My Bibliography

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Vinson DA, Stephens KE, O'Meally RN, Bhat S, Dancy BCR, Cole RN, Yegnasubramanian S, Taverna SD. De novo methylation of histone H3K23 by the methyltransferases EHMT1/GLP and EHMT2/G9a. Epigenetics Chromatin. 2022 Nov 21;15(1):36. doi: 10.1186/s13072-022-00468-1. PubMed PMID: 36411491; PubMed Central PMCID: PMC9677696.

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Stephens KE, Zhou W, Renfro Z, Ji Z, Ji H, Guan Y, Taverna SD. Global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain. J Neuroinflammation. 2021 Aug 26;18(1):185. doi: 10.1186/s12974-021-02228-6. PubMed PMID: 34446036; PubMed Central PMCID: PMC8390277.

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Xu J, Zhao X, Mao F, Basrur V, Ueberheide B, Chait BT, Allis CD, Taverna SD, Gao S, Wang W, Liu Y. A Polycomb repressive complex is required for RNAi-mediated heterochromatin formation and dynamic distribution of nuclear bodies. Nucleic Acids Res. 2021 Jun 4;49(10):5407-5425. doi: 10.1093/nar/gkaa1262. PubMed PMID: 33412588; PubMed Central PMCID: PMC8191774.

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Rizzardi LF, Hickey PF, Idrizi A, Tryggvadóttir R, Callahan CM, Stephens KE, Taverna SD, Zhang H, Ramazanoglu S, Hansen KD, Feinberg AP. Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits. Genome Biol. 2021 Apr 22;22(1):116. doi: 10.1186/s13059-021-02335-w. PubMed PMID: 33888138; PubMed Central PMCID: PMC8061076.

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Waldrip ZJ, Jenjaroenpun P, DeYoung O, Nookaew I, Taverna SD, Raney KD, Tackett AJ. Genome-wide Cas9 binding specificity in Saccharomyces cerevisiae. PeerJ. 2020;8:e9442. doi: 10.7717/peerj.9442. eCollection 2020. PubMed PMID: 32821531; PubMed Central PMCID: PMC7395602.

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Storey AJ, Hardman RE, Byrum SD, Mackintosh SG, Edmondson RD, Wahls WP, Tackett AJ, Lewis JA. Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome Using Tandem Mass Tags. J Proteome Res. 2020 Mar 6;19(3):1183-1195. doi: 10.1021/acs.jproteome.9b00704. Epub 2020 Feb 19. PubMed PMID: 32027144; PubMed Central PMCID: PMC7241437.

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West KL, Byrum SD, Mackintosh SG, Edmondson RD, Taverna SD, Tackett AJ. Proteomic characterization of the arsenic response locus in S. cerevisiae. Epigenetics. 2019 Feb;14(2):130-145. doi: 10.1080/15592294.2019.1580110. Epub 2019 Mar 1. PubMed PMID: 30739529; PubMed Central PMCID: PMC6557609.

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Stephens KE, Zhou W, Ji Z, Chen Z, He S, Ji H, Guan Y, Taverna SD. Sex differences in gene regulation in the dorsal root ganglion after nerve injury. BMC Genomics. 2019 Feb 19;20(1):147. doi: 10.1186/s12864-019-5512-9. PubMed PMID: 30782122; PubMed Central PMCID: PMC6381758.

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Stephens KE, Chen Z, Sivanesan E, Raja SN, Linderoth B, Taverna SD, Guan Y. RNA-seq of spinal cord from nerve-injured rats after spinal cord stimulation. Mol Pain. 2018 Jan-Dec;14:1744806918817429. doi: 10.1177/1744806918817429. Epub 2018 Nov 19. PubMed PMID: 30451078; PubMed Central PMCID: PMC6293371.

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Bhat S, Hwang Y, Gibson MD, Morgan MT, Taverna SD, Zhao Y, Wolberger C, Poirier MG, Cole PA. Hydrazide Mimics for Protein Lysine Acylation To Assess Nucleosome Dynamics and Deubiquitinase Action. J Am Chem Soc. 2018 Aug 1;140(30):9478-9485. doi: 10.1021/jacs.8b03572. Epub 2018 Jul 24. PubMed PMID: 29991262; PubMed Central PMCID: PMC6070418.

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Hartman JH, Miller GP, Caro AA, Byrum SD, Orr LM, Mackintosh SG, Tackett AJ, MacMillan-Crow LA, Hallberg LM, Ameredes BT, Boysen G. 1,3-Butadiene-induced mitochondrial dysfunction is correlated with mitochondrial CYP2E1 activity in Collaborative Cross mice. Toxicology. 2017 Mar 1;378:114-124. doi: 10.1016/j.tox.2017.01.005. Epub 2017 Jan 9. PubMed PMID: 28082109; PubMed Central PMCID: PMC5319481.

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Xiong J, Gao S, Dui W, Yang W, Chen X, Taverna SD, Pearlman RE, Ashlock W, Miao W, Liu Y. Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin. Nucleic Acids Res. 2016 Dec 1;44(21):10091-10105. doi: 10.1093/nar/gkw684. Epub 2016 Aug 3. PubMed PMID: 27488188; PubMed Central PMCID: PMC5137421.

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Hamilton EP, Kapusta A, Huvos PE, Bidwell SL, Zafar N, Tang H, Hadjithomas M, Krishnakumar V, Badger JH, Caler EV, Russ C, Zeng Q, Fan L, Levin JZ, Shea T, Young SK, Hegarty R, Daza R, Gujja S, Wortman JR, Birren BW, Nusbaum C, Thomas J, Carey CM, Pritham EJ, Feschotte C, Noto T, Mochizuki K, Papazyan R, Taverna SD, Dear PH, Cassidy-Hanley DM, Xiong J, Miao W, Orias E, Coyne RS. Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome. Elife. 2016 Nov 28;5. doi: 10.7554/eLife.19090. PubMed PMID: 27892853; PubMed Central PMCID: PMC5182062.

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Su Z, Wang F, Lee JH, Stephens KE, Papazyan R, Voronina E, Krautkramer KA, Raman A, Thorpe JJ, Boersma MD, Kuznetsov VI, Miller MD, Taverna SD, Phillips GN Jr, Denu JM. Reader domain specificity and lysine demethylase-4 family function. Nat Commun. 2016 Nov 14;7:13387. doi: 10.1038/ncomms13387. PubMed PMID: 27841353; PubMed Central PMCID: PMC5114558.

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Atanassov BS, Mohan RD, Lan X, Kuang X, Lu Y, Lin K, McIvor E, Li W, Zhang Y, Florens L, Byrum SD, Mackintosh SG, Calhoun-Davis T, Koutelou E, Wang L, Tang DG, Tackett AJ, Washburn MP, Workman JL, Dent SY. ATXN7L3 and ENY2 Coordinate Activity of Multiple H2B Deubiquitinases Important for Cellular Proliferation and Tumor Growth. Mol Cell. 2016 May 19;62(4):558-71. doi: 10.1016/j.molcel.2016.03.030. Epub 2016 Apr 28. PubMed PMID: 27132940; PubMed Central PMCID: PMC4874879.

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Ayyadevara S, Mercanti F, Wang X, Mackintosh SG, Tackett AJ, Prayaga SV, Romeo F, Shmookler Reis RJ, Mehta JL. Age- and Hypertension-Associated Protein Aggregates in Mouse Heart Have Similar Proteomic Profiles. Hypertension. 2016 May;67(5):1006-13. doi: 10.1161/HYPERTENSIONAHA.115.06849. Epub 2016 Mar 14. PubMed PMID: 26975704; PubMed Central PMCID: PMC4833546.

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Ringel AE, Cieniewicz AM, Taverna SD, Wolberger C. Nucleosome competition reveals processive acetylation by the SAGA HAT module. Proc Natl Acad Sci U S A. 2015 Oct 6;112(40):E5461-70. doi: 10.1073/pnas.1508449112. Epub 2015 Sep 23. PubMed PMID: 26401015; PubMed Central PMCID: PMC4603478.

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Harr JC, Luperchio TR, Wong X, Cohen E, Wheelan SJ, Reddy KL. Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins. J Cell Biol. 2015 Jan 5;208(1):33-52. doi: 10.1083/jcb.201405110. PubMed PMID: 25559185; PubMed Central PMCID: PMC4284222.

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Byrum SD, Taverna SD, Tackett AJ. Purification of specific chromatin loci for proteomic analysis. Methods Mol Biol. 2015;1228:83-92. doi: 10.1007/978-1-4939-1680-1_8. PubMed PMID: 25311124; PubMed Central PMCID: PMC4324170.

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Brown LJ, Baranowski M, Wang Y, Schrey AK, Lenz T, Taverna SD, Cole PA, Sefkow M. Using S-adenosyl-L-homocysteine capture compounds to characterize S-adenosyl-L-methionine and S-adenosyl-L-homocysteine binding proteins. Anal Biochem. 2014 Dec 15;467:14-21. doi: 10.1016/j.ab.2014.08.013. Epub 2014 Aug 27. PubMed PMID: 25172130; PubMed Central PMCID: PMC4315328.

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Cieniewicz AM, Moreland L, Ringel AE, Mackintosh SG, Raman A, Gilbert TM, Wolberger C, Tackett AJ, Taverna SD. The bromodomain of Gcn5 regulates site specificity of lysine acetylation on histone H3. Mol Cell Proteomics. 2014 Nov;13(11):2896-910. doi: 10.1074/mcp.M114.038174. Epub 2014 Aug 8. PubMed PMID: 25106422; PubMed Central PMCID: PMC4223480.

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Gilbert TM, McDaniel SL, Byrum SD, Cades JA, Dancy BC, Wade H, Tackett AJ, Strahl BD, Taverna SD. A PWWP domain-containing protein targets the NuA3 acetyltransferase complex via histone H3 lysine 36 trimethylation to coordinate transcriptional elongation at coding regions. Mol Cell Proteomics. 2014 Nov;13(11):2883-95. doi: 10.1074/mcp.M114.038224. Epub 2014 Aug 6. PubMed PMID: 25104842; PubMed Central PMCID: PMC4223479.

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Waldrip ZJ, Byrum SD, Storey AJ, Gao J, Byrd AK, Mackintosh SG, Wahls WP, Taverna SD, Raney KD, Tackett AJ. A CRISPR-based approach for proteomic analysis of a single genomic locus. Epigenetics. 2014 Sep;9(9):1207-11. doi: 10.4161/epi.29919. Epub 2014 Jul 18. PubMed PMID: 25147920; PubMed Central PMCID: PMC4169012.

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Papazyan R, Voronina E, Chapman JR, Luperchio TR, Gilbert TM, Meier E, Mackintosh SG, Shabanowitz J, Tackett AJ, Reddy KL, Coyne RS, Hunt DF, Liu Y, Taverna SD. Methylation of histone H3K23 blocks DNA damage in pericentric heterochromatin during meiosis. Elife. 2014 Aug 26;3:e02996. doi: 10.7554/eLife.02996. PubMed PMID: 25161194; PubMed Central PMCID: PMC4141274.

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Zhu B, Zhang M, Byrum SD, Tackett AJ, Davie JK. TBX2 blocks myogenesis and promotes proliferation in rhabdomyosarcoma cells. Int J Cancer. 2014 Aug 15;135(4):785-97. doi: 10.1002/ijc.28721. Epub 2014 Jan 27. PubMed PMID: 24470334; PubMed Central PMCID: PMC4051830.

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Prusevich P, Kalin JH, Ming SA, Basso M, Givens J, Li X, Hu J, Taylor MS, Cieniewicz AM, Hsiao PY, Huang R, Roberson H, Adejola N, Avery LB, Casero RA Jr, Taverna SD, Qian J, Tackett AJ, Ratan RR, McDonald OG, Feinberg AP, Cole PA. A selective phenelzine analogue inhibitor of histone demethylase LSD1. ACS Chem Biol. 2014 Jun 20;9(6):1284-93. doi: 10.1021/cb500018s. Epub 2014 Apr 7. PubMed PMID: 24707965; PubMed Central PMCID: PMC4076021.

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Byrum SD, Taverna SD, Tackett AJ. Purification of a specific native genomic locus for proteomic analysis. Nucleic Acids Res. 2013 Nov;41(20):e195. doi: 10.1093/nar/gkt822. Epub 2013 Sep 11. PubMed PMID: 24030711; PubMed Central PMCID: PMC3814360.

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Yan G, Eller MS, Elm C, Larocca CA, Ryu B, Panova IP, Dancy BM, Bowers EM, Meyers D, Lareau L, Cole PA, Taverna SD, Alani RM. Selective inhibition of p300 HAT blocks cell cycle progression, induces cellular senescence, and inhibits the DNA damage response in melanoma cells. J Invest Dermatol. 2013 Oct;133(10):2444-2452. doi: 10.1038/jid.2013.187. Epub 2013 Apr 18. PubMed PMID: 23698071; PubMed Central PMCID: PMC4380234.

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Papazyan R, Taverna SD. Separation and purification of multiply acetylated proteins using cation-exchange chromatography. Methods Mol Biol. 2013;981:103-13. doi: 10.1007/978-1-62703-305-3_8. PubMed PMID: 23381856; PubMed Central PMCID: PMC3779653.

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Byrum SD, Raman A, Taverna SD, Tackett AJ. ChAP-MS: a method for identification of proteins and histone posttranslational modifications at a single genomic locus. Cell Rep. 2012 Jul 26;2(1):198-205. doi: 10.1016/j.celrep.2012.06.019. Epub 2012 Jul 20. PubMed PMID: 22840409; PubMed Central PMCID: PMC3408609.

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Dancy BC, Ming SA, Papazyan R, Jelinek CA, Majumdar A, Sun Y, Dancy BM, Drury WJ 3rd, Cotter RJ, Taverna SD, Cole PA. Azalysine analogues as probes for protein lysine deacetylation and demethylation. J Am Chem Soc. 2012 Mar 21;134(11):5138-48. doi: 10.1021/ja209574z. Epub 2012 Mar 12. PubMed PMID: 22352831; PubMed Central PMCID: PMC3313494.

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Li R, Zhu J, Xie Z, Liao G, Liu J, Chen MR, Hu S, Woodard C, Lin J, Taverna SD, Desai P, Ambinder RF, Hayward GS, Qian J, Zhu H, Hayward SD. Conserved herpesvirus kinases target the DNA damage response pathway and TIP60 histone acetyltransferase to promote virus replication. Cell Host Microbe. 2011 Oct 20;10(4):390-400. doi: 10.1016/j.chom.2011.08.013. PubMed PMID: 22018239; PubMed Central PMCID: PMC3253558.

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Byrum SD, Taverna SD, Tackett AJ. Quantitative analysis of histone exchange for transcriptionally active chromatin. J Clin Bioinforma. 2011 Jul 7;1(1):17. doi: 10.1186/2043-9113-1-17. PubMed PMID: 21884633; PubMed Central PMCID: PMC3164610.

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Blair LP, Avaritt NL, Huang R, Cole PA, Taverna SD, Tackett AJ. MassSQUIRM: An assay for quantitative measurement of lysine demethylase activity. Epigenetics. 2011 Apr;6(4):490-9. doi: 10.4161/epi.6.4.14531. Epub 2011 Apr 1. PubMed PMID: 21273814; PubMed Central PMCID: PMC3230537.

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Byrum S, Mackintosh SG, Edmondson RD, Cheung WL, Taverna SD, Tackett AJ. Analysis of Histone Exchange during Chromatin Purification. J Integr OMICS. 2011 Feb 1;1(1):61-65. doi: 10.5584/jiomics.v1i1.26. PubMed PMID: 21709819; PubMed Central PMCID: PMC3119864.

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Taverna SD, Cole PA. Drug discovery: Reader's block. Nature. 2010 Dec 23;468(7327):1050-1. doi: 10.1038/4681050a. PubMed PMID: 21179160.

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Gradolatto A, Smart SK, Byrum S, Blair LP, Rogers RS, Kolar EA, Lavender H, Larson SK, Aitchison JD, Taverna SD, Tackett AJ. A noncanonical bromodomain in the AAA ATPase protein Yta7 directs chromosomal positioning and barrier chromatin activity. Mol Cell Biol. 2009 Sep;29(17):4604-11. doi: 10.1128/MCB.00160-09. Epub 2009 Jul 6. PubMed PMID: 19581291; PubMed Central PMCID: PMC2725702.

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Smart SK, Mackintosh SG, Edmondson RD, Taverna SD, Tackett AJ. Mapping the local protein interactome of the NuA3 histone acetyltransferase. Protein Sci. 2009 Sep;18(9):1987-97. doi: 10.1002/pro.212. PubMed PMID: 19621382; PubMed Central PMCID: PMC2777373.

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Gradolatto A, Rogers RS, Lavender H, Taverna SD, Allis CD, Aitchison JD, Tackett AJ. Saccharomyces cerevisiae Yta7 regulates histone gene expression. Genetics. 2008 May;179(1):291-304. doi: 10.1534/genetics.107.086520. PubMed PMID: 18493054; PubMed Central PMCID: PMC2390607.

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Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol. 2007 Nov;14(11):1025-1040. doi: 10.1038/nsmb1338. Epub 2007 Nov 5. Review. PubMed PMID: 17984965; PubMed Central PMCID: PMC4691843.

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Liu Y, Taverna SD, Muratore TL, Shabanowitz J, Hunt DF, Allis CD. RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena. Genes Dev. 2007 Jun 15;21(12):1530-45. doi: 10.1101/gad.1544207. PubMed PMID: 17575054; PubMed Central PMCID: PMC1891430.

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Song X, Gjoneska E, Ren Q, Taverna SD, Allis CD, Gorovsky MA. Phosphorylation of the SQ H2A.X motif is required for proper meiosis and mitosis in Tetrahymena thermophila. Mol Cell Biol. 2007 Apr;27(7):2648-60. doi: 10.1128/MCB.01910-06. Epub 2007 Jan 22. PubMed PMID: 17242195; PubMed Central PMCID: PMC1899910.

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Taverna SD, Ueberheide BM, Liu Y, Tackett AJ, Diaz RL, Shabanowitz J, Chait BT, Hunt DF, Allis CD. Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini. Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2086-91. doi: 10.1073/pnas.0610993104. Epub 2007 Feb 6. PubMed PMID: 17284592; PubMed Central PMCID: PMC1892956.

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Taverna SD, Ilin S, Rogers RS, Tanny JC, Lavender H, Li H, Baker L, Boyle J, Blair LP, Chait BT, Patel DJ, Aitchison JD, Tackett AJ, Allis CD. Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol Cell. 2006 Dec 8;24(5):785-796. doi: 10.1016/j.molcel.2006.10.026. PubMed PMID: 17157260; PubMed Central PMCID: PMC4690528.

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Barber CM, Turner FB, Wang Y, Hagstrom K, Taverna SD, Mollah S, Ueberheide B, Meyer BJ, Hunt DF, Cheung P, Allis CD. The enhancement of histone H4 and H2A serine 1 phosphorylation during mitosis and S-phase is evolutionarily conserved. Chromosoma. 2004 May;112(7):360-71. doi: 10.1007/s00412-004-0281-9. Epub 2004 May 7. PubMed PMID: 15133681.

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Morshead KB, Ciccone DN, Taverna SD, Allis CD, Oettinger MA. Antigen receptor loci poised for V(D)J rearrangement are broadly associated with BRG1 and flanked by peaks of histone H3 dimethylated at lysine 4. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11577-82. doi: 10.1073/pnas.1932643100. Epub 2003 Sep 19. PubMed PMID: 14500909; PubMed Central PMCID: PMC208800.

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Taverna SD, Coyne RS, Allis CD. Methylation of histone h3 at lysine 9 targets programmed DNA elimination in tetrahymena. Cell. 2002 Sep 20;110(6):701-11. doi: 10.1016/s0092-8674(02)00941-8. PubMed PMID: 12297044.

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Jacobs SA, Taverna SD, Zhang Y, Briggs SD, Li J, Eissenberg JC, Allis CD, Khorasanizadeh S. Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J. 2001 Sep 17;20(18):5232-41. doi: 10.1093/emboj/20.18.5232. PubMed PMID: 11566886; PubMed Central PMCID: PMC125272.