Xiaodong Cheng, Ph.D.

Peer-Reviewed Articles

1. Hong T, Li J, Guo L, Cavalier M, Wang T, Dou Y, DeLaFuente A, Fang S, Guzman A, Wohlan K, Kapadia C, Rosas C, Yang Y, Yin CC, Li S, You MJ, Cheng X, Goodell MA, Zhou Y, Huang Y. TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells. Nat Aging 3(11):1387-1400, 2023. e-Pub 2023. PMID: 37884767.
2. Zhang X, Xia F, Zhang X, Blumenthal RM, Cheng X. C2H2 Zinc Finger Transcription Factors Associated with Hemoglobinopathies. J Mol Biol:168343. e-Pub 2023. PMID: 37924864.
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. Valverde de Morales HG, Wang HV, Garber K, Cheng X, Corces VG, Li H. Expansion of the genotypic and phenotypic spectrum of CTCF-related disorder guides clinical management: 43 new subjects and a comprehensive literature review. Am J Med Genet A 191(3):718-729, 2023. e-Pub 2022. PMID: 36454652.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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 17(9):1-12, 2022. e-Pub 2021. PMID: 34523387.
13. Huang P, Peslak SA, Ren R, Khandros E, Qin K, Keller CA, Giardine B, Bell HW, Lan X, Sharma M, Horton JR, Abdulmalik O, Chou ST, Shi J, Crossley M, Hardison RC, Cheng X, Blobel GA. HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription. Nat Genet 54(9):1417-1426, 2022. e-Pub 2022. PMID: 35941187.
14. Cheng X, Blumenthal RM. Mediating and maintaining methylation while minimizing mutation: Recent advances on mammalian DNA methyltransferases. Curr Opin Struct Biol 75:102433, 2022. e-Pub 2022. PMID: 35914495.
15. 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.
16. 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):1005-1013. e-Pub 2022. PMID: 35605980.
17. 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, 2022. e-Pub 2022. PMID: 35189146.
18. 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.
19. Huang YH, Chen CW, Sundaramurthy V, Slabicki M, Hao D, Watson CJ, Tovy A, Reyes JM, Dakhova O, Crovetti BR, Galonska C, Lee M, Brunetti L, Zhou Y, Tatton-Brown K, Huang Y, Cheng X, Meissner A, Valk PJM, Van Maldergem L, Sanders MA, Blundell JR, Li W, Ebert BL, Goodell MA. Systematic profiling of DNMT3A variants reveals protein instability mediated by the DCAF8 E3 ubiquitin ligase adaptor. Cancer Discov 12(1):220-235, 2022. e-Pub 2021. PMID: 34429321.
20. 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.
21. Yang Y, Ren R, Ly LC, Horton JR, Li F, Quinlan KGR, Crossley M, Shi Y, Cheng X. Structural basis for human ZBTB7A action at the fetal globin promoter. Cell Rep 36(13):109759, 2021. PMID: 34592153.
22. Chen D, Meng Y, Yu D, Noinaj N, Cheng X, Huang R. Chemoproteomic Study Uncovers HemK2/KMT9 As a New Target for NTMT1 Bisubstrate Inhibitors. ACS Chem Biol 16(7):1234-1242, 2021. e-Pub 2021. PMID: 34192867.
23. Ichino L, Boone BA, Strauskulage L, Harris CJ, Kaur G, Gladstone MA, Tan M, Feng S, Jami-Alahmadi Y, Duttke SH, Wohlschlegel JA, Cheng X, Redding S, Jacobsen SE. MBD5 and MBD6 couple DNA methylation to gene silencing through the J-domain protein SILENZIO. Science 372(6549):1434-1439. e-Pub 2021. PMID: 34083448.
24. 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. e-Pub 2021. PMID: 34086966.
25. 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.
26. 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.
27. Chen J, Horton J, Sagum C, Zhou J, Cheng X, Bedford MT. Histone H3 N-terminal mimicry drives a novel network of methyl-effector interactions. Biochem J 478(10):1943-1958, 2021. PMID: 33969871.
28. Zhang X, Blumenthal RM, Cheng X. A Role for N6-Methyladenine in DNA Damage Repair. Trends Biochem Sci 46(3):175-183, 2021. e-Pub 2020. PMID: 33077363.
29. 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.
30. Lan X, Ren R, Feng R, Ly LC, Lan Y, Zhang Z, Aboreden N, Qin K, Horton JR, Grevet JD, Mayuranathan T, Abdulmalik O, Keller CA, Giardine B, Hardison RC, Crossley M, Weiss MJ, Cheng X, Shi J, Blobel GA. ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression. Mol Cell 81(2):239-254.e8, 2021. e-Pub 2020. PMID: 33301730.
31. 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.
32. 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.
33. 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.
34. 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.
35. 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.
36. 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.
37. Hardikar S, Ying Z, Zeng Y, Zhao H, Liu B, Veland N, McBride K, Cheng X, Chen T. The ZBTB24-CDCA7 axis regulates HELLS enrichment at centromeric satellite repeats to facilitate DNA methylation. Protein Cell 11(3):214-218, 2020. PMID: 31970665.
38. 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 48(3):1466-1478, 2020. PMID: 31879785.
39. 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.
40. Wu X, Liu S, Sagum C, Chen J, Singh R, Chaturvedi A, Horton JR, Kashyap TR, Fushman D, Cheng X, Bedford MT, Wang B. Crosstalk between Lys63- and Lys11-polyubiquitin signaling at DNA damage sites is driven by Cezanne. Genes Dev 33(23-24):1702-1717, 2019. e-Pub 2019. PMID: 31699778.
41. Zoeller EL, Pedro B, Konen J, Dwivedi B, Rupji M, Sundararaman N, Wang L, Horton JR, Zhong C, Barwick BG, Cheng X, Martinez ED, Torres MP, Kowalski J, Marcus AI, Vertino PM. Genetic heterogeneity within collective invasion packs drives leader and follower cell phenotypes. J Cell Sci 132(19), 2019. e-Pub 2019. PMID: 31515279.
42. 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.
43. Yang J, Zhang X, Blumenthal RM, Cheng X. Detection of DNA Modifications by Sequence-Specific Transcription Factors. J Mol Biol. e-Pub 2019. PMID: 31626807.
44. 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.
45. 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.
46. 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.
47. Milite C, Feoli A, Horton JR, Rescigno D, Cipriano A, Pisapia V, Viviano M, Pepe G, Amendola G, Novellino E, Cosconati S, Cheng X, Castellano S, Sbardella G. Discovery of a Novel Chemotype of Histone Lysine Methyltransferase EHMT1/2 (GLP/G9a) Inhibitors: Rational Design, Synthesis, Biological Evaluation, and Co-crystal Structure. J Med Chem 62(5):2666-2689, 2019. e-Pub 2019. PMID: 30753076.
48. 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.
49. 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.
50. 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.
51. 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.
52. Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X. Detecting and interpreting DNA methylation marks. Curr Opin Struct Biol 53:88-99, 2018. e-Pub 2018. PMID: 30031306.
53. 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.
54. Wu L, Cao J, Cai WL, Lang SM, Horton JR, Jansen DJ, Liu ZZ, Chen JF, Zhang M, Mott BT, Pohida K, Rai G, Kales SC, Henderson MJ, Hu X, Jadhav A, Maloney DJ, Simeonov A, Zhu S, Iwasaki A, Hall MD, Cheng X, Shadel GS, Yan Q. KDM5 histone demethylases repress immune response via suppression of STING. PLoS Biol 16(8):e2006134, 2018. e-Pub 2018. PMID: 30080846.
55. 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.
56. 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.
57. 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.
58. 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.
59. Youngblood B, Hale JS, Kissick HT, Ahn E, Xu X, Wieland A, Araki K, West EE, Ghoneim HE, Fan Y, Dogra P, Davis CW, Konieczny BT, Antia R, Cheng X, Ahmed R. Effector CD8 T cells dedifferentiate into long-lived memory cells. Nature 552(7685):404-409, 2017. e-Pub 2017. PMID: 29236683.
60. Lee CC, Peng SH, Shen L, Lee CF, Du TH, Kang ML, Xu GL, Upadhyay AK, Cheng X, Yan YT, Zhang Y, Juan LJ. The Role of N-α-acetyltransferase 10 Protein in DNA Methylation and Genomic Imprinting. Mol Cell 68(1):89-103.e7, 2017. e-Pub 2017. PMID: 28943313.
61. 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.
62. 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.
63. Head PE, Zhang H, Bastien AJ, Koyen AE, Withers AE, Daddacha WB, Cheng X, Yu DS. Sirtuin 2 mutations in human cancers impair its function in genome maintenance. J Biol Chem 292(24):9919-9931, 2017. e-Pub 2017. PMID: 28461331.
64. Yang P, Wang Y, Hoang D, Tinkham M, Patel A, Sun MA, Wolf G, Baker M, Chien HC, Lai KN, Cheng X, Shen CJ, Macfarlan TS. A placental growth factor is silenced in mouse embryos by the zinc finger protein ZFP568. Science 356(6339):757-759, 2017. PMID: 28522536.
65. 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.
66. 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.
67. 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.
68. 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.
69. Horton JR, Liu X, Gale M, Wu L, Shanks JR, Zhang X, Webber PJ, Bell JS, 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):769-81, 2016. e-Pub 2016. PMID: 27427228.
70. 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.
71. 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.
72. Estève PO, Zhang G, Ponnaluri VK, Deepti K, Chin HG, Dai N, Sagum C, Black K, Corrêa IR, Bedford MT, Cheng X, Pradhan S. Binding of 14-3-3 reader proteins to phosphorylated DNMT1 facilitates aberrant DNA methylation and gene expression. Nucleic Acids Res 44(4):1642-56, 2016. e-Pub 2015. PMID: 26553800.
73. 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.
74. Hong S, Cheng X. DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications. Adv Exp Med Biol 945:321-341, 2016. PMID: 27826845.
75. Zeng Y, Yao B, Shin J, Lin L, Kim N, Song Q, Liu S, Su Y, Guo JU, Huang L, Wan J, Wu H, Qian J, Cheng X, Zhu H, Ming GL, Jin P, Song H. Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression. Mol Cell 61(1):153-60, 2016. e-Pub 2015. PMID: 26711009.
76. 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.
77. 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. e-Pub 2015. PMID: 26152719.
78. Pais JE, Dai N, Tamanaha E, Vaisvila R, Fomenkov AI, Bitinaite J, Sun Z, Guan S, Corrêa IR, Noren CJ, Cheng X, Roberts RJ, Zheng Y, Saleh L. Biochemical characterization of a Naegleria TET-like oxygenase and its application in single molecule sequencing of 5-methylcytosine. Proc Natl Acad Sci U S A 112(14):4316-21, 2015. e-Pub 2015. PMID: 25831492.
79. 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.
80. Myrick LK, Hashimoto H, Cheng X, Warren ST. Human FMRP contains an integral tandem Agenet (Tudor) and KH motif in the amino terminal domain. Hum Mol Genet 24(6):1733-40, 2015. e-Pub 2014. PMID: 25416280.
81. Daugherty AB, Horton JR, Cheng X, Lutz S. Structural and functional consequences of circular permutation on the active site of old yellow enzyme. ACS Catal 5(2):892-899, 2015. PMID: 25692074.
82. Myrick LK, Deng PY, Hashimoto H, Oh YM, Cho Y, Poidevin MJ, Suhl JA, Visootsak J, Cavalli V, Jin P, Cheng X, Warren ST, Klyachko VA. Independent role for presynaptic FMRP revealed by an FMR1 missense mutation associated with intellectual disability and seizures. Proc Natl Acad Sci U S A 112(4):949-56, 2015. e-Pub 2015. PMID: 25561520.
83. 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):3703-12, 2014. e-Pub 2014. PMID: 25240767.
84. Myrick LK, Nakamoto-Kinoshita M, Lindor NM, Kirmani S, Cheng X, Warren ST. Fragile X syndrome due to a missense mutation. Eur J Hum Genet 22(10):1185-9, 2014. e-Pub 2014. PMID: 24448548.
85. 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.
86. 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.
87. 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.
88. Cheng X. Structural and functional coordination of DNA and histone methylation. Cold Spring Harb Perspect Biol 6(8), 2014. e-Pub 2014. PMID: 25085914.
89. 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.
90. 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.
91. 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.
92. 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.
93. 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.
94. Rotili D, Tarantino D, Marrocco B, Gros C, Masson V, Poughon V, Ausseil F, Chang Y, Labella D, Cosconati S, Di Maro S, Novellino E, Schnekenburger M, Grandjenette C, Bouvy C, Diederich M, Cheng X, Arimondo PB, Mai A. Properly substituted analogues of BIX-01294 lose inhibition of G9a histone methyltransferase and gain selective anti-DNA methyltransferase 3A activity. PLoS One 9(5):e96941, 2014. e-Pub 2014. PMID: 24810902.
95. 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.
96. 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.
97. Liu Y, Zhang X, Blumenthal RM, Cheng X. A common mode of recognition for methylated CpG. Trends Biochem Sci 38(4):177-83, 2013. e-Pub 2013. PMID: 23352388.
98. 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.
99. Sun Z, Terragni J, Jolyon T, Borgaro JG, Liu Y, Yu L, Guan S, Wang H, Sun D, Cheng X, Zhu Z, Pradhan S, Zheng Y. High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells. Cell Rep 3(2):567-76, 2013. e-Pub 2013. PMID: 23352666.
100. Nicholson TB, Singh AK, Su H, Hevi S, Wang J, Bajko J, Li M, Valdez R, Goetschkes M, Capodieci P, Loureiro J, Cheng X, Li E, Kinzel B, Labow M, Chen T. A hypomorphic lsd1 allele results in heart development defects in mice. PLoS One 8(4):e60913, 2013. e-Pub 2013. PMID: 23637775.
101. 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.
102. 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.
103. 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.
104. 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.
105. 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.
106. 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.
107. 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.
108. 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.
109. Szulwach KE, Li X, Li Y, Song CX, Wu H, Dai Q, Irier H, Upadhyay AK, Gearing M, Levey AI, Vasanthakumar A, Godley LA, Chang Q, Cheng X, He C, Jin P. 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat Neurosci 14(12):1607-16, 2011. e-Pub 2011. PMID: 22037496.
110. 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.
111. 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.
112. 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.
113. 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.
114. 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. Lysine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling. Nat Immunol 12(1):29-36, 2011. e-Pub 2010. PMID: 21131967.
115. Estève PO, Chang Y, Samaranayake M, Upadhyay AK, Horton JR, Feehery GR, Cheng X, Pradhan S. A methylation and phosphorylation switch between an adjacent lysine and serine determines human DNMT1 stability. Nat Struct Mol Biol 18(1):42-8, 2011. e-Pub 2010. PMID: 21151116.
116. Hashimoto H, Vertino PM, Cheng X. Molecular coupling of DNA methylation and histone methylation. Epigenomics 2(5):657-69, 2010. PMID: 21339843.
117. Lee CF, Ou DS, Lee SB, Chang LH, Lin RK, Li YS, Upadhyay AK, Cheng X, Wang YC, Hsu HS, Hsiao M, Wu CW, Juan LJ. hNaa10p contributes to tumorigenesis by facilitating DNMT1-mediated tumor suppressor gene silencing. J Clin Invest 120(8):2920-30, 2010. e-Pub 2010. PMID: 20592467.
118. 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.
119. Collins R, Cheng X. A case study in cross-talk: the histone lysine methyltransferases G9a and GLP. Nucleic Acids Res 38(11):3503-11, 2010. e-Pub 2010. PMID: 20159995.
120. Cheng X, Blumenthal RM. Coordinated chromatin control: structural and functional linkage of DNA and histone methylation. Biochemistry 49(14):2999-3008, 2010. PMID: 20210320.
121. 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.
122. Qian Z, Horton JR, Cheng X, Lutz S. Structural redesign of lipase B from Candida antarctica by circular permutation and incremental truncation. J Mol Biol 393(1):191-201, 2009. e-Pub 2009. PMID: 19683009.
123. 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.
124. 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.
125. 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.
126. Jurkowska RZ, Anspach N, Urbanke C, Jia D, Reinhardt R, Nellen W, Cheng X, Jeltsch A. Formation of nucleoprotein filaments by mammalian DNA methyltransferase Dnmt3a in complex with regulator Dnmt3L. Nucleic Acids Res 36(21):6656-63, 2008. e-Pub 2008. PMID: 18945701.
127. 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.
128. 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.
129. Subramanian K, Jia D, Kapoor-Vazirani P, Powell DR, Collins RE, Sharma D, Peng J, Cheng X, Vertino PM. Regulation of estrogen receptor alpha by the SET7 lysine methyltransferase. Mol Cell 30(3):336-47, 2008. PMID: 18471979.
130. 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.
131. Cheng X, Blumenthal RM. Mammalian DNA methyltransferases: a structural perspective. Structure 16(3):341-50, 2008. PMID: 18334209.
132. Dhayalan A, Jurkowski TP, Laser H, Reinhardt R, Jia D, Cheng X, Jeltsch A. Mapping of protein-protein interaction sites by the 'absence of interference' approach. J Mol Biol 376(4):1091-9, 2008. e-Pub 2007. PMID: 18191145.
133. 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.
134. 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.
135. Rathert P, Cheng X, Jeltsch A. Continuous enzymatic assay for histone lysine methyltransferases. Biotechniques 43(5):602, 604, 606 passim, 2007. PMID: 18072589.
136. 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.
137. Liebert K, Horton JR, Chahar S, Orwick M, Cheng X, Jeltsch A. Two alternative conformations of S-adenosyl-L-homocysteine bound to Escherichia coli DNA adenine methyltransferase and the implication of conformational changes in regulating the catalytic cycle. J Biol Chem 282(31):22848-55, 2007. e-Pub 2007. PMID: 17545164.
138. Lan F, Collins RE, De Cegli R, Alpatov R, Horton JR, Shi X, Gozani O, Cheng X, Shi Y. Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature 448(7154):718-22, 2007. PMID: 17687328.
139. Ooi SK, Qiu C, Bernstein E, Li K, Jia D, Yang Z, Erdjument-Bromage H, Tempst P, Lin SP, Allis CD, Cheng X, Bestor TH. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448(7154):714-7, 2007. PMID: 17687327.
140. Higashimoto K, Kuhn P, Desai D, Cheng X, Xu W. Phosphorylation-mediated inactivation of coactivator-associated arginine methyltransferase 1. Proc Natl Acad Sci U S A 104(30):12318-23, 2007. e-Pub 2007. PMID: 17640894.
141. 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.
142. 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.
143. Cheng X, Zhang X. Structural dynamics of protein lysine methylation and demethylation. Mutat Res 618(1-2):102-15, 2007. e-Pub 2007. PMID: 17374386.
144. Wu H, Horton JR, Battaile K, Allali-Hassani A, Martin F, Zeng H, Loppnau P, Vedadi M, Bochkarev A, Plotnikov AN, Cheng X. Structural basis of allele variation of human thiopurine-S-methyltransferase. Proteins 67(1):198-208, 2007. PMID: 17243178.
145. Collins RE, Cheng X. Structural and biochemical advances in mammalian RNAi. J Cell Biochem 99(5):1251-66, 2006. PMID: 16927374.
146. Mercante J, Suzuki K, Cheng X, Babitzke P, Romeo T. Comprehensive alanine-scanning mutagenesis of Escherichia coli CsrA defines two subdomains of critical functional importance. J Biol Chem 281(42):31832-42, 2006. e-Pub 2006. PMID: 16923806.
147. Horton JR, Liebert K, Bekes M, Jeltsch A, Cheng X. Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase. J Mol Biol 358(2):559-70, 2006. e-Pub 2006. PMID: 16524590.
148. Reyes-Turcu FE, Horton JR, Mullally JE, Heroux A, Cheng X, Wilkinson KD. The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin. Cell 124(6):1197-208, 2006. PMID: 16564012.
149. 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.
150. Zhang X, Cheng X. Structure of protein arginine methyltransferases. Enzymes 24:105-21, 2006. e-Pub 2007. PMID: 26718038.
151. Schubert HL, Blumenthal RM, Cheng X. Protein Methyltransferases: Their Distribution Among the Five Structural Classes of AdoMet-Dependent Methyltransferases. Enzymes 24:3-28, 2006. e-Pub 2007. PMID: 26718035.
152. Horton JR, Sawada K, Nishibori M, Cheng X. Structural basis for inhibition of histamine N-methyltransferase by diverse drugs. J Mol Biol 353(2):334-344, 2005. PMID: 16168438.
153. Collins RE, Cheng X. Structural domains in RNAi. FEBS Lett 579(26):5841-9, 2005. e-Pub 2005. PMID: 16107250.
154. 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.
155. Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X. Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase. Cell 121(3):349-61, 2005. PMID: 15882618.
156. 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.
157. Yang Z, Horton JR, Maunus R, Wilson GG, Roberts RJ, Cheng X. Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI. Nucleic Acids Res 33(6):1892-901, 2005. e-Pub 2005. PMID: 15805123.
158. 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.
159. Amor JC, Swails J, Zhu X, Roy CR, Nagai H, Ingmundson A, Cheng X, Kahn RA. The structure of RalF, an ADP-ribosylation factor guanine nucleotide exchange factor from Legionella pneumophila, reveals the presence of a cap over the active site. J Biol Chem 280(2):1392-400, 2005. e-Pub 2004. PMID: 15520000.
160. Dillon SC, Zhang X, Trievel RC, Cheng X. The SET-domain protein superfamily: protein lysine methyltransferases. Genome Biol 6(8):227, 2005. e-Pub 2005. PMID: 16086857.
161. 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.
162. Yang Z, Shipman L, Zhang M, Anton BP, Roberts RJ, Cheng X. Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase. J Mol Biol 340(4):695-706, 2004. PMID: 15223314.
163. 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.
164. 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.
165. Horton JR, Ratner G, Banavali NK, Huang N, Choi Y, Maier MA, Marquez VE, MacKerell AD, Cheng X. Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase. Nucleic Acids Res 32(13):3877-86, 2004. e-Pub 2004. PMID: 15273274.
166. 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.
167. 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.
168. Schubert HL, Blumenthal RM, Cheng X. Many paths to methyltransfer: a chronicle of convergence. Trends Biochem Sci 28(6):329-35, 2003. PMID: 12826405.
169. 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.
170. 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.
171. 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.
172. 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.
173. 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.
174. 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.
175. Zhou L, Cheng X, Connolly BA, Dickman MJ, Hurd PJ, Hornby DP. Zebularine: a novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferases. J Mol Biol 321(4):591-9, 2002. PMID: 12206775.
176. 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.
177. 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.
178. 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.
179. Cheng X, Blumenthal RM. Cytosines do it, thymines do it, even pseudouridines do it--base flipping by an enzyme that acts on RNA. Structure 10(2):127-9, 2002. PMID: 11839295.
180. Amor JC, Horton JR, Zhu X, Wang Y, Sullards C, Ringe D, Cheng X, Kahn RA. Structures of yeast ARF2 and ARL1: distinct roles for the N terminus in the structure and function of ARF family GTPases. J Biol Chem 276(45):42477-84, 2001. e-Pub 2001. PMID: 11535602.
181. Cheng X, Roberts RJ. AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res 29(18):3784-95, 2001. PMID: 11557810.
182. 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.
183. Blumenthal RM, Cheng X. A Taq attack displaces bases. Nat Struct Biol 8(2):101-3, 2001. PMID: 11175890.
184. 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.
185. Vilkaitis G, Dong A, Weinhold E, Cheng X, Klimasauskas S. Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase. J Biol Chem 275(49):38722-30, 2000. PMID: 11102456.
186. 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.
187. Horton JR, Cheng X. PvuII endonuclease contains two calcium ions in active sites. J Mol Biol 300(5):1049-56, 2000. PMID: 10903853.
188. Liu Y, Gong W, Huang CC, Herr W, Cheng X. Crystal structure of the conserved core of the herpes simplex virus transcriptional regulatory protein VP16. Genes Dev 13(13):1692-703, 1999. PMID: 10398682.
189. 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.
190. Sheikhnejad G, Brank A, Christman JK, Goddard A, Alvarez E, Ford H, Marquez VE, Marasco CJ, Sufrin JR, O'gara M, Cheng X. Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine. J Mol Biol 285(5):2021-34, 1999. PMID: 9925782.
191. V.E. Marquez, A. Goddard, E. Alvarez, H. Ford Jr., J.K. Christmas, G. Sheikhnejad, A. Brank, C.J. Marasco, J. R. Suffrin, M. O'Gara, X. Cheng. Oligonucleotides containing 5, 6-dihydro-5-azacytosine at CpG sites can produce potent inhibition of DNA cytosine-C5-methyltransferase without covalently binding to the enzyme. Antisense & Nucleic Acid Drug Development 9:415-421, 1999.
192. Horton JR, Nastri HG, Riggs PD, Cheng X. Asp34 of PvuII endonuclease is directly involved in DNA minor groove recognition and indirectly involved in catalysis. J Mol Biol 284(5):1491-504, 1998. PMID: 9878366.
193. O'Gara M, Horton JR, Roberts RJ, Cheng X. Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base. Nat Struct Biol 5(10):872-7, 1998. PMID: 9783745.
194. Horton JR, Bonventre J, Cheng X. How is modification of the DNA substrate recognized by the PvuII restriction endonuclease?. Biol Chem 379(4-5):451-8, 1998. PMID: 9628337.
195. Roberts RJ, Cheng X. Base flipping. Annu Rev Biochem 67:181-98, 1998. PMID: 9759487.
196. O'Gara M, Adams GM, Gong W, Kobayashi R, Blumenthal RM, Cheng X. Expression, purification, mass spectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific). Eur J Biochem 247(3):1009-18, 1997. PMID: 9288926.
197. Gong W, O'Gara M, Blumenthal RM, Cheng X. Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res 25(14):2702-15, 1997. PMID: 9207015.
198. Kumar S, Horton JR, Jones GD, Walker RT, Roberts RJ, Cheng X. DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase. Nucleic Acids Res 25(14):2773-83, 1997. PMID: 9207024.
199. Xu RM, Jokhan L, Cheng X, Mayeda A, Krainer AR. Crystal structure of human UP1, the domain of hnRNP A1 that contains two RNA-recognition motifs. Structure 5(4):559-70, 1997. PMID: 9115444.
200. Xu RM, Koch C, Liu Y, Horton JR, Knapp D, Nasmyth K, Cheng X. Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis. Structure 5(3):349-58, 1997. PMID: 9083114.
201. Lloyd RS, Cheng X. Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping. Biopolymers 44(2):139-51, 1997. PMID: 9354758.
202. O'Gara M, Roberts RJ, Cheng X. A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase. J Mol Biol 263(4):597-606, 1996. PMID: 8918941.
203. O'Gara M, Klimasauskas S, Roberts RJ, Cheng X. Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaL methyltransferase-DNA-AdoHcy complexes. J Mol Biol 261(5):634-45, 1996. PMID: 8800212.
204. Xu RM, Carmel G, Kuret J, Cheng X. Structural basis for selectivity of the isoquinoline sulfonamide family of protein kinase inhibitors. Proc Natl Acad Sci U S A 93(13):6308-13, 1996. PMID: 8692811.
205. Cheng X, Blumenthal RM. Finding a basis for flipping bases. Structure 4(6):639-45, 1996. PMID: 8805547.
206. Malone T, Blumenthal RM, Cheng X. Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J Mol Biol 253(4):618-32, 1995. PMID: 7473738.
207. O'Gara M, McCloy K, Malone T, Cheng X. Structure-based sequence alignment of three AdoMet-dependent DNA methyltransferases. Gene 157(1-2):135-8, 1995. PMID: 7607477.
208. Cheng X, Balendiran K, Schildkraut I, Anderson JE. Crystal structure of the PvuII restriction endonuclease. Gene 157(1-2):139-40, 1995. PMID: 7607478.
209. Schluckebier G, O'Gara M, Saenger W, Cheng X. Universal catalytic domain structure of AdoMet-dependent methyltransferases. J Mol Biol 247(1):16-20, 1995. PMID: 7897657.
210. Xu RM, Carmel G, Sweet RM, Kuret J, Cheng X. Crystal structure of casein kinase-1, a phosphate-directed protein kinase. EMBO J 14(5):1015-23, 1995. PMID: 7889932.
211. Cheng X. DNA modification by methyltransferases. Curr Opin Struct Biol 5(1):4-10, 1995. PMID: 7773746.
212. Cheng X. Structure and function of DNA methyltransferases. Annu Rev Biophys Biomol Struct 24:293-318, 1995. PMID: 7663118.
213. Cheng X, Balendiran K, Schildkraut I, Anderson JE. Structure of PvuII endonuclease with cognate DNA. EMBO J 13(17):3927-35, 1994. PMID: 8076590.
214. 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.
215. Carmel G, Leichus B, Cheng X, Patterson SD, Mirza U, Chait BT, Kuret J. Expression, purification, crystallization, and preliminary x-ray analysis of casein kinase-1 from Schizosaccharomyces pombe. J Biol Chem 269(10):7304-9, 1994. PMID: 8125945.
216. Klimasauskas S, Kumar S, Roberts RJ, Cheng X. HhaI methyltransferase flips its target base out of the DNA helix. Cell 76(2):357-69, 1994. PMID: 8293469.
217. S. Kumar, X. Cheng, S.Klimasauskas, S. Mi, J. Posfai, R. J. Robers, G.G. Wilson. The DNA (cytosine-5) Methyltransferases. Nucleic Acids Res 22:1-10, 1994.
218. Cheng X, Kumar S, Posfai J, Pflugrath JW, Roberts RJ. Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine. Cell 74(2):299-307, 1993. PMID: 8343957.
219. Cheng X, Kumar S, Klimasauskas S, Roberts RJ. Crystal structure of the HhaI DNA methyltransferase. Cold Spring Harb Symp Quant Biol 58:331-8, 1993. PMID: 7956046.
220. Kumar S, Cheng X, Pflugrath JW, Roberts RJ. Purification, crystallization, and preliminary X-ray diffraction analysis of an M.HhaI-AdoMet complex. Biochemistry 31(36):8648-53, 1992. PMID: 1390649.
221. X. Cheng, Schoenborn BP. Neutron diffraction study of carbonmonoxymyoglobin. J Mol Biol 220(2):381-99, 1991. PMID: 1856864.
222. X. Cheng B.P. Schoenbom. Repulsive restraints for hydrogen bonding in least-squares refinement of protein crystals. Acta Cryst A47:314-317, 1991.
223. X. Cheng, B.P. Schoenbom. Hydration in protein crystals. A neutron diffraction analysis of carbonmonoxymyoglobin. Acta Cryst B46:195-208, 1990.
224. Z. Xu, X. Cheng. The mass of neutrino and the Schwarzchild’s internal solution when  not equal to 0. Journal of Central China Normal University (Natural Sciences Edition, in Chinese 2:12, 1981.

Book Chapters

1. Ren R, Horton JR, Hong S, Cheng X. Recent Advances on DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications. In: Adv Exp Med Biol, 295-315, 2022.
2. Horton JR, Gale M, Yan Q, Cheng X. The Molecular Basis of Histone Demethylation. In: DNA and Histone Methylation as Cancer Targets. Book Series: Cancer Drug Discovery and Development. Humana Press, Cham, 151-219, 2017.
3. Cheng X and Trievel RC. JmjC Lysine Demethylases. In: 2-Oxoglutarate-Dependent Oxygenases. The Royal Society of Chemistry, 210-245, 2015.
4. Collins RE, Cheng X. Methyl-Lysine Recognition by Ankyrin-Repeat Proteins. In: Histone Recognition. Springer, Cham: Switzerland, 101-124, 2015.
5. 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. Academic Press, 9-24, 2011.
6. Upadhyay AK, Cheng X. Dynamics of histone lysine methylation: structures of methyl writers and erasers. In: Prog Drug Res, 107-124, 2011.
7. Cheng X, Blumenthal RM. Epiphanies in epigenetics. In: Prog. Mol. Biol. Transl. Sci, 1-21, 2011.
8. Cheng X, Blumenthal RM. Structures and activities of mammalian DNA methyltransferases. In: DNA and RNA Modification Enzymes: Structure, Mechanism, Function, and Evolution. Landes Bioscience, 87-96, 2009.
9. Cheng X, Blumenthal RM. Structural and Biochemical Advances in Mammalian DNA Methylation. In: Epigenomics. Springer Dordrect, 85-100, 2009.
10. Jia D, Cheng X. Methylation on the nucleosome: from DNA to Histone. In: Nutrients and Epigenetics. CRC Press, 7-35, 2009.
11. Horton JR, Blumenthal M, Cheng X. Restriction endonucleases: structure of the conserved catalytic and the role of metal ions in DNA cleavage. In: Restriction Endonucleases. Book Series: Nucleic Acids and Molecular Biology. Springer-Verlag: Berlin, Heidelberg, 361-392, 2004.
12. Blumenthal RM, Cheng X. Restriction-Modification Systems. In: Modern Microbial Genetics. 2. Wiley: New York, 177-225, 2002.
13. Fauman EB, Blumenthal RM, Cheng X. Structure and evolution of AdoMet-dependent methyltransferases. In: S-Adenosylmethionine-dependent methyltransferases: structures and functions. World Scientific Publishing Co Ptc. Ltd: New Jersey, 1-38, 1999.
14. Schoenbom, BP and Cheng X. The localization of solvent in protein crystals. In: Protein: Structure, Dynamics and Design. ESCOM Science Publishers B.V, 367-371, 1991.

Books (edited and written)

1. Cheng X, Blumenthal RM. Prog. Mol. Biol. Transl. Sci. In: Epiphanies in epigenetics, 2011.
2. Cheng X, Blumenthal RM. AdoMet-dependent methyltransferases: structures and functions. World Scientific: New Jersey, 1999.
3. Marshak, D.R., Cheng, X. Techniques in Protein Chemistry VIII. Academic Press, 1996.
4. Marshak, D.R., Cheng, X. Techniques in Protein Chemistry VII. Academic Press, 1995.