone lysine methyltransferases. J Mol Biol 400(1):1-7, 2010. e-Pub 2010. PMID: 20434463.
78. Blackwell E, Zhang X, Ceman S. Arginines of the RGG box regulate FMRP association with polyribosomes and mRNA. Hum Mol Genet 19(7):1314-23, 2010. e-Pub 2010. PMID: 20064924.
79. Horton JR, Upadhyay AK, Qi HH, Zhang X, Shi Y, Cheng X. Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Nat Struct Mol Biol 17(1):38-43, 2010. e-Pub 2009. PMID: 20023638.
80. Gao T, Collins RE, Horton JR, Zhang X, Zhang R, Dhayalan A, Tamas R, Jeltsch A, Cheng X. The ankyrin repeat domain of Huntingtin interacting protein 14 contains a surface aromatic cage, a potential site for methyl-lysine binding. Proteins 76(3):772-7, 2009. PMID: 19434754.
81. Chang Y, Zhang X, Horton JR, Upadhyay AK, Spannhoff A, Liu J, Snyder JP, Bedford MT, Cheng X. Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294. Nat Struct Mol Biol 16(3):312-7, 2009. e-Pub 2009. PMID: 19219047.
82. Hashimoto H, Horton JR, Zhang X, Cheng X. UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications. Epigenetics 4(1):8-14, 2009. e-Pub 2009. PMID: 19077538.
83. Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen SE, Cheng X. The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature 455(7214):826-9, 2008. e-Pub 2008. PMID: 18772888.
84. Rathert P, Dhayalan A, Murakami M, Zhang X, Tamas R, Jurkowska R, Komatsu Y, Shinkai Y, Cheng X, Jeltsch A. Protein lysine methyltransferase G9a acts on non-histone targets. Nat Chem Biol 4(6):344-6, 2008. e-Pub 2008. PMID: 18438403.
85. Collins RE, Northrop JP, Horton JR, Lee DY, Zhang X, Stallcup MR, Cheng X. The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules. Nat Struct Mol Biol 15(3):245-50, 2008. e-Pub 2008. PMID: 18264113.
86. Rathert P, Zhang X, Freund C, Cheng X, Jeltsch A. Analysis of the substrate specificity of the Dim-5 histone lysine methyltransferase using peptide arrays. Chem Biol 15(1):5-11, 2008. PMID: 18215768.
87. Osborne TC, Obianyo O, Zhang X, Cheng X, Thompson PR. Protein arginine methyltransferase 1: positively charged residues in substrate peptides distal to the site of methylation are important for substrate binding and catalysis. Biochemistry 46(46):13370-81, 2007. e-Pub 2007. PMID: 17960915.
88. Jia D, Jurkowska RZ, Zhang X, Jeltsch A, Cheng X. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449(7159):248-51, 2007. e-Pub 2007. PMID: 17713477.
89. Lee DY, Ianculescu I, Purcell D, Zhang X, Cheng X, Stallcup MR. Surface-scanning mutational analysis of protein arginine methyltransferase 1: roles of specific amino acids in methyltransferase substrate specificity, oligomerization, and coactivator function. Mol Endocrinol 21(6):1381-93, 2007. e-Pub 2007. PMID: 17426288.
90. Horton JR, Elgar SJ, Khan SI, Zhang X, Wade PA, Cheng X. Structure of the SANT domain from the Xenopus chromatin remodeling factor ISWI. Proteins 67(4):1198-202, 2007. PMID: 17377988.
91. Zhang X, Cheng X. 4 Structure of protein arginine methyltransferases. Enzymes 24:105-21, 2006. e-Pub 2007. PMID: 26718038.
92. Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X. DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion. Nucleic Acids Res 34(3):939-48, 2006. e-Pub 2006. PMID: 16473850.
93. Gowher H, Zhang X, Cheng X, Jeltsch A. Avidin plate assay system for enzymatic characterization of a histone lysine methyltransferase. Anal Biochem 342(2):287-91, 2005. PMID: 15935324.
94. Collins RE, Tachibana M, Tamaru H, Smith KM, Jia D, Zhang X Selker EU, Shinkai Y, Cheng X. In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases. J Biol Chem 280(7):5563-70, 2005. e-Pub 2004. PMID: 15590646.
95. Sawada K, Yang Z, Horton JR, Collins RE, Zhang X, Cheng X. Structure of the conserved core of the yeast Dot1p, a nucleosomal histone H3 lysine 79 methyltransferase. J Biol Chem 279(41):43296-306, 2004. e-Pub 2004. PMID: 15292170.
96. Zhang X, Studier FW. Multiple roles of T7 RNA polymerase and T7 lysozyme during bacteriophage T7 infection. J Mol Biol 340(4):707-30, 2004. PMID: 15223315.
97. Dong A, Zhou L, Zhang X, Stickel S, Roberts RJ, Cheng X. Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions. Biol Chem 385(5):373-9, 2004. PMID: 15195996.
98. Jackson JP, Johnson L, Jasencakova Z, Zhang X, PerezBurgos L, Singh PB, Cheng X, Schubert I, Jenuwein T, Jacobsen SE. Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma 112(6):308-15, 2004. e-Pub 2004. PMID: 15014946.
99. Yang Z, Horton JR, Zhou L, Zhang XJ, Dong A, Zhang X, Schlagman SL, Kossykh V, Hattman S, Cheng X. Structure of the bacteriophage T4 DNA adenine methyltransferase. Nat Struct Biol 10(10):849-55, 2003. e-Pub 2003. PMID: 12937411.
100. Zhang X, Yang Z, Khan SI, Horton JR, Tamaru H, Selker EU, Cheng X. Structural basis for the product specificity of histone lysine methyltransferases. Mol Cell 12(1):177-85, 2003. PMID: 12887903.
101. Zhang X, Cheng X. Structure of the predominant protein arginine methyltransferase PRMT1 and analysis of its binding to substrate peptides. Structure 11(5):509-20, 2003. PMID: 12737817.
102. Tamaru H, Zhang X, McMillen D, Singh PB, Nakayama J, Grewal SI, Allis CD, Cheng X, Selker EU. Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat Genet 34(1):75-9, 2003. PMID: 12679815.
103. Wu P, Qiu C, Sohail A, Zhang X, Bhagwat AS, Cheng X. Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4. J Biol Chem 278(7):5285-91, 2003. e-Pub 2002. PMID: 12456671.
104. Whitehead SE, Jones KW, Zhang X, Cheng X, Terns RM, Terns MP. Determinants of the interaction of the spinal muscular atrophy disease protein SMN with the dimethylarginine-modified box H/ACA small nucleolar ribonucleoprotein GAR1. J Biol Chem 277(50):48087-93, 2002. e-Pub 2002. PMID: 12244096.
105. Min J, Zhang X, Cheng X, Grewal SI, Xu RM. Structure of the SET domain histone lysine methyltransferase Clr4. Nat Struct Biol 9(11):828-32, 2002. PMID: 12389037.
106. Zhang X, Tamaru H, Khan SI, Horton JR, Keefe LJ, Selker EU, Cheng X. Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase. Cell 111(1):117-27, 2002. PMID: 12372305.
107. Lee YH, Koh SS, Zhang X, Cheng X, Stallcup MR. Synergy among nuclear receptor coactivators: selective requirement for protein methyltransferase and acetyltransferase activities. Mol Cell Biol 22(11):3621-32, 2002. PMID: 11997499.
108. Green DM, Marfatia KA, Crafton EB, Zhang X, Cheng X, Corbett AH. Nab2p is required for poly(A) RNA export in Saccharomyces cerevisiae and is regulated by arginine methylation via Hmt1p. J Biol Chem 277(10):7752-60, 2002. e-Pub 2002. PMID: 11779864.
109. Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nat Struct Biol 9(3):217-24, 2002. PMID: 11836534.
110. Horton JR, Sawada K, Nishibori M, Zhang X, Cheng X. Two polymorphic forms of human histamine methyltransferase: structural, thermal, and kinetic comparisons. Structure 9(9):837-49, 2001. PMID: 11566133.
111. Dong A, Yoder JA, Zhang X, Zhou L, Bestor TH, Cheng X. Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA. Nucleic Acids Res 29(2):439-48, 2001. PMID: 11139614.
112. Zhang X, Zhou L, Cheng X. Crystal structure of the conserved core of protein arginine methyltransferase PRMT3. EMBO J 19(14):3509-19, 2000. PMID: 10899106.
113. O'Gara M, Zhang X, Roberts RJ, Cheng X. Structure of a binary complex of HhaI methyltransferase with S-adenosyl-L-methionine formed in the presence of a short non-specific DNA oligonucleotide. J Mol Biol 287(2):201-9, 1999. PMID: 10080885.
114. Zhang X, Studier FW. Mechanism of inhibition of bacteriophage T7 RNA polymerase by T7 lysozyme. J Mol Biol 269(1):10-27, 1997. PMID: 9192997.
115. Zhang X, Studier FW. Isolation of transcriptionally active mutants of T7 RNA polymerase that do not support phage growth. J Mol Biol 250(2):156-68, 1995. PMID: 7608967.
116. Cheng X, Zhang X, Pflugrath JW, Studier FW. The structure of bacteriophage T7 lysozyme, a zinc amidase and an inhibitor of T7 RNA polymerase. Proc Natl Acad Sci U S A 91(9):4034-8, 1994. PMID: 8171031.

Other Articles

1. Zhang X, Blumenthal RM, Cheng X DNA-binding proteins from MBD through ZF to BEN: recognition of cytosine methylation status by one arginine with two conformations. Nucleic Acids Res 52(19):11442-11454, 2024. PMID: 39329271.
2. Zhang, X, Blumenthal, RM, Cheng, X Keep Fingers on the CpG Islands. Epigenomes 8(2), 2024. PMID: 38920624.
3. Zhang X, Blumenthal RM, Cheng X Updated understanding of the protein-DNA recognition code used by C2H2 zinc finger proteins. Curr Opin Struct Biol 87:102836. PMID: 38754172.
4. Zhang X, Xia F, Zhang X, Blumenthal RM, Cheng X C2H2 zinc finger transcription factors associated with hemoglobinopathies. J Mol Biol 436(7):168343, 2024. PMID: 37924864.
5. Zhang X, Blumenthal RM, Cheng X A Role for N6-Methyladenine in DNA Damage Repair. Trends Biochem Sci 46(3):175-183, 2021. PMID: 33077363.
6. Woodcock CB, Horton JR, Zhang X, Blumenthal RM, Cheng X Beta class amino methyltransferases from bacteria to humans: evolution and structural consequences. Nucleic Acids Res 48(18):10034-10044, 2020. PMID: 32453412.
7. Yang J, Zhang X, Blumenthal RM, Cheng X Detection of DNA Modifications by Sequence-Specific Transcription Factors. J Mol Biol. PMID: 31626807.
8. Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X Detecting and interpreting DNA methylation marks. Curr Opin Struct Biol 53:88-99, 2018. PMID: 30031306.
9. Hashimoto H, Zhang X, Vertino PM, Cheng X The Mechanisms of Generation, Recognition, and Erasure of DNA 5-Methylcytosine and Thymine Oxidations. J Biol Chem 290(34):20723-33, 2015. PMID: 26152719.
10. Liu Y, Zhang X, Blumenthal RM, Cheng X A common mode of recognition for methylated CpG. Trends Biochem Sci 38(4):177-83, 2013. PMID: 23352388.
11. Cheng X, Zhang X Structural dynamics of protein lysine methylation and demethylation. Mutat Res 618(1-2):102-15, 2007. PMID: 17374386.
12. Cheng X, Collins RE, Zhang X Structural and sequence motifs of protein (histone) methylation enzymes. Annu Rev Biophys Biomol Struct 34:267-94, 2005. PMID: 15869391.
13. Dillon SC, Zhang X, Trievel RC, Cheng X The SET-domain protein superfamily: protein lysine methyltransferases. Genome Biol 6(8):227, 2005. PMID: 16086857.

Book Chapters

1. Cheng X, Hashimoto H, Horton JR, Zhang X. Mechanisms of DNA methylation, methyl-CpG recognition, and demethylation in mammals. In: Handbook of Epigenetics: The New Molecular and Medical Genetics. None. Oxford: Academic Press, 9-24, 2010.