Publications
*=Co-first, #=Co-corresponding.
39. Finkin-Groner E, Al-Kachak A, Agustinus A, Bastle R, Lepack A, Lyu Y, Maze I#, David Y#.Flexible and site-specific manipulation of histones in live animals. bioRxiv. 2023 Mar 20:2023.03.19.533378. doi: 10.1101/2023.03.19.533378. Preprint. https://www.biorxiv.org/content/10.1101/2023.03.19.533378v1.
38. Prescott NA, Mansisidor A, Bram Y, Lemmon AA, Lim C, Risca VI, Schwartz RE#, David Y#.A nucleosome switch primes Hepatitis B Virus infection. bioRxiv. 2023. https://www.biorxiv.org/content/10.1101/2023.03.03.531011v1. In revision.
37. Zheng Q, Bastle RM, Zhao S, Kong L, Vostal L, Ramakrishnan A, Shen L, Fulton SL, Wang H, Zhang B, Thompson RE, Molina H, Stransky S, Sidoli S, Muir TW, Li H#, David Y#, Maze I#. Histone monoaminylation dynamics are regulated by a single enzyme and promote neural rhythmicity. bioRxiv. 2022. https://www.biorxiv.org/content/10.1101/2022.12.06.519310v1. In revision.
36. Agustinus A, Raviram R, Dameracharla B, Luebeck J, Stransky S, Scipioni L, Myers R, Di Bona M, Duran M, Weigelt B, Yomtoubian S, Toufektchan E, Mischel P, Mittal V, Shah S, Maciejowski J, Gratton E, Ly P, Bakhoum M, Landau D, Bafna V, Sidoli S, David Y#, Bakhoum S#. Epigenetic dysregulation from chromosomal transit in micronuclei. bioRxiv. 2022 .https://www.biorxiv.org/content/10.1101/2022.01.12.475944v1. Nature. 2023 Jul;619(7968):176-183. doi: 10.1038/s41586-023-06084-7. Epub 2023 Jun 7.
35. Corless BC, Geißen R, Prescott NA, David Y, Scheinberg DA, Tan DS. Chemoenzymatic Synthesis of Novel Cytotoxic Epoxyketones Using the Eponemycin Biosynthetic Enzyme EpnF. https://pubmed.ncbi.nlm.nih.gov/37172287/. ACS Chem Biol. 2023 Jun 16;18(6):1360-1367. doi: 10.1021/acschembio.3c00080.Epub 2023 May 12.
34. Pihl R, Zheng Q#, David Y#.Nature-inspired protein ligation and its applications. https://www.nature.com/articles/s41570-023-00468-z. Nat Rev Chem. 2023 Apr;7(4):234-255. doi: 10.1038/s41570-023-00468-z. Epub 2023 Feb 21.
33. Knörlein A, Xiao Y, David Y#. Leveraging histone glycation for cancer diagnostics and therapeutics. Trends Cancer. 2023 May;9(5):410-420. doi: 10.1016/j.trecan.2023.01.005. Epub 2023 Feb 18. https://www.sciencedirect.com/science/article/pii/S2405803323000079?via%3Dihub.
32. Pluta R, Aragón E, Prescott NA, Ruiz L, Mees RA, Baginski B, Flood JR, Martin-Malpartida P, Massagué J, David Y, Macias MJ.
Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1. Nat Commun. 2022 Nov 26;13(1):7279. doi: 10.1038/s41467-022-34925-y. https://www.nature.com/articles/s41467-022-34925-y.
31. Ray D*, Jennings E*, Maksimovic I, Chai X, Galligan J#, David Y#, Zheng Q#. Chemical Labeling and Enrichment of Histone Glyoxal Adducts.. ACS Chem Bio, 2022.https://pubs.acs.org/doi/10.1021/acschembio.1c00864
30. Leicher R* , Osunsade A*, Chua G*, Faulkner S*, Latham A, Watters J, Nguyen T, Beckwitt E, Christodoulou-Rubalcava S, Young P, Zhang B, David Y# and Liu S#. https://www.biorxiv.org/content/10.1101/2021.03.17.435841v1. Nature Structure & Molecular Biology, 2022. In press.
29. Maksimovic I, Finkin-Groner E, Fukase Y, Zheng Q, Sun S, Michino M, Huggins DJ, Myers RW, David Y#. Deglycase-activity oriented screening to identify DJ-1 inhibitors. RSC Med Chem. 2021 Jun 2;12(7):1232-1238. doi: 10.1039/d1md00062d. eCollection 2021 Jul 21
28. Wu A., Zhi J., Tian T., Cihan A., Cevher MA., Liu Z., David Y., Muir TW., Roeder RG., Yu M. DOT1L complex regulates transcriptional initiation in human erythroleukemic cells. Proc Natl Acad Sci U S A. 2021 Jul 6;118(27):e2106148118. doi: 10.1073/pnas.2106148118.
27. Faulkner S., Maksimovic I. and David Y#. A chemical field guide to histone nonenzymatic modifications. Current Opinion in Chemical Biology, 2021 Jun 19;63:180-187. doi: 10.1016/j.cbpa.2021.05.002.
26. Maksimovic I. and David Y#. Non-enzymatic Covalent Modifications as a New Chapter in the Histone code. Trends in Biochemical Sciences, May 5:S0968-0004(21)00070-0. doi: 10.1016/j.tibs.2021.04.004. Online ahead of print.
25. Yusufova, N., Kloetgen, A., Teater, M. et al. Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture. Nature, 2021 Jan;589(7841):299-305. doi: 10.1038/s41586-020-3017-y. PMID: 33299181
24. Willcockson, M.A., Healton, S.E., Weiss, C.N. et al. H1 histones control the epigenetic landscape by local chromatin compaction. Nature, 2021 Jan;589(7841):293-298. doi: 10.1038/s41586-020-3032-z. PMID: 33299182
23. Zheng Q, Osunsade A, David Y#. Protein arginine deiminase 4 antagonizes methylglyoxal-induced histone glycation. Nat. Commun. 11, 3241. 2020 Jun 26;11(1):3241. doi: 10.1038/s41467-020-17066-y. PMID: 32591537
22. Maksimovic I, Zheng Q, Trujillo MN, Galligan JJ, David Y#. An azidoribose probe to track ketoamine adducts in histone ribose glycation. J. Am. Chem. Soc. 2020, 142, 22, 9999–10007.
Highlighted in Synfacts and recommended in Faculty Opinions
21. Zheng Q, Maksimovic I, Upad A, David Y#. Non-enzymatic covalent modifications: a new link between metabolism and epigenetics. Protein & Cell, 2020, 11, 401-416.
Highlighted as a Cover Story.
Featured in Today's Science Sparks on the library website of MSKCC (June 12th, 2020).
20. Prescott NA, David Y#. In vivo histone labeling using ultrafast trans-splicing inteins. Methods Mol. Biol., 2020, 2133, 201-219.
19. Zheng Q, Maksimovic I, Upad A, Guber D, David Y#. Synthesis of an alkynyl methylglyoxal probe to investigate nonenzymatic histone glycation. J. Org. Chem., 2020, 85, 1691-1697.
Part of the Modern Peptide and Protein Chemistry special issue.
18. Prescott NA, Bram Y, Schwartz RE, David Y#. Targeting hepatitis B virus covalently closed circular DNA and hepatitis B virus X protein: Recent advances and new approaches. ACS Infect. Dis., 2019, 5, 1657-1667.
17. Maksimovic I, Ray D, Zheng Q, David Y#. Utilizing intein trans-splicing for in vivo generation of site-specifically modified proteins. Methods Enzymol., 2019, 626, 203-222.
16. Zheng Q, Omans ND, Leicher R, Osunsade A, Agustinus AS, Finkin-Groner E, D’Ambrosio H, Liu B, Chandarlapaty S, Liu S, David Y#. Reversible histone glycation is associated with disease-related changes in chromatin architecture. Nat. Commun., 2019, 10, 1289.
Selected by Nat. Commun. Editors’ Highlights.
Selected to 10 Remarkable Basic Science Breakthroughs of MSKCC in 2019.
Highlighted by Diao X. Histone glycation: Linking metabolic perturbation with epigenetic misregulation in cancer. AIMS Genet., 2019, 6, 14-16.
15. Zheng Q, Prescott NA, Maksimovic I, David Y#. (De)Toxifying the epigenetic code. Chem. Res. Toxicol., 2019, 32, 796-807.
Part of the Epigenetics in Toxicology special issue.
14. Osunsade A, Prescott NA, Hebert JM, Ray DM and David Y#. A robust method for the purification and characterization of the human histone H1 variants. Biochemistry, 2019, 58, 171-176.
Part of Future of Biochemistry: The International Issue.
13. Oslund RC, Su X, Haugbro M, Kee JM, Esposito M, David Y, Wang B, Ge E, Perlman DH, Kang Y, Muir TW, Rabinowitz JD. Bisphosphoglycerate mutase controls serine pathway flux via 3-phosphoglycerate. Nat. Chem. Biol., 2017, 13, 1081-1087.
12. David Y#, Muir TW#. Emerging chemistry strategies for engineering native chromatin. J. Am. Chem. Soc., 2017, 139, 9090-9096.
11. Liszczak GP, Brown ZZ, Kim SH, Oslund RC, David Y, Muir TW. Genomic targeting of epigenetic probes using a chemically tailored Cas9 system. Proc. Natl. Acad. Sci. USA., 2017, 114, 681-686.
10. Holt M, David Y, Pollock S, Tang Z, Jeon J, Kim J, Roeder RG, Muir TW. Identification of a functional hotspot on ubiquitin required for stimulation of methyltransferase activity on chromatin. Proc. Natl. Acad. Sci. USA., 2015, 112, 10365-10370.
9. David Y, Vila-Perelló M, Verma S, Muir TW. Chemical tagging and customizing of cellular chromatin states using ultrafast trans-splicing inteins. Nat. Chem. 2015, 7, 394-402.
Featured in Nature Methods Research Highlights: Doerr A, ‘Chemical Biology: Tinkering with chromatin’. Nature Methods. 2015 May:12, 491.
Featured in Nature Chemistry News and Views: Fischle W, Schwarzer D, Mootz HD. ‘Chemical biology: Chromatin chemistry goes cellular’. Nature Chemistry. 2015 May;7(5):371-3
Featured in EurekAlert AAAS, PhysOrg Science news (Chemistry), Science Newsline and others: Nguyen T. ‘Decoding the cell’s genetic filing system’.
8. Altun M, Walter TS, Kramer HB, Herr P, Iphöfer A, Boström J, David Y, Komsany A, Ternette N, Navon A, Stuart DI, Ren J, Kessler BM. The human otubain2-ubiquitin structure provides insights into the cleavage specificity of poly-ubiquitin-linkages. PLoS One, 2015, 10, e0115344.
7. Nguyen UT, Bittova L, Müller MM, Fierz B, David Y, Houck-Loomis B, Feng V, Dann GP, Muir TW. Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Nat. Methods, 2014, 11, 834-840.
6. Berko D, Herkon O, Braunstein I, Isakov E, David Y, Ziv T, Navon A, Stanhill A. Inherent asymmetry in the 26S proteasome is defined by the ubiquitin receptor RPN13. J. Bio. Chem., 2014, 289, 5609-5618.
5. Shahar-Pomerantz Y, Elbaz J, Kirenberg I, Reizel Y, David Y, Galiani D, Nevo N, Navon A, Dekel N. From ubiquitin-proteasomal degradation to CDK1 inactivation: Requirements for the first polar body extrusion in mouse oocytes. FASEB J., 2012, 26, 4495-4505.
4. David Y*, Ternette N*, Edelmann M, Ziv T, Gayer B, Sertchook R, Dadon Y, Kessler BM, Navon A. E3 ligases determine the ubiquitination site and chain type by enforcing specificity on E2 enzymes. J. Biol. Chem., 2011, 286, 44104-44115.
3. Shimshon L, Michaeli A, Hadar R, Nutt SL, David Y, Navon A, Waisman A, Tirosh B. SUMOylation of Blimp-1 promotes its proteasomal degradation. FEBS Lett., 2011, 585, 2405-2409.
2. David Y, Ziv T, Admon A, Navon A. The E2 ubiquitin conjugating enzymes direct polyubiquitination to preferred lysines. J. Biol. Chem., 2010, 285, 8595-8604.
1. Shtiegman K, Kochupurakkal BS, Zwang Y, Pines G, Starr A, Vexler A, Citri A, Katz M, Lavi S, Ben-Basat Y, Benjamin S, Corso S, Gan J, Yosef RB, Giordano S, Yarden Y. (2007) Defective ubiquitylation of EGFR mutants of lung cancer confers prolonged signaling. Oncogene, 2007, 26, 6968-6978.