Xiaodong Cheng, Ph.D.
Department of Epigenetics and Molecular Carcinogenesis, Division of Discovery Science
Present Title & Affiliation
Primary Appointment
Professor, Department of Epigenetics and Molecular Carcinogenesis, Division of Discovery Science, The University of Texas MD Anderson Cancer Center, Houston, TX
Education & Training
Degree-Granting Education
| 1989 | State University of New York, Stony Brook, New York, US, PhD, 1984-1989 in Protein Crystallography |
| 1982 | Fudan University, Shanghai, CN, BS, 1978-1982 in Physics |
Postgraduate Training
| 2004-2004 | "A Short Course on Cryo-HRSEM/STEM/TEM" (July 28-30, 2004), Organized by Dr. Robert P. Apkarian, Integrated Microscopy & Microanalytical Faculty, Emory University, Atlanta, Georgia |
| 2002-2002 | "Effective Teaching Workshop" (January 17-19, 2002), Organized by Richard M. Felder and Rebecca Brent, North Carolina State University, Raleigh, North Carolina |
| 1990-1991 | Postdoctoral, Protein Crystallography, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York |
Experience & Service
Academic Appointments
Professor, Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 2016 - 2019
Professor of Biochemistry and Georgia Research Alliance Eminent Scholar, Emory University School of Medicine, Atlanta, GA, 1997 - 2017
Senior Staff Investigator (Associate Professor) and W.M. Keck Foundation Endowed Professor, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1994 - 1997
Staff Investigator (Assistant Professor), Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1992 - 1993
Administrative Appointments/Responsibilities
Program Leader, Department of Cancer Center Support Grant (CCSG), The University of Texas MD Anderson Cancer Center, Houston, Texas, 2020 - 2024
Co-Director, Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, 2018 - Present
Institutional Committee Activities
Reviewer, Inquiry Committee, 2024 - Present
Committee member, Search Committee for Department Chair of Biostatistics, 2023 - 2024
Committee member, Senior Faculty Committee, 2023 - Present
Member, Faculty Recruitment Panel (also known as the Jim Allison Committee), 2022 - 2022
Board Member, Core Facilities Oversight Board, 2022 - Present
Member, Research Policy Advisory Council, 2021 - 2023
Committee Member, SCRB5 Research Steering Committee - Structural Biology/Cryo-EM, 2021 - Present
Committee member, Advanced Technology Core for Macromolecular X-ray Crystallography, 2020 - Present
Review Committee Member, Promotion and Tenure Committee, 2020 - 2022
Scientific Advisory, Advanced Technology Core for Macromolecular X-ray Crystallography, 2020 - Present
Advisory, CryoEM Core Facility at McGovern Medical School, 2020 - Present
Scientific Peer Reviewer, Proposal Review Committee, 2020 - 2021
Committee Member, G&E Graduate Program Steering Committee, 2020 - Present
Committee member, TMC3 Science Think Tank Facility Group, 2020 - Present
Member, Technology Task Force Committee, 2020 - Present
Member, Shared Resource Executive Committee, 2020 - 2021
Reviewer, UT Stars Program, 2019 - 2023
Advisory, Core for Biomolecular Structure and Function, 2017 - 2020
Member at-Large, Keck Executive Committee, 2017 - Present
Committee member, BCDB Executive Committee, 2012 - 2016
Reviewer, Department of Thoracic & Cardiovascular Surgery Mid-Tenure Review Committee
Member, TMC3 Science Think Thank Facility Group
Member, Planning Committee, SCRB5 Core Facilities
External Reviewer, Tenure and Promotion Committee
External Reviewer, Tenure and Promotion Committee
Honors & Awards
| 2023 | Nechay Memorial Lecture, Pharmacology & Toxicology Scholar Organization |
| 2022 | MDACC President's Recognition of Faculty Excellence - Research Excellence, The University of Texas MD Anderson Cancer Center |
| 2019 | Keynote, Symposium on Structural Biology, Van Andel Research Institute |
| 2018 | Keynote, UNC Chromatin and Epigenetics Symposium (12/6/2018), University of North Carolina |
| 2017 | CPRIT Scholar in Cancer Research (MDACC), Cancer Prevention and Research Institute of Texas |
| 2017 | Wall-of-Science in MDACC, The University of Texas MD Anderson Cancer Center |
| 2016 | SER-CAT Impact Award, SouthEast Regional Collaborative Access Team |
| 2015 | SER-CAT Outstanding Science Award, SouthEast Regional Collaborative Access Team |
| 2012 | AAAS Fellow Elected |
| 2008 | Albert E. Levy Awards for Excellence in Scientific Research, Emory University |
| 1997 | Georgia Research Alliance Eminent Scholar, Emory University |
| 1997 | Visiting Professorship, Max-Planck Institute fur Molecular Genetik |
| 1994 | Keck Foundation Endowed Professor, Cold Spring Harbor Laboratory |
Selected Publications
Peer-Reviewed Articles
- Zhou, J, Chen, Q, Ren, R, Yang, J, Liu, B, Horton, JR, Chang, C, Li, C, Maksoud, L, Yang, Y, Rotili, D, Jain, A, 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 Chemical Biology 31(12):2112-2127.e6, 2024. e-Pub 2024. PMID: 39437789.
- 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. e-Pub 2024. PMID: 39329271.
- 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. e-Pub 2024. PMID: 39178265.
- Zhang, X, Blumenthal, RM, Cheng, X. Updated understanding of the protein–DNA recognition code used by C2H2 zinc finger proteins. Current Opinion in Structural Biology 87, 2024. e-Pub 2024. PMID: 38754172.
- Wang, Y, Zhou, J, He, W, Fu, R, Shi, L, Dang, NK, Liu, B, Xu, H, Cheng, X, Bedford, MT. SART3 reads methylarginine-marked glycine- and arginine-rich motifs. Cell Reports 43(7), 2024. e-Pub 2024. PMID: 38985674.
- Zhang, X, Blumenthal, RM, Cheng, X. Keep Fingers on the CpG Islands. Epigenomes 8(2), 2024. e-Pub 2024. PMID: 38920624.
- 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. e-Pub 2024. PMID: 37924864.
- Zhou, J, Chen, T, Cheng, X. One form and two functions. Structure 32(3):258-260, 2024. e-Pub 2024. PMID: 38458157.
- 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.
- 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. e-Pub 2023. PMID: 37439339.
- 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. Author Correction: HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription. Nat Genet 55(9):1608, 2023. e-Pub 2023. PMID: 37524792.
- 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.
- 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.
- 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.
- 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. e-Pub 2023. PMID: 36660822.
- 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.
- 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 2023. PMID: 36596360.
- 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 2023. PMID: 36581322.
- 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):970-981, 2022. e-Pub 2022. PMID: 34523387.
- 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.
- 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.
- 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, 2022. e-Pub 2022. PMID: 35605980.
- 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, 2022. e-Pub 2022. PMID: 35255310.
- 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.
- 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 2022. PMID: 34429321.
- 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. e-Pub 2021. PMID: 34086966.
- 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.
- 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. e-Pub 2021. PMID: 34592153.
- 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.
- 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.
- 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, 2021. e-Pub 2021. PMID: 34083448.
- 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. e-Pub 2021. PMID: 33877329.
- 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. e-Pub 2021. PMID: 33969871.
- 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 2021. PMID: 33301730.
- 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.
- 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.
- 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. e-Pub 2020. PMID: 32663306.
- 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.
- 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.
- 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.
- 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. e-Pub 2020. PMID: 31970665.
- 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. e-Pub 2020. PMID: 31879785.
- 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.
- 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.
- 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.
- 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.
- 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. e-Pub 2019. PMID: 31081034.
- 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. e-Pub 2019. PMID: 31226215.
- 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.
- 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.
- 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. e-Pub 2019. PMID: 30566668.
- 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 2019. PMID: 30626964.
- 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.
- 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.
- 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.
- 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.
- 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. e-Pub 2018. PMID: 29294058.
- 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.
- 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.
- 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. e-Pub 2018. PMID: 29228259.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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. e-Pub 2017. PMID: 28522536.
- 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. e-Pub 2017. PMID: 28158710.
- 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. e-Pub 2017. PMID: 27903915.
- 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.
- 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.
- 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.
- 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 2016. PMID: 26645689.
- 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 2016. PMID: 26553800.
- 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. e-Pub 2016. PMID: 26833727.
- 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 2016. PMID: 26711009.
- 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.
- 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.
- 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.
- 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.
- 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 2015. PMID: 25416280.
- 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. e-Pub 2015. PMID: 25692074.
Invited Articles
- Cheng X, Hashimoto H, Stainbrook SC. Enzymes | Mammalian DNA methyltransferase structural themes. Encyclopedia of Biological Chemistry: third edition, 3, 330-335. In: Encyclopedia of Biological Chemistry III (Third Edition). Jez J (ed). Elsevier. pp. 330-335. https://doi.org/10.1016/B978-0-12-819460-7.00285-1, 2021. e-Pub 2021.
Other Articles
- 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. PMID: 36454652.
- Cheng X, Blumenthal RM Mediating and maintaining methylation while minimizing mutation: Recent advances on mammalian DNA methyltransferases. Curr Opin Struct Biol 75:102433, 2022. PMID: 35914495.
- 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.
- 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.
- Yang J, Zhang X, Blumenthal RM, Cheng X Detection of DNA Modifications by Sequence-Specific Transcription Factors. J Mol Biol, 2020. PMID: 31626807.
- 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.
- 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.
- 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.
Book Chapters
- 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.
- 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.
Grant & Contract Support
| Date: | 2025 - 2030 |
| Title: | Epigenetic regulations of DNA and histone methylation and deMethylation: Structures and Mechanisms |
| Funding Source: | NIH/NIGMS |
| Role: | PI |
| ID: | R35GM134744-A101 |
| Date: | 2024 - 2029 |
| Title: | Interrogating the Role of Bacterial Methylmodifying Enzymes in Pathoadaptation and Host Epigenetic Interference in Cancer |
| Funding Source: | NIH |
| Role: | Co-I |
| ID: | R01CA290034-01A1 |
| Date: | 2023 - 2025 |
| Title: | Preclinical studies of non-nucleoside DNMT3A/3B inhibitors |
| Funding Source: | NIH/NCI |
| Role: | PD/PI |
| ID: | R21CA277152 |
| Date: | 2023 - 2028 |
| Title: | Mechanisms of action and therapeutic targeting of the CARM1-NFIB axis in small cell lung cancer |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | R01CA272843-01A1 |
| Date: | 2023 - 2026 |
| Title: | Mutual reinforcement between somatic mutations and transcription factors in clonal hematopoiesis |
| Funding Source: | Texas A & M University |
| Role: | MPI |
| ID: | R01DK132386 |
| Date: | 2022 - 2025 |
| Title: | Prevention of omental metastasis of ovarian cancer by targeting a linkage between innate and adaptive immunity |
| Funding Source: | Department of Defense (DOD) |
| Role: | PD/PI |
| ID: | OC210175 |
| Date: | 2020 - 2024 |
| Title: | Epigenetic regulations of DNA and histone methylation and deMethylation: Structures and Mechanisms |
| Funding Source: | NIH/NIGMS |
| Role: | PI |
| ID: | R35-GM134744 |
Patient Reviews
CV information above last modified March 19, 2025