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For: Wang T, Holt MV, Young NL. Early butyrate induced acetylation of histone H4 is proteoform specific and linked to methylation state. Epigenetics 2018;13:519-535. [PMID: 29940793 DOI: 10.1080/15592294.2018.1475979] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]  Open
Number Cited by Other Article(s)
1
Chowdhury T, Cupp-Sutton KA, Guo Y, Gao K, Zhao Z, Burgett A, Wu S. Quantitative Top-down Proteomics Revealed Kinase Inhibitor-Induced Proteoform-Level Changes in Cancer Cells. J Proteome Res 2025;24:303-314. [PMID: 39620430 DOI: 10.1021/acs.jproteome.4c00778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
2
Poncha KF, Paparella AT, Young NL. Normalized and Directional Interplay Scoring for the Interrogation of Proteoform Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.18.624157. [PMID: 39605462 PMCID: PMC11601473 DOI: 10.1101/2024.11.18.624157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
3
Phillips M, Malone KL, Boyle BW, Montgomery C, Kressy IA, Joseph FM, Bright KM, Boyson SP, Chang S, Nix JC, Young NL, Jeffers V, Frietze S, Glass KC. Impact of Combinatorial Histone Modifications on Acetyllysine Recognition by the ATAD2 and ATAD2B Bromodomains. J Med Chem 2024;67:8186-8200. [PMID: 38733345 PMCID: PMC11149620 DOI: 10.1021/acs.jmedchem.4c00210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
4
Taylor BC, Steinthal LH, Dias M, Yalamanchili HK, Ochsner SA, Zapata GE, Mehta NR, McKenna NJ, Young NL, Nuotio-Antar AM. Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress. Epigenetics Chromatin 2024;17:12. [PMID: 38678237 PMCID: PMC11055387 DOI: 10.1186/s13072-024-00536-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024]  Open
5
Taylor BC, Steinthal LH, Dias M, Yalamanchili HK, Ochsner SA, Zapata GE, Mehta NR, McKenna NJ, Young NL, Nuotio-Antar AM. Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.30.551059. [PMID: 38328142 PMCID: PMC10849524 DOI: 10.1101/2023.07.30.551059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
6
Silva-Ochoa AD, Velasteguí E, Falconí IB, García-Solorzano VI, Rendón-Riofrio A, Sanguña-Soliz GA, Vanden Berghe W, Orellana-Manzano A. Metabolic syndrome: Nutri-epigenetic cause or consequence? Heliyon 2023;9:e21106. [PMID: 37954272 PMCID: PMC10637881 DOI: 10.1016/j.heliyon.2023.e21106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 09/08/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023]  Open
7
Ho YH, Huang R. Effects of Oncohistone Mutations and PTM Crosstalk on the N-Terminal Acetylation Activities of NatD. ACS Chem Biol 2023;18:693-700. [PMID: 35044762 PMCID: PMC9294072 DOI: 10.1021/acschembio.1c00840] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
8
Taylor BC, Young NL. Histone H4 proteoforms and post-translational modifications in the Mus musculus brain with quantitative comparison of ages and brain regions. Anal Bioanal Chem 2023;415:1627-1639. [PMID: 36754872 PMCID: PMC10165947 DOI: 10.1007/s00216-023-04555-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/08/2022] [Accepted: 01/18/2023] [Indexed: 02/10/2023]
9
Huang CJ, Lyu X, Kang J. The molecular characteristics and functional roles of microspherule protein 1 (MCRS1) in gene expression, cell proliferation, and organismic development. Cell Cycle 2023;22:619-632. [PMID: 36384428 PMCID: PMC9980701 DOI: 10.1080/15384101.2022.2145816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/21/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022]  Open
10
Luo C, Wang Z, Wang J, Yun F, Lu F, Fu J, Liu Q, Shi D. Individual variation in buffalo somatic cell cloning efficiency is related to glycolytic metabolism. SCIENCE CHINA. LIFE SCIENCES 2022;65:2076-2092. [PMID: 35366153 DOI: 10.1007/s11427-021-2039-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
11
Hess L, Moos V, Lauber AA, Reiter W, Schuster M, Hartl N, Lackner D, Boenke T, Koren A, Guzzardo PM, Gundacker B, Riegler A, Vician P, Miccolo C, Leiter S, Chandrasekharan MB, Vcelkova T, Tanzer A, Jun JQ, Bradner J, Brosch G, Hartl M, Bock C, Bürckstümmer T, Kubicek S, Chiocca S, Bhaskara S, Seiser C. A toolbox for class I HDACs reveals isoform specific roles in gene regulation and protein acetylation. PLoS Genet 2022;18:e1010376. [PMID: 35994477 PMCID: PMC9436093 DOI: 10.1371/journal.pgen.1010376] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 09/01/2022] [Accepted: 08/06/2022] [Indexed: 02/07/2023]  Open
12
Pedersen SS, Prause M, Williams K, Barrès R, Billestrup N. Butyrate inhibits IL-1β-induced inflammatory gene expression by suppression of NF-κB activity in pancreatic beta cells. J Biol Chem 2022;298:102312. [PMID: 35921894 PMCID: PMC9428856 DOI: 10.1016/j.jbc.2022.102312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/05/2022]  Open
13
van der Vossen EWJ, Bastos D, Stols-Gonçalves D, de Goffau MC, Davids M, Pereira JPB, Li Yim AYF, Henneman P, Netea MG, de Vos WM, de Jonge W, Groen AK, Nieuwdorp M, Levin E. Effects of fecal microbiota transplant on DNA methylation in subjects with metabolic syndrome. Gut Microbes 2022;13:1993513. [PMID: 34747338 PMCID: PMC8583152 DOI: 10.1080/19490976.2021.1993513] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]  Open
14
Sansores-España LD, Melgar-Rodríguez S, Olivares-Sagredo K, Cafferata EA, Martínez-Aguilar VM, Vernal R, Paula-Lima AC, Díaz-Zúñiga J. Oral-Gut-Brain Axis in Experimental Models of Periodontitis: Associating Gut Dysbiosis With Neurodegenerative Diseases. FRONTIERS IN AGING 2021;2:781582. [PMID: 35822001 PMCID: PMC9261337 DOI: 10.3389/fragi.2021.781582] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022]
15
Thomas SP, Denu JM. Short-chain fatty acids activate acetyltransferase p300. eLife 2021;10:72171. [PMID: 34677127 PMCID: PMC8585482 DOI: 10.7554/elife.72171] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023]  Open
16
Rommelfanger S, Zhou M, Shaghasi H, Tzeng SC, Evans BS, Paša-Tolić L, Umen JG, Pesavento JJ. An Improved Top-Down Mass Spectrometry Characterization of Chlamydomonas reinhardtii Histones and Their Post-translational Modifications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021;32:1671-1688. [PMID: 34165968 PMCID: PMC9236284 DOI: 10.1021/jasms.1c00029] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 06/01/2023]
17
Holt MV, Wang T, Young NL. Expeditious Extraction of Histones from Limited Cells or Tissue Samples and Quantitative Top-Down Proteomic Analysis. Curr Protoc 2021;1:e26. [PMID: 33534192 DOI: 10.1002/cpz1.26] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
18
Lysines Acetylome and Methylome Profiling of H3 and H4 Histones in Trichostatin A-Treated Stem Cells. Int J Mol Sci 2021;22:ijms22042063. [PMID: 33669725 PMCID: PMC7921975 DOI: 10.3390/ijms22042063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 12/13/2022]  Open
19
Combinations of histone post-translational modifications. Biochem J 2021;478:511-532. [DOI: 10.1042/bcj20200170] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 01/13/2021] [Accepted: 01/18/2021] [Indexed: 12/20/2022]
20
Demetriadou C, Koufaris C, Kirmizis A. Histone N-alpha terminal modifications: genome regulation at the tip of the tail. Epigenetics Chromatin 2020;13:29. [PMID: 32680559 PMCID: PMC7367250 DOI: 10.1186/s13072-020-00352-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/09/2020] [Indexed: 01/07/2023]  Open
21
Yang Z, Shen X, Chen D, Sun L. Toward a Universal Sample Preparation Method for Denaturing Top-Down Proteomics of Complex Proteomes. J Proteome Res 2020;19:3315-3325. [PMID: 32419461 DOI: 10.1021/acs.jproteome.0c00226] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
22
Evans LW, Stratton MS, Ferguson BS. Dietary natural products as epigenetic modifiers in aging-associated inflammation and disease. Nat Prod Rep 2020;37:653-676. [PMID: 31993614 PMCID: PMC7577396 DOI: 10.1039/c9np00057g] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
23
Cupp-Sutton KA, Wu S. High-throughput quantitative top-down proteomics. Mol Omics 2020;16:91-99. [PMID: 31932818 DOI: 10.1039/c9mo00154a] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
24
Holt MV, Wang T, Young NL. High-Throughput Quantitative Top-Down Proteomics: Histone H4. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019;30:2548-2560. [PMID: 31741267 DOI: 10.1007/s13361-019-02350-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 10/03/2019] [Accepted: 10/05/2019] [Indexed: 06/10/2023]
25
Holt MV, Wang T, Young NL. One-Pot Quantitative Top- and Middle-Down Analysis of GluC-Digested Histone H4. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019;30:2514-2525. [PMID: 31147891 DOI: 10.1007/s13361-019-02219-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/27/2019] [Accepted: 04/27/2019] [Indexed: 05/28/2023]
26
Marchione DM, Garcia BA, Wojcik J. Proteomic approaches for cancer epigenetics research. Expert Rev Proteomics 2018;16:33-47. [PMID: 30482069 DOI: 10.1080/14789450.2019.1550363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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