Research

24. Zhang X, Blumenthal RM, Cheng X. (2024) Keep Fingers on the CpG Island. Epigenomes 8(2): 23. doi: 10.3390/epigenomes8020023 [2024 June 19]

23. Zhang X, Xia F, Zhang X, Blumenthal RM, Cheng X. (2023) C2H2 zinc finger transcription factors associated with hemoglobinopathies. J Mol Biol. doi: 10.1016/j.jmb.2023.168343 [Epub 2023 Nov 2]

22. Yang J, Horton JR, Liu B, Corces VG, Blumenthal RM, Zhang X, Cheng X. (2023) Structures of CTCF-DNA complexes including all 11 zinc fingers. Nucleic Acids Res. 51(16): 8447-8462. doi: 10.1093/nar/gkad594. [Epub 2023 July 13]

21. 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. (2023) 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. :gkac1274. doi: 10.1093/nar/gkac1274. [Epub 2023 Jan 20]

20. Ren R, Horton JR, Chen Q, Yang J, Liu B, Huang Y, Blumenthal RM, Zhang X, Cheng X. (2023) 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. doi: 10.1016/j.jbc.2023.102885. [Epub 2023 Jan 7]

19. 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. (2022) HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription. Nat Genet. 54(9): 1417-1426. doi: 10.1038/s41588-022-01152-6. [Epub 2022 Aug 8]

18. Yang Y, Ren R, Ly LC, Horton JR, Li F, Quinlan KGR, Crossley M, Shi Y, Cheng X. (2021) Structural basis for human ZBTB7A action at the fetal globin promoter. Cell Rep. 36(13): 109759. doi: 10.1016/j.celrep.2021.109759 [Epub 2021 Sep 28]

17. 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 (2021) ZNF410 uniquely activates the NuRD component CHD4 to silence fetal hemoglobin expression. Mol Cell 81(2): 239-254 [Epub 2020 Dec 9]

16. Yang J, Zhang X, Blumenthal RM, Cheng X (2020) Detection of DNA modifications by sequence-specific transcription factors. J Mol Biol. 432: 1661-1673. [Epub 2019 Oct 15]

15. 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 (2019). Structural basis of specific DNA binding by the transcription factor ZBTB24. Nucleic Acids Res. 47(16): 8388-8398. doi: 10.1093/nar/gkz557. [Epub 2019 June 21]

14. Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X (2018) Detecting and interpreting DNA methylation marks. Curr Opin Struct Biol. 53: 88-99

13. Patel A, Yang P, Tinkham M, Pradhan M, Sun MA, Wang Y, Hoang D, Wolf G, Horton JR, Zhang X, Macfarlan T, Cheng X (2018) DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins. Cell 173(1): 221-233 [Epub 2018 Mar 15]

12. Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X, Cheng X (2018) 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 [Epub 2017 Dec 27]

11. Patel A, Zhang X, Blumenthal RM, Cheng X (2017) Structural basis of human PRDM9 allele C specific recognition of its cognate DNA sequence. J Biol Chem. 292(39): 15994-16002 [Epub 2017 Aug 11]

10. Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X (2017) Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA. Mol Cell 66(5): 711-720 [Epub 2017 May 18]

9. Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X (2016) Distinctive Klf4 mutants determine preference for DNA methylation status. Nucleic Acids Res. 44(21): 10177-10185 [Epub 2016 Sep 4]

8. Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng X (2016) 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 [Epub 2016 Sep 4]

7. Patel A, Hashimoto H, Zhang X, Cheng X (2016) Characterization of How DNA Modifications Affect DNA Binding by C2H2 Zinc Finger Proteins. Methods in Enzymology 573: 387-401 [Epub 2016 Feb 16]

6. Patel A, Horton JR, Wilson GG, Zhang X, Cheng X (2016) Structural basis for human PRDM9 action at recombination hot spots. Genes Dev. 30(3): 257-65. [Epub 2016 Feb 1]

5. Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X (2014) Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence. Genes Dev. 28(20): 2304-13 [Epub 2014 Sept 25]

4. Liu Y, Olanrewaju YO, Zheng Y, Hashimoto H, Blumenthal RM, Zhang X, Cheng X (2014) Structural basis for Klf4 recognition of methylated DNA. Nucleic Acids Res. 42(8): 4859-67 [Epub 2014 Feb 11]

3. Liu Y, Olanrewaju YO, Zhang X, Cheng X (2013) DNA recognition of 5-carboxylcytosine by a Zfp57 mutant at atomic resolution of 0.97 angstrom. Biochemistry 52: 9301-7 [Epub 2013 Nov 15]

2. Liu Y, Zhang X, Blumenthal RM, Cheng X (2013) A common mode of recognition for methylated CpG. Trends Biochem Sci. 38: 177-183 [Epub 2013 Jan 22]

1. Liu Y, Toh H, Sasaki H, Zhang X, Cheng X (2012) An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence. Genes Dev. 26, 2374-9 [Epub 2012 Oct 11]

Base flipping involves rotation of backbone bonds in double-stranded deoxyribonucleic acid (DNA) to expose an out-of-stack base, which can then be a substrate for an enzyme-catalyzed chemical reaction or for a specific protein binding interaction. The phenomenon was first observed for a DNA methyltransferase in 1994 (reference 1), and is now widespread for enzymes or proteins that require access to unpaired, mismatched, damaged or modified bases or even undamaged and unmodified bases for specific functions.

1. Klimasauskas S, Kumar S, Roberts RJ, Cheng X (1994) HhaI methyltransferase flips its target base out of the DNA helix. Cell 76, 357-69

2. M. O’Gara, J. R. Horton, R. J. Roberts, X. Cheng (1998) Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base. Nature Struct. Biol. 5, 872-7

3. Jia D, Jurkowska RZ, Zhang X, Jeltsch A, Cheng X (2007) Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449, 248-51

4. Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen S, Cheng X (2008) The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature 455, 826-9

5. Hashimoto H, Pais JE, Zhang X, Saleh L, Fu ZQ, Dai N, Corrêa IR, Zheng Y, Cheng X (2014) Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA. Nature 506, 391-5

6. Horton JR, Woodcock CB, Opot SB, Reich NO, Zhang X, Cheng X (2019) The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site. Nat Commun. 10(1): 4600. doi: 10.1038/s41467-019-12498-7. [Epub Oct 10]

7. Zeng Y, Ren R, Kaur G, Hardikar S, Ying Z, Babcock L, Gupta E, Zhang X, Chen T, Cheng X. (2020) The inactive Dnmt3b3 isoform preferentially enhances Dnmt3b-mediated DNA methylation. Genes Dev. 34: 1546-1558 doi: 10.1101/gad.341925.120 [Epub Oct 1]

8. Zhou J, Horton JR, Blumenthal RM, Zhang X, Cheng X. (2021) Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix. Nat Commun. 12(1): 3436. doi: 10.1038/s41467-021-23693-w. [Epub Jun 8]

S-adenosyl-l-methionine (AdoMet or SAM) is the second most commonly used enzyme cofactor after ATP. The AdoMet-dependent methyltransferases act on a wide variety of target molecules, including DNA, RNA, proteins, polysaccharides, lipids, and a range of small molecules involved in metabolism. We determined the first structure of a DNA methyltransferase (1993), the first structure of protein arginine methyltransferase (2000), the first structure of a protein (histone) lysine methyltransferase (2002) and its complex with histone peptide substrate (2003). In addition, we determined structures of PvuII, a DNA cytosine-N4 methyltransferase (1997), DNMT2 - a tRNA cytosine methyltransferase (2001), HNMT - a small molecule (histamine) methyltransferase (2001), HemK - a protein glutamine methyltransferase (2004), Dot1p - a histone H3 lysine79 methyltransferase (2004), and SETD6 - a non-histone lysine methyltransferase (2011).

1. Cheng X, Kumar S, Posfai J, Pflugrath JW, Roberts RJ (1993) Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-l-methionine. Cell 74, 299-307

2. W. Gong, M. O’Gara, R. M. Blumenthal, X. Cheng (1997) Structure of PvuII DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res. 25, 2702-2715

3. Zhang X, Zhou L, Cheng X (2000) Crystal structure of the conserved core of the protein arginine methyltransferase PRMT3. EMBO J. 19, 3509-19

4. X. Zhang and X. Cheng (2003) Structure of the predominant protein arginine methyltransferase PRMT1 and analysis of its binding to substrate peptides. Structure 11, 509-520

5. Dong A, Yoder JA, Zhou L, Zhang X, Bestor T, Cheng X (2001) Structure of human DNMT2, an enigmatic DNA methyltransferase homologue that displays denaturant-resistant binding to DNA. Nucleic Acids Res. 29, 439-448.

6. Horton JR, Sawada K, Nishibori M, Zhang X, Cheng X (2001) Two polymorphic forms of human histamine methyltransferase: structural, thermal and kinetic comparisons. Structure, 837-849.

7. Zhang X, Tamaru H, Khan SI, Horton JR, Keefe LJ, Selker EU, Cheng X (2002) Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase. Cell 111, 117-27

8. Zhang X, Yang Z, Khan SI, Horton JR, Tamaru H, Selker EU, Cheng X (2003) Structural basis for the product specificity of histone lysine methyltransferases. Molecular Cell 12, 177-185

9. Yang Z, Shipman L, Zhang M, Anton B, Roberts RJ, Cheng X (2004) Structural characterization and comparative phylogenetic analysis of E. coli HemK, a Protein (N5)-Glutamine Methyltransferase. J. Mol. Biol. 340, 695-706

10. Sawada K, Yang Z, Horton JR, Collins RE, Zhang X, and Cheng X (2004) Structure of the conserved core of the Yeast Dot1p, a nucleosomal histone H3 lysine79 methyltransferase. J. Biol. Chem. 279, 43296-43306

11. Chang Y, Levy D, Horton JR, Peng J, Zhang X, Gozani O, Cheng X (2011) Structural basis of SETD6-mediated regulation of the NF-kB network via methyl-lysine signaling. Nucleic Acids Res. 39, 6380-9

12. Wilkinson AE, 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* (2019) SETD3 is an actin histidine methyltransferase that prevents primary dystocia. *Co-corresponding authors. Nature 565(7739): 372-376 [Epub Dec 10, 2018] see comment by P. Lappalainen: Protein modification fine-tunes the cell's force producers. Nature 565(7739): 297-298 (2019) and has been recommended in F1000Prime as being of special significance in its field by F1000 Faculty Member Pekka Lappalainen.

13. Dai S, Horton JR, Woodcock CB, Wilkinson AW, Zhang X, Gozani O, Cheng X (2019) Structural basis for the target specificity of actin histidine methyltransferase SETD3. Nat Commun. 10(1): 3541. doi: 10.1038/s41467-019-11554-6 [Epub Aug 6]

14. Zhou J, Horton JR, Kaur G, Chen Q, Li X, Mendoza F, Wu T, Blumenthal RM, Zhang X, Cheng X. (2023) 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. doi: 10.1016/j.jbc.2023.105017. [Epub 2023 Jul 5]

In addition to cytosine C5 modification (5mC) in DNA and RNA, the exocyclic amino group of adenine in DNA and RNA is also methylated, resulting in N6-methyl-adenine (N6mA).

1. Malone T, Blumenthal RM, Cheng X (1995) Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J. Mol. Biol. 253, 618-32

2. Yang Z, Horton JR, Zhou L, Zhang XJ, Dong A, Zhang X, Schlagman SL, Kossykh V, Hattman S, Cheng X (2003) Structure of the bacteriophage T4 DNA adenine methyltransferase. Nature Struct. Biol. 10, 849-855

3. Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X (2005) Transition from nonspecific to specific DNA interaction along the substrate recognition pathway of Dam methyltransferase. Cell 121, 349-61

4. Horton JR, Liebert K, Bekes M, Jeltsch A, Cheng X (2006) Structure and Substrate Recognition of the E. coli DNA Adenine Methyltransferase. J. Mol. Biol. 358, 559-570

5. Horton JR, Zhang X, Blumenthal RM, Cheng X (2015) 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

6. Murray IA, Morgan RD, Luyten Y, Fomenkov A, Corrêa IR Jr, Dai N, Allaw MB, Zhang X, Cheng X, Roberts RJ (2017) The non-specific adenine DNA methyltransferase M.EcoGII. Nucleic Acids Res. doi: 10.1093/nar/gkx1191. [Epub 2017 Dec 8]

7. Woodcock CB, Yu D, Zhang X, Cheng X (2019) Human HemK2/KMT9/N6AMT1 is an active protein methyltransferase, but does not act on DNA in vitro, in the presence of Trm112. Cell Discovery 5: 50. doi: 10.1038/s41421-019-0119-5 [Epub Sept 10]

8. Woodcock CB, Yu D, Hajian T, Li J, Huang Y, Dai N, Correa IR Jr, Wu T, Vedadi M, Zhang X, Cheng X (2019) Human MettL3–MettL14 complex is a sequence-specific DNA adenine methyltransferase active on single-strand and unpaired DNA in vitro. Cell Discov. 5: 63. doi: 10.1038/s41421-019-0136-4 [Epub Dec 24]

9. Woodcock CB, Horton JR, Zhang X, Blumenthal RM, Cheng X. (2020) Beta Class Amino Methyltransferases From Bacteria to Humans: Evolution and Structural Consequence. Nucleic Acids Res. 48(18): 10034-10044 doi: 10.1093/nar/gkaa446 [Epub May 26]

10. Woodcock CB, Horton JR, Zhou J, Bedford MT, Blumenthal RM, Zhang X, Cheng X. (2020) Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA. Nucleic Acids Res. 48(18): 10329-10341 doi: 10.1093/nar/gkaa604 [Epub July 14]  

11. Zhang X, Blumenthal RM, Cheng X. (2021) A role for N6-methyladenine in DNA damage repair. Trends in Biochemical Sciences 46(3): 175-183 https://doi.org/10.1016/j.tibs.2020.09.007 [Epub Oct 16, 2020]

12. Yu D, Horton JR, Yang J, Hajian T, Vedadi M, Sagum CA, Bedford MT, Blumenthal RM, Zhang X, Cheng X. (2021) Human MettL3-MettL14 RNA adenine methyltransferase complex is active on double-stranded DNA containing lesions. Nucleic Acids Res. doi: 10.1093/nar/gkab460 [Epub Jun 4]

13. Yu D, Kaur G, Blumenthal RM, Zhang X, Cheng X. (2021) Enzymatic characterization of three human RNA adenosine methyltransferases reveals diverse substrate affinities and reaction optima. J Biol Chem. 296: 100270. doi: 10.1016/j.jbc.2021.100270. [Epub Jan 8]

14. Yu D, Dai N, Wolf EJ, Corrêa IR Jr, Zhou J, Wu T, Blumenthal RM, Zhang X, Cheng X. (2022) Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs. J Biol Chem. 298(4): 101751. doi: 10.1016/j.jbc.2022.101751 [Epub Feb 18]

15. Yu D, Zhou J, Chen Q, Wu T, Blumenthal RM, Zhang X, Cheng X. (2022) Enzymatic Characterization of In Vitro Activity of RNA Methyltransferase PCIF1 on DNA. Biochemistry  doi: 10.1021/acs.biochem.2c00134. [Epub May 23]

1. X. Cheng, K. Balendiran, I. Schildkraut, J. E. Anderson (1994) Structure of PvuII endonuclease with cognate DNA. EMBO J. 13, 3927-3935

2. Z. Yang, J.R. Horton, R. Maunus, G.G. Wilson, R.J. Roberts and X. Cheng (2005) Structure of HinP1I Endonuclease Reveals a Striking Similarity to the Monomeric Restriction Enzyme MspI. Nucleic Acids Res. 33, 1892-1901

3. J. R. Horton, X. Zhang, R. Maunus, Z. Yang, G. G. Wilson, R. J. Roberts and X. Cheng (2006) DNA nicking by HinP1I endonuclease: bending, base flipping, and minor groove expansion. Nucleic Acids Res. 34, 938-948

4. Horton JR, Mabuchi MY, Cohen-Kamo D, Zhang, X, Griggs RM, Samaranayake M, Roberts RJ, Zheng Y, Cheng X (2012) Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease. Nucleic Acids Res. 40, 9763-73

5. 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 (2014) Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI. Sci Rep. 4:4246

6. Horton JR, Borgaro JG, Griggs RM, Quimby A, Guan S, Zhang X, Wilson GG, Zheng Y, Zhu Z, Cheng X (2014) Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA. Nucleic Acids Res. 42(12): 7947-59

7. Horton JR, Wang H, Mabuchi MY, Zhang X, Roberts RJ, Zheng Y, Wilson GG, Cheng X (2014) Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix. Nucleic Acids Res. 42(19): 12092-101

8.  Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A, Wilson GG, Roberts RJ, Cheng X (2020) Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å. Nucleic Acids Res. 48(3): 1466-1478 doi: 10.1093/nar/gkz1195. [Epub Dec 27, 2019] - published as cover on 20 February 2020

Chromatin regulates transcriptional processes through postsynthetic modifications of both of its components: DNA and histones. Much remains to be learned about how the combination of these modifications (or lack thereof) facilitates or silences transcription. One broad theme has emerged that a web of interactions tightly coordinates the modification of a segment of DNA and its associated histones, affecting local chromatin structure and determining the functional states. We are the first to illustrate the mechanistic insights of anti-correlation of histone H3 lysine 4 (H3K4) methylation and DNA methylation (2007), coordinated methylations of H3K9 and DNA (2011), and a methyl-and-phospho switch in DNMT1 (2011).

1. Tamaru H, Zhang X, McMillen D, Singh P, Nakayama J, Grewal SI, Allis CD, Cheng X, Selker EU (2003) Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nature Genetics, 34, 75-79

2. Jackson JP, Johnson L, Jasencakova Z, Zhang X, PerezBurgos L, Singh PB, Cheng X, Schubert I, Jenuwein T, Jacobsen SE. (2004) Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma. 112, 308-315

3. 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 (2007) DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714-717

4. 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 (2011) MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a. Nature Commun. 2: 533

5. Estève PO, Chang Y, Samaranayake M, Upadhyay AK, Horton JR, Feehery GR, Cheng X, Pradhan S (2011) A methylation and phosphorylation switch between an adjacent lysine and serine determines human DNMT1 stability. Nature Struct. Mol. Biol. 18, 42-8

6. Estève PO, Zhang G, Ponnaluri VK, Deepti K, Chin HG, Dai N, Sagum C, Black K, Corrêa IR Jr, Bedford MT, Cheng X, Pradhan S. (2015) Binding of 14-3-3 reader proteins to phosphorylated DNMT1 facilitates aberrant DNA methylation and gene expression. Nucleic Acids Res. 44(4): 1642-56

In principle, epigenetic modifications alter the interaction with DNA binding proteins by strengthening, weakening, or abolishing the interaction altogether. This, in turn, can modulate gene expression and control cellular metabolism and is believed to be one of the principal mechanisms underlying epigenetic processes such as differentiation, development, aging, and disease. We have identified and determined structures of reader domains recognizing histone and DNA modifications (or lack thereof).

1. C. Qiu, K. Sawada, X. Zhang, X. Cheng (2002) The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature Struct. Biol. 9, 217-224

2. Hashimoto H, Liu Y, Upadhyay AK, Chang Y, Howerton SB, Vertino PM, Zhang X, Cheng X (2012) Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation. Nucleic Acids Res. 40, 4841-9

3. Liu Y, Toh H, Sasaki H, Zhang X, Cheng X (2012) An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence. Genes Dev. 26, 2374-2379

4. Liu Y, Zhang X, Blumenthal RM, Cheng X (2013) A common mode of recognition for methylated CpG. Trends Biochem Sci. 38, 177-183

5. Liu Y, Olanrewaju YO, Zhang X, Cheng X (2013) DNA recognition of 5-carboxylcytosine by a Zfp57 mutant at atomic resolution of 0.97 angstrom. Biochemistry 52, 9301-7

6. Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X (2014) Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence. Genes Dev. 28, 2304-2313

7. Liu Y, Olanrewaju YO, Zheng Y, Hashimoto H, Blumenthal RM, Zhang X, Cheng X (2014) Structural basis for Klf4 recognition of methylated DNA. Nucleic Acids Res. 42(8), 4859-67

8. Patel A, Horton JR, Wilson GG, Zhang X, Cheng X (2016) Structural basis for human PRDM9 action at recombination hot spots. Genes Dev. 30(3): 257-265

9. Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X (2016) Distinctive Klf4 mutants determine preference for DNA methylation status. Nucleic Acids Res. 44(21): 10177-10185

10. Wang D, Hashimoto H, Zhang X, Barwick BG, Lonial S, Boise LH, Vertino PM, Cheng X (2017) MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma. Nucleic Acids Res. 45(5): 2396-2407

11. Hong S, Wang D, Horton JR, Zhang X, Speck SH, Blumenthal RM, Cheng X (2017) 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  

12. Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X (2017) Structural basis for the versatile and methylation-dependent binding of CTCF to DNA. Mol. Cell 66(5): 711-720

13. Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang Y, Zhang X, Blumenthal RM, Cheng X (2019) Structural basis for effects of CpA modifications on C/EBPb binding of DNA. Nucleic Acids Res. 47(4): 1774-1785 [Epub Dec 19, 2018]

14. Yang J, Horton JR, Li J, Huang Y, Zhang X, Blumenthal RM, Cheng X (2019) Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine. Nucleic Acids Res. 47(16): 8375-8387. doi: 10.1093/nar/gkz381 [Epub May 13]

15. Woodcock CB, Horton JR, Zhou J, Bedford MT, Blumenthal RM, Zhang X, Cheng X. (2020) Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA. Nucleic Acids Res. 48(18): 10329-10341 doi: 10.1093/nar/gkaa604 [Epub July 14]

16. Yang J, Horton JR, Akdemir KC, Li J, Huang Y, Kumar J, Blumenthal RM, Zhang X, Cheng X. (2021) Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations. Nucleic Acids Res. 49(9): 5084-5094. doi: 10.1093/nar/gkab276 [Epub Apr 20]

17. 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. (2021) MBD5 and MBD6 couple DNA methylation to gene silencing through the J-domain protein SILENZIO. Science doi: 10.1126/science.abg6130. [Epub Jun 3]

18. Yang J, Gupta E, Horton JR, Blumenthal RM, Zhang X, Cheng X. (2022) 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. doi: 10.1016/j.dnarep.2022.103306. [Epub Feb 26]

19. 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. (2024) 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. doi: 10.1126/sciadv.adr0036. [Epub 2024 Aug 23]

We illustrated the mechanistic insight of anti-correlation of H3K4 and H3K9 methylation by PHF8 (2010). The crosstalk between different modifications also applies to non-histone proteins such as ERα (2008) and NF-κB (2011).

1. Lan F, Collins RE, De Cegli R, Alpatov R, Horton JR, Shi X, Gozani O, Cheng X, Shi Y (2007) Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature 448, 718-722

2. Collins RE, Northrop JP, Horton JR, Lee DY, Zhang X, Stallcup MR, Cheng X (2008) The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules. Nature Struct. Mol. Biol. 15, 245-50

3. Subramanian K, Jia D, Kapoor-Vazirani P, Powell DR, Collins RE, Sharma D, Peng J, Cheng X, Vertino PM (2008) Regulation of estrogen receptor alpha by the SET7 lysine methyltransferase. Mol. Cell 30, 336-347

4. Horton JR, Upadhyay AK, Qi HH, Zhang X, Shi Y, Cheng X (2010) Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Nature Struct. Mol. Biol. 17, 38-43

5. Chang Y, Horton JR, Bedford MT, Zhang X, Cheng X (2011) Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9: potential effect of phosphorylation on methyl-lysine binding. J. Mol. Biol. 408, 807-14

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

7. Mahgoub M, Paiano J, Bruno M, Wu W, Pathuri S, Zhang X, Ralls S, Cheng X, Nussenzweig A, Macfarlan TS. (2020) Dual Histone Methyl Reader ZCWPW1 Facilitates Repair of Meiotic Double Strand Breaks in Male Mice. Elife 9: e53360. doi: 10.7554/eLife.53360 [Epub Apr 30] [bioRxiv: https://doi.org/10.1101/821603. Posted October 29, 2019] [see Insight by Mathilde Blot and Bernard de Massy]

8. Chen J, Horton J, Sagum C, Zhou J, Cheng X, Bedford MT. (2021) Histone H3 N-terminal mimicry drives a novel network of methyl-effector interaction. Biochem J. 478(10): 1943-1958. doi: 10.1042/BCJ20210203 [Epub May 10]

9. Horton JR, Zhou J, Chen Q, Zhang X, Bedford MT, Cheng X. (2023) A complete methyl-lysine binding aromatic cage constructed by two domains of PHF2. J Biol Chem. 299(2):102862. doi: 10.1016/j.jbc.2022.102862. [Epub 2022 Dec 31]

1. Wu P, Qiu C, Sohail A,  Zhang X, Bhagwat AS, Cheng X (2003) 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, 5285-5291

2. Hashimoto H, Zhang X, Cheng X (2012) Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation. Nucleic Acids Res. 40, 8276-84

3. Hashimoto H, Hong S, Bhagwat AS, Zhang X, Cheng X (2012) 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, 10203-14

4. Hashimoto H, Zhang X, Cheng X (2013) Selective excision of 5-carboxylcytosine by a thymine DNA glycosylase mutant. J. Mol. Biol. 425(6): 971-6

5. Hashimoto H, Zhang X, Cheng X (2013) Activity and crystal structure of human thymine DNA glycosylase mutant N140A with 5-carboxylcytosine DNA at low pH. DNA Repair 12, 535-540

6. Hong S, Hashimoto H, Kow YW, Zhang X, Cheng X (2014) The carboxy-terminal domain of ROS1 is essential for 5-methylcytosine DNA glycosylase activity. J. Mol. Biol. 426: 3703-12

7. Yang J, Horton JR, Akdemir KC, Li J, Huang Y, Kumar J, Blumenthal RM, Zhang X, Cheng X. (2021) Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations. Nucleic Acids Res. 49(9): 5084-5094. doi: 10.1093/nar/gkab276 [Epub Apr 20]

8. Yang J, Gupta E, Horton JR, Blumenthal RM, Zhang X, Cheng X. (2022) 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. doi: 10.1016/j.dnarep.2022.103306. [Epub Feb 26]

Histone lysine methylation is often compromised in cancers, and the corresponding enzymes (methyltransferases and demethylases) have since become important therapeutic targets, particularly in human cancers where these enzymes are frequently mutated and/or misregulated.

1. Xu R, Carmel G, Kuret J, Cheng X (1996) Structural basis for selectivity of the isoquinoline sulfonamide family of protein kinase inhibitors. Proc. Natl. Acad. Sci. USA 93, 6308-6313

2. Chang Y, Zhang X, Horton JR, Upadhyay AK, Spannhoff A, Liu J, Snyder JP, Bedford MT, Cheng X (2009) Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294. Nature Struct. Mol. Biol. 16, 312-7 (PMC2676930)

3. Chang Y, Ganesh T, Horton JR, Spannhoff A, Liu J, Sun A, Zhang X, Bedford MT, Shinkai Y, Snyder JP, Cheng X (2010) Adding a lysine mimic in the design of potent inhibitors of histone lysine methyltransferases. J Mol Biol. 400, 1-7

4. 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 (2011) Discovery and structural characterization of a small molecule 14-3-3 protein-protein interaction inhibitor. Proc Natl Acad Sci U S A. 108, 16212-6

5. Upadhyay AK, Rotili D, Han JW, Hu R, Chang Y, Labella D, Zhang X, Yoon YS, Mai A, Cheng X (2012) An Analog of BIX-01294 Selectively Inhibits a Family of Histone H3 Lysine 9 Jumonji Demethylases. J. Mol. Biol. 416, 319-327

6. 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 (2014) Selective non-nucleoside inhibitors of human DNA methyltransferases active in cancer including cancer stem cells. J. Med. Chem. 57, 701-13

7. 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. (2014) 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  

8. Horton JR, Engstrom A, Zoeller EL, Liu X, Shanks JR, Zhang X, Johns MA, Vertino PM, Fu H, Cheng X. (2016) Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases. J. Biol. Chem. 291(6): 2631-46

9. 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 (2016) Structural basis for KDM5A histone lysine demethylase inhibition by diverse compounds. Cell Chem. Biol. 23(7): 769-81

10. 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 (2018) Insights into the action of inhibitor enantiomers against histone lysine demethylase 5A. J Med Chem. 61(7): 3193-3208 [Epub Mar 14]

11. 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 (2018) KDM5 histone demethylases repress immune response via suppression of STING. PLoS Biol. 16(8): e2006134. eCollection 2018 Aug.

12. 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 (2018) Structure-based engineering of irreversible inhibitors against histone lysine demethylase KDM5A. J Med Chem. 61(23): 10588–10601 [Epub Nov 3]

13. 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. (2019) 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 [Epub Feb 12]

14. Chen D, Meng Y, Yu D, Noinaj N, Cheng X, Huang R (2021) Chemoproteomic study uncovers HemK2/KMT9 as a new target for NTMT1 bisubstrate inhibitors. ACS Chem Biol. 16(7):1234-1242. doi: 10.1021/acschembio.1c00279 [Epub Jun 30] BioRxiv doi: https://doi.org/10.1101/2021.04.13.439666 [Posted April 13, 2021]

15. Zhou J, Horton JR, Yu D, Ren R, Blumenthal RM, Zhang X, Cheng X. (2021) Repurposing epigenetic inhibitors to target the Clostridioides difficile- specific DNA adenine methyltransferase and sporulation regulator CamA. Epigenetics doi: 10.1080/15592294.2021.1976910. [Epub Sep 15]

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 (2021) Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia. Nature Cancer 2(10): 1002-1017. https://doi.org/10.1038/s43018-021-00249-x [Epub Sep 27 2021] (see in brief - A safe and effective DNA hypomethylating agent)

17. Horton JR, Pathuri S, Wong K, Ren R, Rueda L, Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB, Zhang X, King BW, Cheng X. (2022) Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors. Structure. 30(6):793-802.e5. doi: 10.1016/j.str.2022.03.009. [Epub April 7]

18. 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. (2023) 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. doi: 10.1021/acs.jmedchem.2c01789. [Epub 2022 Dec 29]

19. 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. (2023) 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. doi: 10.1021/acschembio.3c00035. [Epub 2023 Feb 22].

20. Chen Q, Liu B, Zeng Y, Hwang JW, Dai N, Corrêa IR Jr, Estecio MR, Zhang X, Santos MA, Chen T, Cheng X. (2023) GSK-3484862 targets DNMT1 for degradation in cells. NAR Cancer. 5(2): zcad022. doi: 10.1093/narcan/zcad022. [Epub 2023 May 17]