Publications

254. Zhou J, Chen Q, Ren R, Yang J, Liu B, Horton JR, Chang C, Li C, Maksoud L, Yang Y, Rotili D, Zhang X, Blumenthal RM, Chen T, Gao Y, Valente S, Mai A, Cheng X. (2024) Quinoline-based compounds can inhibit diverse enzymes that act on DNA. Cell Chem Biol. S2451-9456(24)00403-3. doi: 10.1016/j.chembiol.2024.09.007 [Epub 2024 Oct 21] BioRxiv preprint doi: https://doi.org/10.1101/2024.04.03.587980 [posted on 2024 April 3]

253. Zhang X, Blumenthal RM, Cheng X. (2024) 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. doi: 10.1093/nar/gkae832. [Epub 2024 Sep 26]

252. 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] [BioRxiv preprint doi: 10.1101/2023.12.15.571946 on 2023 Dec 15][see MD Anderson Research Highlights for September 4, 2024]

251. Wang Y, Zhou J, He W, Fu R, Shi L, Dang NK, Liu B, Xu H, Cheng X, Bedford MT. (2024) SART3 reads methylarginine-marked glycine- and arginine-rich motifs. Cell Rep. 43(7):114459. doi: 10.1016/j.celrep.2024.114459. [Epub 2024 Jul 9]

250. Zhang X, Blumenthal RM, Cheng X. (2024) Keep fingers on the CpG islands. Epigenomes 8(2): 23. https://doi.org/10.3390/epigenomes8020023 [Epub 2024 Jun 19]

249. Zhang X, Blumenthal RM, Cheng X. (2024) Updated understanding of the protein-DNA recognition code used by C2H2 zinc finger proteins. Curr Opin Struct Biol. 87:102836. doi: 10.1016/j.sbi.2024.102836. [Epub 2024 May 15]

248. Zhou J, Chen T, Cheng X. (2024) One form and two functions: MBD of SETDB2 is a protein-interacting domain. Structure 32(3): 258-260. doi: 10.1016/j.str.2024.01.009 [2024 Mar 7]

247. Do C, Jiang G, Cova G, Katsifis CC, Narducci DN, Yang J, Sakellaropoulos T, Vidal R, Lhoumaud P, Fara Regis F, Kakabadze N, Nora EP, Noyes M, Cheng X, Hansen AS, Skok JA. (2024) Brain and cancer associated binding domain mutations provide insight into CTCF's relationship with chromatin and its ability to act as a chromatin organizer. BioRxiv preprint. doi: 10.1101/2024.01.11.575070 [2024 Feb 5].

246. Zhang X, Xia F, Zhang X, Blumenthal RM, Cheng X. (2024) C2H2 Zinc Finger Transcription Factors Associated with Hemoglobinopathies. J Mol Biol. 436(7): 168343. doi: 10.1016/j.jmb.2023.168343. [Epub 2023 Nov 2]

245. 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. (2023) TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells. Nature Aging. 3(11): 1387-1400. doi: 10.1038/s43587-023-00505-y. [Epub 2023 Oct 26]

244. 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 Jul 13]

243. 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 4]. Editors' Pick.

242. 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/zcad0222023 [Epub 2023 May 17]

241. 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 Methyltransferas.  ACS Chem Biol. 18(4): 734-745. doi: 10.1021/acschembio.3c00035. [Epub 2023 Feb 22].

240. 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. 51(4):1674-1686. doi: 10.1093/nar/gkac1274. [Epub 2023 Jan 20]

239. 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].

238. 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].

237. 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]

236. Valverde de Morales HG, Wang HV, Garber K, Cheng X, Corces VG, Li H. (2023) 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. doi: 10.1002/ajmg.a.63065. [Epub 2022 Dec 1]

235. Ren R, Horton JR, Hong S, Cheng X. (2022) Recent Advances on DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications. Adv Exp Med Biol. 1389: 295-315. doi: 10.1007/978-3-031-11454-0_12.

234. 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. Nature Genet. 54(9): 1417-1426. doi: 10.1038/s41588-022-01152-6. [Epub 2022 Aug 8]

233. Cheng X, Blumenthal RM. (2022) Mediating and maintaining methylation while minimizing mutation: Recent advances on mammalian DNA methyltransferases. Curr Opin Struct Biol. 75: 102433. doi: 10.1016/j.sbi.2022.102433. [Epub 2022 July 29]

232. 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 61(11): 1005-13. doi: 10.1021/acs.biochem.2c00134. [Epub 2022 May 23]

231. 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): 793-902.e5. doi: 10.1016/j.str.2022.03.009. [Epub 2022 April 7]

230. 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 2022 Feb 26]

229. 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 2022 Feb 18]

228. 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]

227. 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 2021 Sep 27] (see in brief - A safe and effective DNA hypomethylating agent)

226. Zhou J, Horton JR, Yu D, Ren R, Blumenthal RM, Zhang X, Cheng X. (2022) Repurposing epigenetic inhibitors to target the Clostridioides difficile- specific DNA adenine methyltransferase and sporulation regulator CamA. Epigenetics 17(9): 970-981. doi: 10.1080/15592294.2021.1976910. [Epub 2021 Sep 15]

225. 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 (2022) Systematic profiling of DNMT3A variants reveals protein instability mediated by the DCAF8 E3 ubiquitin ligase adaptor. Cancer Discov. 12(1): 220-235 doi: 10.1158/2159-8290.CD-21-0560 [Epub 2021 Aug 24]

224. 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 2021 Jun 30] BioRxiv doi: 10.1101/2021.04.13.439666 [Posted 2021 April 13]

223. 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 2021 Jun 8] Featured in Editors' highlights and MD Anderson Research Highlights.

222. 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. 49(20): 11629-11642. doi: 10.1093/nar/gkab460 [Epub 2021 Jun 4] (appeared in a cover on November 18, 2021 issue)

221. 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 372(6549): 1434-1439. doi: 10.1126/science.abg6130. [Epub 2021 Jun 3]

220. 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 2021 May 10] - see commentary by Y. Yu, H. Wen and X. Shi on Histone mimics: more tales to read.

219. 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 2021 Apr 20]

218. 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 2021 Jan 8]

217. 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] [bioRxiv: https://doi.org/10.1101/2020.08.31.274324. Posted 2020 August 31] Referred to by Juhyun Kim, Ann Dean. A Zinc Finger Transcription Factor Faithfully Dedicated to Only a Single Target Gene in Erythroid Cells Mol Cell, 81(2): 218-219 (21 January 2021)

216. 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 2020 Oct 16]

215. 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 2020 Oct 1]

214. 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 2020 July 14]

213. Dai S, Holt MV, Horton JR, Woodcock CB, Patel A, Zhang X, Young NL, Wilkinson AW, Cheng X. (2020) Characterization of SETD3 methyltransferase mediated methionine methylation. J Biol Chem. 295(32): 10901-10910 doi:10.1074/jbc.RA120.014072 [Epub 2020 June 5] - see cover photo

212. 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 2020 May 26] - published as cover on 9 October 2020

211. Kumar J, Kaur G, Ren R, Lu Y, Lin K, Li J, Huang Y, Patel A, Barton MC, Macfarlan T, Zhang X, Cheng X. (2020) KRAB domain of ZFP568 disrupts TRIM28-mediated abnormal interactions in cancer cells. NAR Cancer 2(2): zcaa007 [Epub 2020 May 18]

210. 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 2020 Apr 30] [bioRxiv: https://doi.org/10.1101/821603. Posted 2019 October 29] [see Insight by Mathilde Blot and Bernard de Massy]

209. Chen H, Liu Q, Yu D, Natchiar K, Zhou C, Hsu C-H, Hsu P-H, Zhang X, Klaholz B, Gregory RI, Cheng X, Shi Y. METTL5, an 18S rRNA-specific m6A methyltransferase, modulates expression of stress response genes. BioRxiv doi: https://doi.org/10.1101/2020.04.27.064162 [posted 2020 April 28]

208. Hardikar S, Ying Z, Zeng Y, Zhao H, Liu B, Veland N, McBride K, Cheng X, Chen T. (2020) The ZBTB24-CDCA7 axis regulates HELLS enrichment at centromeric satellite repeats to facilitate DNA methylation. Protein Cell. 11(3): 214-218 doi: 10.1007/s13238-019-00682-w. [Epub 2020 Jan. 22]

207. Dai S, Horton JR, Wilkinson AW, Gozani O, Zhang X, Cheng X. (2020) An engineered variant of SETD3 methyltransferase alters target specificity from histidine to lysine methylation. J Biol Chem. 295(9): 2582-2589 doi: 10.1074/jbc.RA119.012319. [Epub 2020 Jan 7]

206. 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

205. 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]

204. Wu X, Liu S, Sagum C, Chen J, Singh R, Chaturvedi A, Horton JR, Kashyap TR, Fushman D, Cheng X, Bedford MT, Wang B (2019) Crosstalk between Lys63- and Lys11-polyubiquitin signaling at DNA damage sites is driven by Cezanne. Genes Dev. 33(23-24): 1702-1717. [Epub Nov 7] - see Outlook by Rona G and Pagano M (2019) Mixed ubiquitin chains regulate DNA repair. Genes Dev. 33(23-24): 1615-1616

203. 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 Oct 15, 2019]

202. 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]

201. 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 (2019) Genetic heterogeneity within collective invasion packs drives leader and follower cell phenotypes. J Cell Sci. 132(19). pii: jcs.231514. doi: 10.1242/jcs.231514. [Epub Sept 12] See cover image

200. 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]

199. 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]

198. 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 June 21]

197. 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]

196. 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]

195. 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]

194. 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.

193. 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]

192. 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.

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

190. 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 Mar 15]

189. 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]

188. Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X, Cheng X (2018) Role for the 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]

187. Murray IA, Morgan RD, Luyten Y, Fomenkov A, Corrêa IR Jr, Dai N, Allaw MB, Zhang X, Cheng X, Roberts RJ (2018) The non-specific adenine DNA methyltransferase M.EcoGII. Nucleic Acids Res. 46(2): 840-848 [Epub 2017 Dec 8]

186. 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, Anata R, Cheng X, Ahmed R (2017) Effector CD8 T cells dedifferentiate into long-lived memory cells. Nature 552(7685): 404-409 [Epub Dec 13]

185. Lee CC, Peng SH, Shen L, Lee CF, Du TH, Kang ML, Xu GL, Upadhyay AK, Cheng X, Yan YT, Zhang Y, Juan LJ. (2017) The Role of N-α-acetyltransferase 10 Protein in DNA Methylation and Genomic Imprinting. Mol Cell 68(1): 89-103 [Epub Sep 21]

184. Horton JR, Gale M, Yan Q, Cheng X (2017) The Molecular Basis of Histone Demethylation. In DNA and Histone Methylation as Cancer Targets (A. Kaneda, Y.-i. Tsukada, eds., Cancer Drug Discovery and Development, DOI 10.1007/978-3-319-59786-7_7), pp 151-219

183. 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 Aug 11]

182. 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 (2017) A placental growth factor is silenced in mouse embryos by the zinc finger protein ZFP568. Science 356(6339): 757-759 [Epub May19]

181. 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 May 18]

180. Head PE, Zhang H, Bastien AJ, Koyen AE, Withers AE, Daddacha WB, Cheng X, Yu DS (2017) Sirtuin 2 mutations in human cancers impair its function in genome maintenance. J. Biol. Chem. 292(24): 9919-9931 [Epub May 1]

179. 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 [Epub Feb 1, 2017] This paper was published as the cover story in the 17 March 2017 issue of Nucleic Acids Research

178. 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 [Epub Nov 28, 2016]

177. Hong S, Cheng X (2016) DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications. Adv. Exp. Med. Biol. 945: 321-341

176. 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 Sep 4]

175. 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 Sep 4]

174. 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 [Epub Jul 14]

173. 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 Feb 16]

172. 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 Feb 1] This paper was published as the cover story in the February 1, 2016 issue of Genes & Development.

171. 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. (2016) Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression. Mol Cell. 61(1): 153-60 [Epub 2015 Dec 16]

170. Horton JR, Engstrom A, Zoeller EL, Liu X, Shanks JR, Zhang X, Johns MA, Vertino PM, Fu H, Cheng X. (2015) Characterization of a linked Jumonji domain of the KDM5/JARID1 family of histone H3 lysine 4 demethylases. J. Biol. Chem. 291(6): 2631-46 [Epub 2015 Dec 8]

169. 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 [Epub 2015 Nov 8]

168. Hashimoto H, Pais JE, Dai N, Corrêa IR Jr, Zhang X, Zheng Y, Cheng X. (2015) Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA. Nucleic Acids Res. 43(22): 10713-21[Epub Aug 31]          

167. Hashimoto H, Zhang X, Vertino PM, Cheng X (2015) The mechanisms of generation, recognition, and erasure of DNA 5-methylcytosine and thymine oxidations. J Biol Chem. 290: 20712-22 [Epub July 7]

166. Collins RE and Cheng X (2015) Methyl-Lysine Recognition by Ankyrin-Repeat Proteins. pp 101-124. In Histone Recognition, M.-M. Zhou (ed.), Springer International Publishing Switzerland. DOI 10.1007/978-3-319-18102-8_5

165. Cheng X and Trievel RC (2015) JmjC Lysine Demethylases. pp 210-245. In 2-Oxoglutarate-Dependent Oxygenases, RSC Metallobiology Series No. 3, Edited by Robert P Hausinger and Christopher J Schofield. The Royal Society of Chemistry. DOI:10.1039/9781782621959-00210

164. 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 [Epub Apr 6]

163. Pais JE, Dai N, Tamanaha E, Vaisvila R, Fomenkov AI, Bitinaite J, Sun Z, Guan S, Corrêa IR Jr, Noren CJ, Cheng X, Roberts RJ, Zheng Y, Saleh L. (2015) 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 [Epub Mar 23]

162. Myrick LK, Deng P, Hashimoto H, Oh YM, Cho Y, Poidevin MJ, Suhl JA, Visootsak J, Cavalli V, Jin P, Cheng X, Warren ST, Klyachko VA (2015) 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): 949-956 [Epub Jan 5]

161. Daugherty AB, Horton JR, Cheng X, Lutz S. (2015) Structural and functional consequences of circular permutation on the active site of old yellow enzyme. ACS Catal. 5: 892-899 [Epub 2014 Dec 9]

160. Myrick LK, Hashimoto H, Cheng X, Warren ST (2015) Human FMRP contains an integral tandem Agenet (Tudor) and KH motif in the amino terminal domain. Hum Mol Genet. 24(6): 1733-40 [Epub 2014 Nov 20]

159. 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 [Epub Sept 27]

158. 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 Sept 25]

157. 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 [Epub Sept. 21]

156. Cheng X, Roberts RJ (2014) Base Flipping. In: eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0002714.pub [Epub Aug 15]

155. Cheng X (2014) Structural and Functional Coordination of DNA and Histone Methylation. Cold Spring Harb Perspect Biol. 6(8). pii: a018747. doi:10.1101/cshperspect.a018747 [Epub Aug 1]

154. 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 (2014) Ectopic DNMT3L triggers assembly of a repressive complex for retroviral silencing in somatic cells. J Virol. 88(18): 10680-95 [Epub Jul 2]

153. 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 [Epub June 3]

152. 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 [Epub May 8]

151. 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 [Epub Mar 7]

150. 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 Feb 11]

149. Myrick LK, Nakamoto-Kinoshita M, Lindor NM, Kirmani S, Cheng X, Warren ST (2014) Fragile X syndrome due to a missense mutation. Eur J Hum Genet. doi: 10.1038/ejhg.2013.311. [Epub 2014 Jan 22]

148. 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 [Epub 2014 Jan 4]

147. 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 [Epub 2013 Dec. 25]

146. 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 Nov 15]

145. 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 [Epub May 13]

144. 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 (2013) A hypomorphic lsd1 allele results in heart development defects in mice. PLoS One. 8(4): e60913 [April 24]

143. Cheng X, Hashimoto H (2013) Mammalian DNA methyltransferase structural themes. Encyclopedia of Biological Chemistry 3: 6-10 [An updated version (2021) 3, pp. 330–335]

142. Sun Z, Terragni J, Borgaro JG, Liu Y, Yu L, Guan S, Wang H, Sun D, Cheng X, Zhu Z, Pradhan S, Zheng Y (2013) High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells. Cell Reports 3: 567-576 [Epub Jan 24]

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

140. Cheng X and Blumenthal RM (2013) Response to Mackay et al.: Is there a telltale RH fingerprint in zinc fingers that recognizes methylated CpG dinucleotides? TiBS 38(9), 423

139. 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 [Epub Jan 19]

138. 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 Oct 11]

137. 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 [Epub Sept 8]

136. 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 [Epub July 30]
This paper was published as the cover story in vol. 40(19) issue of NAR.

135. 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 [Epub June 27]

134. 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 [Epub Feb 22]

133. 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 [Epub Dec 29 2011]
This paper was published as the cover story in the February 24, 2012 issue of JMB.

132. 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. Nat Commun. 2: 533. doi: 10.1038/ncomms1549. [Epub Nov 15]

131. 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 (2011) 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat Neurosci. 14, 1607-16 [Epub Oct 30]

130. 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 [Epub Sept 9]

129. Upadhyaya AK, Horton JR, Du Y, Bai, Y, Cheng X, and Fu H (2013) Reply to Röglin et al.: Synchrotron radiation-induced covalent modification of 14-3-3ζ by diazene compounds containing pyridoxal phosphate. PNAS, 109 (18), E1054

128. Upadhyay AK, Horton JR, Zhang X, Cheng X (2011) Coordinated methyl-lysine erasure: structural and functional linkage of a Jumonji demethylase domain and a reader domain. Curr. Opin. Struct. Biol. 21, 750-760 [Epub Aug 25]

127. Cheng X, Blumenthal RM (2011) Epiphanies in epigenetics. Prog. Mol. Biol. Transl. Sci. 101, 1-21. (Preface for the volume - Modification of Nuclear DNA and its Regulatory Proteins, Cheng and Blumenthal, editors; ISBN 978-0-12-387685-0)

126. 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 [Epub April 22]
This paper was published as the cover story in the August 15, 2011 issue of NAR.

125. 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 [Epub March 23]

124. Horton JR, Upadhyay AK, Hashimoto H, Zhang X, Cheng X (2011) Structural basis for human PHF2 Jumonji domain interaction with metal ions. J. Mol. Biol. 406, 1-8 [Epub 2010 Dec 15]

123. 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. Nat Struct Mol Biol. 18, 42-48 [Epub 2010 Dec 12]

122. 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 [Epub 2010 Dec 5]

121. Upadhyay AK, Cheng X (2011) Dynamics of histone lysine methylation: structures of methyl writers and erasers. In Progress in Drug Research: Epigenetics and Disease (S. Gasser and E. Li, editors) 67, 107-124

120. Hashimoto H, Vertino PM, Cheng X (2010) Molecular coupling of DNA methylation and histone methylation. Epigenomics 2(5), 657-669

119. Cheng X, Hashimoto H, Horton JR, Zhang X (2010) Mechanisms of DNA methylation, methyl-CpG recognition, and demethylation in mammals. In: Handbook of Epigenetics: The New Molecular and Medical Genetics (Trygve Tollefsbol, editor). Oxford: Academic Press (ISBN: 978-0-12-375709-8) (DOI: 10.1016/B978-0-12-375709-8.00002-2) pp 9-24

118. 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 (2010) hNaa10p contributes to tumorigenesis by facilitating DNMT1-mediated tumor suppressor gene silencing. J Clin Invest. 120, 2920-30 [Epub July 1]

117. 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 [Epub Apr 28]
This paper was published as the cover story in the July 2, 2010 issue of JMB.

116. Cheng X and Blumenthal RM (2010) Coordinated Chromatin Control: Structural and Functional Linkage of DNA and Histone Methylation. Biochemistry 49, 2999-3008 [Epub March 8]
This paper was the ten most-accessed articles during the second quarter of 2010.

115. Cheng X and Roberts RJ (2010) Base Flipping. In: ENCYCLOPEDIA OF LIFE SCIENCES 2010, John Wiley & Sons, Ltd: Chichester [DOI: 10.1002/9780470015902.a0002714.pub2]

114. Collins R and Cheng X. (2010) A case study in cross-talk: the histone lysine methyltransferases G9a and GLP. Nucleic Acids Res. 38, 3503-11 [Epub Feb 16]

113. Horton JR, Upadhyay AK, Qi HH, Zhang X, Shi Y, Cheng X (2010) Enzymatic and structural basis for substrate specificity of a family of jumonji histone lysine demethylases. Nat Struct Mol Biol. 17, 38-43 [Epub 2009 Dec 20]

112. Z Qian, JR Horton, X Cheng, S Lutz (2009) Structural redesign of lipase B from Candida antarctica by circular permutation and incremental truncation. J. Mol. Biol. 393, 191-201 [Epub Aug 13]

111. D. Jia, X. Cheng (2009) Methylation on the nucleosome: from DNA to Histone. Nutrients and Epigenetics (CRC Press, editors: Sang Woon Choi and Simonetta Friso) pp 7-35

110. X. Cheng, R.M. Blumenthal (2009) Structural and Biochemical Advances in Mammalian DNA Methylation. Epigenomics (Springer publishers, Editors: Rob Martienssen, John Greally and Anne Ferguson-Smith) pp 85-100

109. T. Gao, R.E. Collins, J.R. Horton, X. Zhang, R. Zhang, A. Dhayalan, R. Tamas, A. Jeltsch, X. Cheng (2009) The ankyrin repeat domain of Huntingtin interacting protein 14 contains a surface aromatic cage, a potential site for methyl-lysine binding. Proteins 76, 772-7 [Epub April 8]

108. 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. Nat Struct Mol Biol. 16, 312-7 [Epub Feb 15]

107. Hashimoto H, Horton JR, Zhang X, Cheng X. (2009) UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications. Epigenetics 4, 8-14

106. Cheng X, Blumenthal RM (2008) Structures and activities of mammalian DNA methyltransferases. In DNA and RNA Modification Enzymes: Comparative Structure, Mechanism, Functions, Cellular Interactions and Evolution (Edited by: Henri Grosjean) ISBN: 978-1-58706-329-9

105. R.Z. Jurkowska, N. Ansbach, C. Urbanke, D. Jia, R. Reinhardt, W. Nellen, X. Cheng, A. Jeltsch (2008) Formation of nucleoprotein filaments by mammalian DNA methyltransferase Dnmt3a in complex with regulator Dnmt3L. Nucleic Acids Res. 36, 6656-63 [Epub Oct 22]

104. H. Hashimoto, J.R. Horton, X. Zhang, M. Bostick, S. Jacobsen, X. Cheng (2008) The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature 455, 826-829 [Epub Sept 3]

103. P. Rathert, A. Dhayalan, M. Murakami, X. Zhang, R. Tamas, R. Jurkowska, Y. Komatsu, Y. Shinkai, X. Cheng, A. Jeltsch (2008) Protein lysine methyltransferase G9a acts on non-histone targets. Nature Chem. Biol. 4, 344-346

102. K. Subramanian, D. Jia, P. Kapoor-Vazirani, D. R. Powell, R. E. Collins, D. Sharma, J. Peng, X. Cheng, P. M. Vertino (2008) Regulation of estrogen receptor alpha by the SET7 lysine methyltransferase. Mol. Cell 30, 336-47

101. X. Cheng, R.M. Blumenthal (2008) Mammalian DNA Methyltransferases: a Structural Perspective. Structure 16, 341-50

100. R. E. Collins, J. P. Northrop, J. R. Horton, D. Y. Lee, X. Zhang, M. R. Stallcup, X. Cheng (2008) The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules. Nature Struct. Mol. Biol. 15, 245-50 [Epub Feb 10] See News and Views by Brent and Marmorstein (2008) Ankyrin for methylated lysines. Nat Struct Mol Biol. 15, 221-2

99. P. Rathert, X. Zhang, C. Freund, X. Cheng, A. Jeltsch (2008) Analysis of the substrate specificity of the Dim-5 histone lysine methyltransferase using peptide arrays. Chemistry & Biology 15, 5-11

98. A. Dhayalan, T. P. Jurkowski, H. Laser, R. Reinhardt, D. Jia, X. Cheng, A. Jeltsch (2008) Mapping of protein-protein interaction sites by the ‘Absence of Interference’ approach. J. Mol. Biol. 376, 1091-99 [Epub Dec 23 2007]

97. P. Rathert, X. Cheng, A. Jeltsch (2007) Continuous enzymatic assay for histone lysine methyltransferases. BioTechniques 43, 602-608

96. T.C. Osborne, O. Obianyo, X. Zhang, X. Cheng, P.R. Thompson (2007) 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, 13370-81 [Epub Oct 26]

95. D. Jia, R. Jurkowska, X. Zhang, A. Jeltsch, X. Cheng (2007) Structure of Dnmt3a bound Dnmt3L suggests a model for de novo DNA methylation. Nature 449, 248-251 [Epub Aug 22]

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

93. SK. Ooi, C. Qiu, E. Bernstein, K. Li, D. Jia, Z. Yang, H. Erdjument-Bromage, P. Tempst, SP. Lin, C. D. Allis, X. Cheng, and T. H. Bestor (2007) DNMT3L Connects Unmethylated Lysine 4 of Histone H3 To De Novo Methylation of DNA. Nature 448, 714-717

92. K. Higashimoto, P. Kuhn, D. Desai, X. Cheng, W. Xu (2007) Phosphorylation-mediated inactivation of coactivator-associated arginine methyltransferase 1. PNAS 104, 12318-12323 [Epub July 17]

91. K. Liebert, J. R. Horton, S. Chahar, M. Orwick, X. Cheng, A. Jeltsch (2007) 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, 22848-22855 [Epub May 31]

90. D.Y. Lee, I. Ianculescu, D. Purcell, X. Zhang, X. Cheng and M.R. Stallcup (2007) Surface-scanning mutational analysis of protein arginine methyltransferase 1: roles of specific amino acids in methyltransferase substrate specificity, oligomerization, and coactivator function. Molecular Endocrinology 21, 1381-1393 [Epub Apr 10]

89. J.R. Horton, S.J. Elgar, S.I. Khan, X. Zhang, P.A. Wade, X. Cheng (2007) Structure of the SANT Domain from the Xenopus chromatin remodeling factor ISWI. Proteins 67, 1198-1202 [Epub March 21]

88. X. Cheng, X. Zhang (2007) Structural dynamics of protein lysine methylation and demethylation. Mutation Res. 618, 102-115 [Epub Jan 21]

87. H. Wu, J. R. Horton, K. Battaile, A. Allali-Hassani, F. Martin, H. Zeng, P. Loppnau, M. Vedadi, A. Bochkarev, A. N. Plotnikov, X. Cheng (2007) Structural basis of allele variation of human thiopurine-S-methyltransferase. Proteins 67, 198-208 [Epub Jan 22]

86. R.E. Collins, X. Cheng (2006) Structural and biochemical advances in mammalian RNAi. J. Cell. Biochem. 99, 1251-1266 [Epub Aug 22]
This review was published as the cover story in the December 1, 2006 issue of JCB.

85. J. Mercante, K. Suzuki, X. Cheng, P. Babitzke, T. Romeo (2006) Comprehensive alanine-scanning mutagenesis of Escherichia coli CsrA defines two subdomains of critical functional importance. J. Biol. Chem. 281, 31832-42 [Epub Aug 21]

84. X. Zhang, X. Cheng (2006) Structure of protein arginine methyltransferases. The Enzymes Vol. 24, pp 101-117

83. H.L. Schubert, R.M. Blumenthal, X. Cheng (2006) Protein methyltransferases: their distribution among the five structural classes of AdoMet-dependent methyltransferases. The Enzymes Vol. 24, pp 1-26

82. F. E. Reyes, J. R. Horton, J. E. Mullally, A. Heroux, X. Cheng, K. D. Wilkinson (2006) The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin. Cell 124, 1197-1208
(see minireview by J. Wade Harper and Brenda A. Schulman (2006) Structural Complexity in Ubiquitin Recognition. Cell 124, 11133-1136

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

80. 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

79. J.R. Horton, K. Sawada, M. Nishibori, and X. Cheng (2005) Structural basis for inhibition of histamine N-methyltransferase by diverse drugs. J. Mol. Biol. 353, 334-344
This paper is published as the cover story in the October 21, 2005 issue of JMB.

78. R. E. Collins, X. Cheng (2005) Structural domains in RNAi. FEBS Letters 579, 5841-5849 [Epub Aug 15]
One of the top 25 most downloaded articles of FEBS Letters in 2005 (Certified by Anthony Newman, Publishing editor for the journal)

77. S.C. Dillon, X. Zhang, R.C. Trievel, X. Cheng (2005) The SET-domain protein superfamily: protein lysine methyltransferases. Genome Biology 6(8): 227 [Epub Aug 2]

76. H. Gowher, X. Zhang, X. Cheng, A. Jeltsch (2005) Avidin-plate assay system for enzymatic characterization of a histone lysine methyltransferase. Analytic Biochemistry 342, 287-291 (Epub May 31)                               

75. J.R. Horton, K. Liebert, S. Hattman, A. Jeltsch, X. Cheng (2005) Transition from nonspecific to specific DNA interaction along the substrate recognition pathway of Dam methyltransferase. Cell, 121, 349-361 (featured in the 2005 annual report of the Advanced Photon Source at Argonne National Laboratory, p105)

74. 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

73. X. Cheng, R.E. Collins, X. Zhang (2005) Structural and sequence motifs of protein (histone) methylation enzymes. Ann. Rev. Biophys. Biomol. Struct. 34, 267-294

72. R.E. Collins, M. Tachibana, H. Tamaru, K.M. Smith, D. Jia, X. Zhang, E.U. Selker, Y. Shinkai, X. Cheng (2005) In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases. J. Biol. Chem. 280, 5563-5570 (epub on Dec. 6, 2004)

71. J.C. Amor, J. Swails, C. R. Roy, H. Nagai, A. Ingmundson, X. Cheng, R. A. Kahn (2005) The structure of RalF, an Arf guanine nucleotide exchange factor from Legionella penumophila, reveals the presence of a cap over the active site. J. Biol. Chem. 280, 1392-1400 (Epub on Nov. 1, 2004)

70. K. Sawada, Z. Yang, J.R. Horton, R.E. Collins, X. Zhang, and X. Cheng (2004) Structure of the conserved core of the Yeast Dot1p, a nucleosomal histone H3 lysine79 methyltransferase. J. Biol. Chem. 279, 43296-43306 (Epub on July 29, 2004).
This paper was published as the cover story in the October 8, 2004 issue of JBC.

69. J.R. Horton, G. Ratner, N.K. Banavali, N.Huang, Y. Choi, M.A. Maier, A.D. MacKerell , V.E. Marquez, X. Cheng (2004) Caught in the act: visualization of an Intermediate in the DNA base flipping pathway induced by HhaI methyltransferase. Nucleic Acids Res. 32, 3877-3886
This paper was published as the cover story in Vol. 32, No. 13 issue of NAR.

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

67. A. Dong, L. Zhou, X. Zhang, S. Stickel, R.J. Roberts, X. Cheng (2004) Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions. Biological Chemistry 385, 373-379

66. 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

65. J.R. Horton, R.M. Blumenthal, X. Cheng (2004) Restriction endonucleases: structure of the conserved catalytic and the role of metal ions in DNA cleavage. In Restriction Endonucleases. Serius: Nucleic Acids and Molecular Biology, Pingoud, A. (ed.) Springer-Verlag Berlin Heidelberg. Vol. 14. pp 361-392

64. Z. Yang, J.R. Horton, L. Zhou, Xu Jia Zhang, A. Dong, Xing Zhang, S.L. Schlagman, V. Kossykh, S. Hattman, X. Cheng (2003) Structure of the bacteriophage T4 DNA adenine methyltransferase. Nature Struct. Biol. 10, 849-855

63. X. Zhang, Z Yang, S.I. Khan, J.R. Horton, H. Tamaru, E.U. Selker, X. Cheng (2003) Structural Basis for the Product Specificity of Histone Lysine Methyltransferases. Molecular Cell 12, 177-185
See preview by: R. N. Dutnall (2003) Cracking the histone codes: one, two, three methyls, you’re out! Molecular Cell 12, 3-4

62. H. L. Schubert, R. M. Blumenthal, X. Cheng (2003) Many paths to methyltransfer: a chronicle of convergence. Trends Biochem. Sci. 28, 329-335

61. 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

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

59. X. Cheng and R. J. Roberts (2003) MHhaI and Base flipping (an essay appears in Benjamin Lewin’s web site at www.ergito.com submitted on 12/16/2002 and last revised on January 6, 2005)

58. P. Wu, C. Qiu, A. Sohail, X. Zhang, A. S. Bhagwat, X. Cheng (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

57. S. E. Whitehead, K. W. Jones, X. Zhang, X. Cheng, R. M. Terns, M. P. Terns (2002) 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, 48087-48093

56. R. M. Blumenthal and X. Cheng (2002) Restriction-Modification Systems. In Modern Microbial Genetics, 2nd edition (Yasbin R.E. and Streips U.N., eds.). New York: Wiley. ISBN 0-471-38665-0 657pp

55. J. Min, X. Zhang, X. Cheng, S. I. S. Grewal, R. Xu (2002) Structure of the SET domain histone lysine methyltransferase Clr4. Nature Struct. Biol. 9, 828-832

54. X. Zhang, H. Tamaru, S. I. Khan, J. R. Horton, L. J. Keefe, E. U. Selker, X. Cheng (2002) Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase. Cell 111, 117-127

53. L. Zhou, X. Cheng, B. A. Connolly, M. J. Dickman, P. J. Hurd, D. P. Hornby (2002) Zebularine: a novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferases. J. Mol. Biol. 321, 591-599

52. Y.-H. Lee, S.S. Koh, X. Zhang, X. Cheng and M.R. Stallcup (2002) Synergy among nuclear receptor coactivators: selective requirement for protein methyltransferase and acetyltransferase activities. Mol. Cell. Biol. 22, 3621-3632

51. X. Cheng and R.M. Blumenthal (2002) Cytosines do it, thymines do it, even pseudouridines do it – base flipping by an enzyme that acts on RNA. Structure 10, 127-130

50. D.M. Green, K.A. Marfatia, E.B. Crafton, X. Zhang, X. Cheng, A.H. Corbett (2002) Nab2p is required for poly(A) RNA export in Saccharomyces cerevisiae and is regulated by arginine methylation via Hmt1p. J. Biol. Chem. 277, 7752-7760

49. 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

48. J.R. Horton, K. Sawada, M. Nishibori, X. Zhang, X. Cheng (2001) Two polymorphic forms of human histamine methyltransferase: structural, thermal and kinetic comparisons. Structure, 837-849
This paper was published as the cover story in the September 2001 issue of Structure.

47. J.C. Amor, J.R. Horton, X. Zhu, Y. Wong, C. Sullards, D. Ringe, X. Cheng, R.A. Kahn (2001) 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, 42477-42484                                                                                         

46. X. Cheng and R.J. Roberts (2001) AdoMet-dependent methylation, DNA methyltransferases, and base flipping. Nuclear Acids Res. 29, 3784-3795.

45. R. M. Blumenthal and X. Cheng (2001) A Taq attack displaces bases. Nature Struct. Biol. 8, 101-103

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

43. X. Cheng and R. J. Roberts (2000) Base flipping. Encyclopedia of Life Sciences / 2001 Nature Publishing Group / www.els.net (number of pages: 6)

42. G. Vilkaitis, A. Dong, E. Weinhold, X. Cheng, S. Klimasauskas (2000) Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase. J. Biol. Chem. 275, 38722-38730

41. J. R. Horton and X. Cheng (2000) PvuII Endonuclease contains two calcium ions in active sites. J. Mol. Biol. 300, 1051-1058

40. X. Zhang, L. Zhou, X. Cheng (2000) Crystal structure of the conserved core of the protein arginine methyltransferase PRMT3. EMBO J. 19, 3509-3519

39. V. E. Marquez, A. Goddard, E. Alvarez, H. Ford Jr., J. K. Christman, G. Sheikhnejad, A. Brank, C. J. Marasco, J. R. Suffrin, M. O’Gara, X. Cheng (1999) 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

38. E. B. Fauman, R. M. Blumenthal, X. Cheng (1999) Structure and evolution of AdoMet-dependent methyltransferases.  In X. Cheng and R. M. Blumenthal (eds.) AdoMet-dependent methyltransferases: structures and functions. (New Jersey: World Scientific. ISBN 981-02-3870-3 420pp) pp. 1-38

37. Y. Liu, W. Gong, C. C. Huang, W. Herr, X. Cheng (1999) Crystal structure of the conserved core of the HSV transcriptional regulatory protein VP16.  Genes & Dev. 13, 1692-1703

36. M. O’Gara, X. Zhang, R. J. Roberts, X. Cheng (1999) Structure of a binary complex of HhaI methyltransferase with S-adenosyl-l-methionine formed in the presence of a short nonspecific DNA oligonucleotide. J. Mol. Biol. 287, 201-210

35. G. Sheikhnejad, A. Brank, J. K. Christman, A. Goddard, E. Alvarez, H. Ford, Jr., V. E. Marquez, C. J. Marasco, J. R. Sufrin, M. O’Gara, X. Cheng (1999) Mechanism of inhibition of DNA-(cytosine C5) methyltransferases by oligodeoxyribonucleotides containing 5, 6-dihydro-5-azacytosine. J. Mol. Biol. 285, 2021-2034

34. J.R. Horton, H.G. Nastri, P.D. Riggs, X. Cheng (1998) Asp34 of PvuII endonuclease is directly involved in DNA minor groove recognition and indirectly involved in catalysis. J. Mol. Biol. 284, 1491-1504

33. J.R. Horton, J. Bonventre, X. Cheng (1998) How is modification of the DNA substrate recognized by the PvuII restriction endonuclease?  Biol. Chem. 379, 451-458

32. 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, 872-877

31. R.J. Roberts and X. Cheng (1998) Base flipping. Annu. Rev. Biochem. 67, 181-198

30. R.S. Lloyd and X. Cheng (1997) Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping. Biopoly. 44, 139-151

29. S. Kumar, J.R. Horton, G. D. Jones, R. T. Walker, R. J. Roberts, X. Cheng (1997) DNA containing 4'-thio-2-deoxycytidine inhibits the methylation of HhaI methyltransferase. Nucleic Acids Res. 25, 2773-2783

28. 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
This paper was published as the cover story in the 15 July 1997 issue of Nucleic Acids Research.

27. M. O’Gara, G. M. Adams, W. Gong, R. Kobayashi, R.M. Blumenthal, X. Cheng (1997) Expression, purification, masspectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific). Eur J. Biochem. 247, 1009-1018

26. R. Xu, L. Jokhan, X. Cheng, A. Mayeda, A.R. Krainer (1997) Crystal structure of human UP1, the domain of hnRNP A1 that contains two RNA-recognition motifs.  Structure 5, 559-570

25. R. Xu, C. Koch, Y. Liu, J. R. Horton, D. Knapp, K. Nasmyth, X. Cheng (1997) Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell cycle control of DNA synthesis. Structure 5, 349-358

24. M. O’Gara, R.J. Roberts, X. Cheng (1996) A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase. J. Mol. Biol. 263, 597-606
This paper was published as the cover story in the 8 November 1996 issue of J. Mol. Biol.

23. M. O’Gara, S. Klimasauskas, R.J. Roberts, X. Cheng (1996) Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaI methyltransferase-DNA-AdoHcy complexes. J. Mol. Biol.  261, 634-645
This paper was published as the cover story in the 6 September 1996 issue of J. Mol. Biol.

22. X. Cheng and R.M. Blumenthal (1996) Finding a basis for flipping bases. Structure 4, 639-645

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

20. R. Xu, G. Carmel, R.M. Sweet, J. Kuret, X. Cheng (1995) Crystal structure of casein kinase-1, a phosphate-directed protein kinase. EMBO J. 14, 1015-1023
This paper was published as the cover story in the March 1, 1995 issue of EMBO J.

19. T. Malone, R.M. Blumenthal, X. Cheng (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, 618-632

18. G. Schluckebier, M. O’Gara, W. Saenger, X. Cheng (1995) Universal catalytic domain structure of AdoMet-dependent methyltransferases. J. Mol. Biol. 247, 16-20

17. X. Cheng (1995) Structure and function of DNA methyltransferases. Annu. Rev. Biophys. Biomol. Struct. 24, 293-31816.  

16. X. Cheng (1995) DNA modification by methyltransferases. Curr. Opin. Struc. Biol. 5, 4-10

15. X. Cheng, K.  Balendiran, I. Schildkraut, J. Anderson (1995) Crystal structure of the PvuII restriction endonuclease. Gene 157, 139-140

14. M. O’Gara, K. McCloy, T. Malone, X. Cheng (1995) Structure-based sequence alignment of three AdoMet-dependent methyltransferases. Gene 157, 135-138

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

12. X. Cheng, X. Zhang, J. W. Pflugrath, F. W. Studier (1994) The structure of bacteriophage T7 lysozyme, a zinc amidase and an inhibitor of T7 RNA polymerase. Proc. Natl. Acad. Sci. USA 91, 4034-4038

11. G. Carmel, B. Leichus, X. Cheng, S. D. Patterson, U. Mirza, B. T. Chait, J. Kuret (1994) Expression, purification, crystallization, and preliminary X-ray analysis of casein kinase-1 from Schizosaccharomyces pombe. J. Biol. Chem. 269, 7304-7309

10. S. Kumar, X. Cheng, S. Klimasauskas, S. Mi, J. Posfai, R. J. Roberts, G. G. Wilson (1994) The DNA (cytosine-5) Methyltransferases. Nucleic Acids Res. 22, 1-10

9. S. Klimasauskas, S. Kumar, R. J. Roberts, X. Cheng (1994) HhaI methyltransferase flips its target base out of the DNA helix. Cell 76, 357-369
This paper was published as the cover story in the January 28, 1994 issue of Cell, and was honored as the cover of the journal Nucleic Acids Research throughout 1994.

8. X. Cheng, S. Kumar, S. Klimasauskas, R. J. Roberts (1993) Crystal structure of the HhaI DNA methyltransferase. Cold Spring Harbor Symp. Quan. Biol. 58, 331-338

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

6. S. Kumar, X. Cheng, J. W. Pflugrath, R. J. Roberts (1992). Purification, crystallization, and preliminary X-ray diffraction analysis of an M.HhaI-AdoMet complex. Biochemistry 31, 8648-8653

5. B. P. Schoenbom and X. Cheng (1991) The localization of solvent in protein crystals. In Protein: Structure, Dynamics and Design (ed. Renugopalakrishnan et al., ESCOM, Leiden) pp.  367-371

4. X. Cheng and B. P. Schoenbom (1991) Repulsive restraints for hydrogen bonding in least-squares refinement of protein crystals. Acta Cryst. A47, 314-317

3. X. Cheng and B. P. Schoenbom (1991) Neutron diffraction study of carbonmonoxymyoglobin. J. Mol. Biol.  220, 381-399

2. X. Cheng and B. P. Schoenbom (1990) Hydration in protein crystals. A neutron diffraction analysis of carbonmonoxymyoglobin. Acta Cryst.  B46, 195-208

1981 (Fudan University)

1. Z. Xu and X. Cheng (1981) The mass of neutrino and the Schwarzchild’s internal solution when l not equal to 0”. Journal of Central China Normal University (Natural Sciences Edition, in Chinese), 2