Cheng Laboratory
Xiaodong Cheng, Ph.D.
Principal Investigator
- Departments, Labs and Institutes
- Labs
- Cheng Laboratory
Areas of Research
- Epigenetics
- DNA Methylation
The Cheng Laboratory is defining the structural and biological effects of epigenetic modifications on DNA and histones.
Our Research
Many of our research projects center on the enzymatic readers, writers and erasers of epigenetic modifications on DNA and histones, as well as the rational design of inhibitors that act on these enzymes. We have additional interests in defining how transcription factors recognize DNA modifications.
Selected Notable Publications
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. 2024 Oct 14:S2451-9456(24)00403-3.
Hardikar S, Ren R, Ying Z, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, 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. 2024 Aug 23;10(34):eadr0036.
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. 2023 Sep 8;51(16):8447-8462.
Chen Q, Liu B, Zeng Y, Hwang JW, Dai N, Corrêa IR Jr, Estecio MR, Zhang X, Santos MA, Chen T, Cheng X. GSK-3484862 targets DNMT1 for degradation in cells. NAR Cancer. 2023 May 17;5(2):zcad022.
Pappalardi MB, Keenan K, Cockerill M, Kellner WA, Stowell A, et al. Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia. Nat Cancer . 2021 Oct;2(10):1002-1017.
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. 2021 Jun 8;12(1):3436.
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. 2020 Nov 1;34(21-22):1546-1558.
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. 2019 Oct 10;10(1):4600.
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. 2019 Aug 6;10(1):3541.
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. 2018 Mar 22;173(1):221-233.e12.
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. 2017 Jun 1;66(5):711-720.e3.