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 https://doi.org/10.1101/2023.03.19.533378.
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 https://doi.org/10.1101/2023.03.03.531011. Cell, in press.
Garg A, On KF, Xiao Y, Elkayam E, Cifani P, David Y, Joshua-Tor L. The molecular basis of Human FN3K mediated phosphorylation of glycated substrate. bioRxiv. 2024 Aug. Nat Commun. 2025 Jan 22;16(1):941. doi: 10.1038/s41467-025-56207-z.
Quarto G, … David Y, Morey L, Jeschke J, Deplus R, Collignon E, Fuks F. Cell. 2025 Jan 15:S0092-8674(24)01422-3. doi: 10.1016/j.cell.2024.12.009. Online ahead of print.
Zheng Q, Bastle RM, Zhao S, Kong L, Vostal L, Ramakrishnan A, Shen L, Fulton SL, Wang H, Zhang B, Upad A, Dierdorff L, 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. Nature. 2025 Jan;637(8047):974-982. doi: 10.1038/s41586-024-08371-3. Epub 2025 Jan 8.
Wortzel I, Akano I, Seo Y, Hebert J, … David Y#, Kim HS# and Lyden D#. Unique structural configuration of EV-DNA primes anti-tumor immunity to prevent metastatic progression. Nat Cancer. 2024 Dec;5(12):1815-1833. doi: 10.1038/s43018-024-00862-6. Epub 2024 Dec 3.
Tiedemann RL, Hrit J, Du Q, Wiseman AK, Eden HE, Dickson BM, Kong X, Chomiak AA, Vaughan RM, Hebert JM, David Y, Zhou W, Baylin SB, Jones PA, Clark SJ, Rothbart SB. UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation. Nucleic Acids Res. 2024 Dec 11;52(22):13733-13756. doi: 10.1093/nar/gkae1105.
Feierman ER, Louzon S, Prescott NA, Biaco T, Gao Q, Qiu Q, Choi K, Palozola KC, Voss AJ, Mehta S, Quaye C, Lynch K, Fuccillo M, Wu H, David Y, Korb E. Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory. Mol Cell. 2024 Aug 8;84(15):2822-2837.e11. doi: 10.1016/j.molcel.2024.06.025. Epub 2024 Jul 17.
Agustinus AS, David Y. Thinking outside the chromosome: epigenetic mechanisms in non-canonical chromatin species. Nat Struct Mol Biol 2024 Jan;31(1):8-10. doi: 10.1038/s41594-023-01200-7.
Agustinus A,…David Y#, Bakhoum S#. Epigenetic dysregulation from chromosomal transit in micronuclei. Nature. 2023 Jul;619(7968):176-183. doi: 10.1038/s41586-023-06084-7. Epub 2023 Jun 7
Corless BC, Geißen R, Prescott NA, David Y, Scheinberg DA, Tan DS. Chemoenzymatic Synthesis of Novel Cytotoxic Epoxyketones Using the Eponemycin Biosynthetic Enzyme EpnF. ACS Chem Biol. 2023 Jun 16;18(6):1360-1367. doi: 10.1021/acschembio.3c00080. Epub 2023 May 12.
Pihl R, Zheng Q#, David Y#. Nature-inspired Protein Ligation and Its Applications. Invited review, Nature Reviews in Chemistry. 2023 Apr;7(4):234-255. doi: 10.1038/s41570-023-00468-z. Epub 2023 Feb 21.
Knoerlein A, Xiao Y, and David Y. Histone Glycation as a New Avenue 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.
Pluta R, Aragón E, Prescott NA, Ruiz L, Mees R, Baginski B, Flood JR, Martin-Malpartida P, Massagué J, David Y, and Macias MJ. Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1. Nature Commun. 2022 Nov 26;13(1):7279. doi: 10.1038/s41467-022-34925-y.
Ray DM, Flood JR, David Y. Harnessing Split-Inteins as a Tool for the Selective Modification of Surface Receptors in Live Cells. Chembiochem. 2022 Sep 30:e202200487. doi: 10.1002/cbic.202200487. Online ahead of print.
Nguyen T, Li S, Chang J, Watters J, Ng H, Osunsade A, David Y, Liu S. Chromatin sequesters Sox2 pioneer factor from exerting condensation-driven mechanical stress on DNA. Nature Commun, 2022 Jul 9;13(1):3988. doi: 10.1038/s41467-022-31738-x.
Leicher R, Osunsade A, Chua GNL, Faulkner SC, Latham AP, Watters JW, Nguyen T, Beckwitt EC, Christodoulou-Rubalcava S, Young PG, Zhang B, David Y, Liu S. Single-stranded nucleic acid binding and coacervation by linker histone H1. Nat Struct Mol Biol. 2022 Apr 28. doi: 10.1038/s41594-022-00760-4. Epub ahead of print. PMID: 35484234.
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. https://www.biorxiv.org/content/10.1101/2022.01.12.475944v1. In Revision.
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.https://pubs.acs.org/doi/10.1021/acschembio.1c00864.
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 . In press.
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
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.
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.
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.
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
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
Zheng Q, Osunsade A, David Y. Protein arginine deiminase 4 antagonizes methlyglyoxal-induced histone glycation. Nat Commun. 2020 Jun 26;11(1):3241. doi: 10.1038/s41467-020-17066-y.
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 Jun 3;142(22):9999-10007. doi: 10.1021/jacs.0c01325. Epub 2020 May 22.
Zheng Q, Maksimovic I, Upad A, David Y. Non-enzymatic covalent modifications: a new link between metabolism and epigenetics. Protein Cell. 2020 Jun;11(6):401-416. doi: 10.1007/s13238-020-00722-w. Epub 2020 Apr 30. Free PMC article. Review.
Prescott NA, David Y. In Vivo Histone Labeling Using Ultrafast trans-Splicing Inteins. Methods Mol Biol. 2020;2133:201-219. doi: 10.1007/978-1-0716-0434-2_10.
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 Feb 7;85(3):1691-1697. doi: 10.1021/acs.joc.9b02504. Epub 2020 Jan 7.
Maksimovic I, Ray D, Zheng Q and David Y. Utilizing intein trans-splicing for in vivo generation of site-specifically modified proteins. Methods in Enzymology. 2019;626:203-222. doi: 10.1016/bs.mie.2019.07.015. Epub 2019 Aug 2.
Prescott NA and David Y. Utilizing intein trans-splicing for in vivo generation of site-specifically modified proteins. Methods in Molecular Biology. 2020;2133:201-219. doi: 10.1007/978-1-0716-0434-2_10.
Maksimovic I, Ray D, Zheng Q and David Y. Utilizing intein trans-splicing for in vivo generation of site-specifically modified proteins. Methods in Enzymology. doi.org/10.1016/bs.mie.2019.07.015
Prescott NA and David Y. Utilizing intein trans-splicing for in vivo generation of site-specifically modified proteins. Methods in Molecular Biology. In press.
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 Mar 20;10(1):1289. doi: 10.1038/s41467-019-09192-z
Zheng Q, Prescott NA, Maksimovic I, David Y. (De)Toxifying the Epigenetic Code. Chem Res Toxicol. 2019 Mar 18. doi: 10.1021/acs.chemrestox.9b00013.
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. 2018 Dec 26. doi: 10.1021/acs.biochem.8b01060.
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 Oct;13(10):1081-1087. doi: 10.1038/nchembio.2453. Epub 2017 Aug 7.
David Y, Muir TW. Emerging Chemistry Strategies for Engineering Native Chromatin J Am Chem Soc. 2017 Jul 12;139(27):9090-9096. doi: 10.1021/jacs.7b03430. Epub 2017 Jun 27.
Liszczak GP, Brown ZZ, Kim SH, Oslund RC, David Y, Muir TW. Genomic targeting of epigenetic probes using a chemically tailored Cas9 system. PNAS. 2017 Jan 24;114(4):681-686
Matthew Holt, Yael_David, Sam Pollock, Zhanyun Tang, Jongcheol Jeon, Jaehoon Kim, Robert G. Roeder and Tom W. Muir. Identification of a Functional Hotspot on Ubiquitin Required for Stimulation of Methyltransferase Activity on Chromatin. Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10365-70.
Yael David, Miquel Vila-Perello, Shivam Verma and Tom Muir. Chemical Tagging and Customizing of Cellular Chromatin States using Ultrafast Trans-Splicing Inteins. Nature Chemistry. 2015 May;7(5):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’.
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 Jan 15;10(1):e0115344
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. Nature Methods. 2014 Aug;11(8):834-40
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 Biol Chem. 2014 Feb 28;289(9):5609-18
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 Nov;26(11):4495-505.
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 Dec 23;286(51):44104-15
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 Aug 4;585(15):2405-9
David Y, Ziv T, Admon A, Navon A. The E2 Ubiquitin Conjugating Enzymes Direct Polyubiquitination to Preferred Lysines. J Biol Chem. 2010 Mar 19;285(12):8595-604. 10.
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 Oct 25;26(49):6968-78