My Bibliography

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Meng FW, Murphy PJ. Canonical and Variant Nucleosome Reprogramming from Sperm to Blastula. Methods Mol Biol. 2025;2923:17-32. doi: 10.1007/978-1-0716-4522-2_2. PubMed PMID: 40418441.

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Park BJ, Hua S, Casler KD, Cefaloni E, Ayers MC, Lake RF, Murphy KE, Vertino PM, O'Connell MR, Murphy PJ. CUT&Tag overcomes biases of ChIP and establishes chromatin patterns for repetitive genomic loci. iScience. 2025 Nov 21;28(11):113757. doi: 10.1016/j.isci.2025.113757. eCollection 2025 Nov 21. PubMed PMID: 41234774; PubMed Central PMCID: PMC12605858.

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Meng FW, Schneider P, Wei X, Ariyasiri K, Halpern ME, Murphy PJ. TransTag enables simple and efficient transgene mapping in zebrafish via tagmentation. Cell Rep Methods. 2025 Jul 21;5(7):101090. doi: 10.1016/j.crmeth.2025.101090. Epub 2025 Jul 8. PubMed PMID: 40633543; PubMed Central PMCID: PMC12296462.

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Blanc RS, Shah N, Hachmer S, Salama NAS, Meng FW, Mousaei A, Puri G, Hwang JH, Wacker EE, Yang BA, Aguilar CA, Chakkalakal JV, Onukwufor JO, Murphy PJ, Calvi LM, Dilworth FJ, Dirksen RT. Epigenetic erosion of H4K20me1 induced by inflammation drives aged stem cell ferroptosis. Nat Aging. 2025 Aug;5(8):1491-1509. doi: 10.1038/s43587-025-00902-5. Epub 2025 Jun 30. PubMed PMID: 40588650; PubMed Central PMCID: PMC12350153.

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Park BJ, Hua S, Casler KD, Cefaloni E, Ayers MC, Lake RF, Murphy KE, Vertino PM, O'Connell MR, Murphy PJ. CUT&Tag Identifies Repetitive Genomic Loci that are Excluded from ChIP Assays. bioRxiv. 2025 Feb 5;. doi: 10.1101/2025.02.03.636299. PubMed PMID: 39974916; PubMed Central PMCID: PMC11838576.

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Das D, Khor ES, Jiang F, He J, Kawakami Y, Wainwright L, Hollinger J, Geiger J, Liu H, Meng F, Porter GA Jr, Jin Z, Murphy P, Yao P. Loss-of-function of RNA-binding protein PRRC2B causes translational defects and congenital cardiovascular malformation. medRxiv. 2024 Sep 27;. doi: 10.1101/2024.09.26.24313895. PubMed PMID: 39398999; PubMed Central PMCID: PMC11469349.

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Duong P, Rodriguez-Parks A, Kang J, Murphy PJ. CUT&Tag applied to zebrafish adult tail fins reveals a return of embryonic H3K4me3 patterns during regeneration. Epigenetics Chromatin. 2024 Jul 20;17(1):22. doi: 10.1186/s13072-024-00547-5. PubMed PMID: 39033118; PubMed Central PMCID: PMC11264793.

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Duong P, Rodriguez-Parks A, Kang J, Murphy PJ. CUT&Tag Applied to Zebrafish Adult Tail Fins Reveals a Return of Embryonic H3K4me3 Patterns During Regeneration. Res Sq. 2024 Apr 3;. doi: 10.21203/rs.3.rs-4189493/v1. PubMed PMID: 38645155; PubMed Central PMCID: PMC11030498.

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Blanc RS, Shah N, Salama NAS, Meng FW, Mousaei A, Yang BA, Aguilar CA, Chakkalakal JV, Onukwufor JO, Murphy PJ, Calvi L, Dirksen R. Epigenetic erosion of H4K20me1 induced by inflammation drives aged stem cell ferroptosis. Res Sq. 2024 Mar 15;. doi: 10.21203/rs.3.rs-3937628/v2. PubMed PMID: 38410478; PubMed Central PMCID: PMC10896381.

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Alexander WB, Wang W, Hill MA, O'Dell MR, Ruffolo LI, Guo B, Jackson KM, Ullman N, Friedland SC, McCall MN, Patel A, Figueroa-Guilliani N, Georger M, Belt BA, Whitney-Miller CL, Linehan DC, Murphy PJ, Hezel AF. Smad4 restricts injury-provoked biliary proliferation and carcinogenesis. Dis Model Mech. 2024 Jun 1;17(6). doi: 10.1242/dmm.050358. Epub 2024 Feb 28. PubMed PMID: 38415925; PubMed Central PMCID: PMC10924230.

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Reda A, Hategan LA, McLean TAB, Creighton SD, Luo JQ, Chen SES, Hua S, Winston S, Reeves I, Padmanabhan A, Dahi TA, Ramzan F, Brimble MA, Murphy PJ, Walters BJ, Stefanelli G, Zovkic IB. Role of the histone variant H2A.Z.1 in memory, transcription, and alternative splicing is mediated by lysine modification. Neuropsychopharmacology. 2024 Jul;49(8):1285-1295. doi: 10.1038/s41386-024-01817-2. Epub 2024 Feb 16. PubMed PMID: 38366138; PubMed Central PMCID: PMC11224360.

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Halblander FN, Meng FW, Murphy PJ. Anp32e protects against accumulation of H2A.Z at Sox motif containing promoters during zebrafish gastrulation. Dev Biol. 2024 Mar;507:34-43. doi: 10.1016/j.ydbio.2023.12.010. Epub 2023 Dec 28. PubMed PMID: 38159623; PubMed Central PMCID: PMC10922954.

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Halblander FN, Meng FW, Murphy PJ. Anp32e protects against accumulation of H2A.Z at Sox motif containing promoters during zebrafish gastrulation. bioRxiv. 2023 Dec 18;. doi: 10.1101/2023.12.18.572196. PubMed PMID: 38187710; PubMed Central PMCID: PMC10769258.

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Murphy PJ, Berger F. The chromatin source-sink hypothesis: a shared mode of chromatin-mediated regulations. Development. 2023 Nov 1;150(21). doi: 10.1242/dev.201989. Epub 2023 Nov 3. PubMed PMID: 37922125; PubMed Central PMCID: PMC10629678.

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Meng FW, Murphy KE, Makowski CE, Delatte B, Murphy PJ. Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression. Development. 2023 Nov 1;150(21). doi: 10.1242/dev.202338. Epub 2023 Nov 8. PubMed PMID: 37938830; PubMed Central PMCID: PMC10651094.

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Chen S, Rosin LF, Pegoraro G, Moshkovich N, Murphy PJ, Yu G, Lei EP. NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization. Nucleic Acids Res. 2022 Aug 12;50(14):7906-7924. doi: 10.1093/nar/gkac600. PubMed PMID: 35819192; PubMed Central PMCID: PMC9371915.

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Meng FW, Murphy KE, Makowski CE, Murphy PJ. Competition for H2A.Z between genes and repetitive elements establishes response to anti-viral immune activation. BioRxiv. 2022 March. doi: 10.1101/2022.03.31.486614.

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Hickey GJ, Wike CL, Nie X, Guo Y, Tan M, Murphy PJ, Cairns BR. Establishment of developmental gene silencing by ordered polycomb complex recruitment in early zebrafish embryos. Elife. 2022 Jan 4;11. doi: 10.7554/eLife.67738. PubMed PMID: 34982026; PubMed Central PMCID: PMC8769650.

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Ruff GL, Murphy KE, Smith ZR, Vertino PM, Murphy PJ. Subtype-Independent ANP32E Reduction During Breast Cancer Progression in Accordance with Chromatin Relaxation. BMC Cancer. 2021 Dec 18;21(1):1342. doi: 10.1186/s12885-021-09077-9. PubMed PMID: 34922480; PubMed Central PMCID: PMC8684129.

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Akdogan-Ozdilek B, Duval KL, Meng FW, Murphy PJ, Goll MG. Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag. Dev Dyn. 2022 Apr;251(4):729-742. doi: 10.1002/dvdy.430. Epub 2021 Oct 23. PubMed PMID: 34647658; PubMed Central PMCID: PMC8976701.

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Stefanelli G, Makowski CE, Brimble MA, Hall M, Reda A, Creighton SD, Leonetti AM, McLean TAB, Zakaria JM, Baumbach J, Greer CB, Davidoff AM, Walters BJ, Murphy PJ, Zovkic IB. The histone chaperone Anp32e regulates memory formation, transcription, and dendritic morphology by regulating steady-state H2A.Z binding in neurons. Cell Rep. 2021 Aug 17;36(7):109551. doi: 10.1016/j.celrep.2021.109551. PubMed PMID: 34407406; PubMed Central PMCID: PMC8422973.

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Meng FW, Murphy PJ. Rolling uphill: in vivo reacquisition of pluripotency during cranial neural crest differentiation. Commun Biol. 2021 May 20;4(1):626. doi: 10.1038/s42003-021-02154-6. PubMed PMID: 34017055; PubMed Central PMCID: PMC8137701.

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Murphy KE, Meng FW, Makowski CE, Murphy PJ. Genome-wide chromatin accessibility is restricted by ANP32E. Nat Commun. 2020 Oct 8;11(1):5063. doi: 10.1038/s41467-020-18821-x. PubMed PMID: 33033242; PubMed Central PMCID: PMC7546623.

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Murphy PJ, Guo J, Jenkins TG, James ER, Hoidal JR, Huecksteadt T, Broberg DS, Hotaling JM, Alonso DF, Carrell DT, Cairns BR, Aston KI. NRF2 loss recapitulates heritable impacts of paternal cigarette smoke exposure. PLoS Genet. 2020 Jun;16(6):e1008756. doi: 10.1371/journal.pgen.1008756. eCollection 2020 Jun. PubMed PMID: 32520939; PubMed Central PMCID: PMC7307791.

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Rougeot J, Chrispijn ND, Aben M, Elurbe DM, Andralojc KM, Murphy PJ, Jansen PWTC, Vermeulen M, Cairns BR, Kamminga LM. Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan. Development. 2019 Sep 30;146(19). doi: 10.1242/dev.178590. PubMed PMID: 31488564; PubMed Central PMCID: PMC6803366.

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Murphy PJ, Wu SF, James CR, Wike CL, Cairns BR. Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming. Cell. 2018 Feb 22;172(5):993-1006.e13. doi: 10.1016/j.cell.2018.01.022. Epub 2018 Feb 15. PubMed PMID: 29456083.

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Guo J, Grow EJ, Yi C, Mlcochova H, Maher GJ, Lindskog C, Murphy PJ, Wike CL, Carrell DT, Goriely A, Hotaling JM, Cairns BR. Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development. Cell Stem Cell. 2017 Oct 5;21(4):533-546.e6. doi: 10.1016/j.stem.2017.09.003. PubMed PMID: 28985528; PubMed Central PMCID: PMC5832720.

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Jenkins TG, James ER, Alonso DF, Hoidal JR, Murphy PJ, Hotaling JM, Cairns BR, Carrell DT, Aston KI. Cigarette smoking significantly alters sperm DNA methylation patterns. Andrology. 2017 Nov;5(6):1089-1099. doi: 10.1111/andr.12416. Epub 2017 Sep 26. PubMed PMID: 28950428; PubMed Central PMCID: PMC5679018.

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Murphy PJ, Cairns BR. Genome-wide DNA methylation profiling in zebrafish. Methods Cell Biol. 2016;135:345-59. doi: 10.1016/bs.mcb.2016.05.002. Epub 2016 Jun 21. PubMed PMID: 27443935.

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Murphy KE, Murphy PJ, Carrell DT. Epigenetic Changes in the Paternal Germline. In: Tollefsbol T, editor. Transgenerational epigenetics Amsterdam ; Boston: Elsevier/Academic Press; 2014. Chapter 5.

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Murphy PJ, Cipriany BR, Wallin CB, Ju CY, Szeto K, Hagarman JA, Benitez JJ, Craighead HG, Soloway PD. Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells. Proc Natl Acad Sci U S A. 2013 May 7;110(19):7772-7. doi: 10.1073/pnas.1218495110. Epub 2013 Apr 22. PubMed PMID: 23610441; PubMed Central PMCID: PMC3651511.

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Benítez JJ, Topolancik J, Tian HC, Wallin CB, Latulippe DR, Szeto K, Murphy PJ, Cipriany BR, Levy SL, Soloway PD, Craighead HG. Microfluidic extraction, stretching and analysis of human chromosomal DNA from single cells. Lab Chip. 2012 Nov 21;12(22):4848-54. doi: 10.1039/c2lc40955k. PubMed PMID: 23018789; PubMed Central PMCID: PMC3954578.

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Cipriany BR, Murphy PJ, Hagarman JA, Cerf A, Latulippe D, Levy SL, Benítez JJ, Tan CP, Topolancik J, Soloway PD, Craighead HG. Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel. Proc Natl Acad Sci U S A. 2012 May 29;109(22):8477-82. doi: 10.1073/pnas.1117549109. Epub 2012 May 14. PubMed PMID: 22586076; PubMed Central PMCID: PMC3365150.

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Park YJ, Herman H, Gao Y, Lindroth AM, Hu BY, Murphy PJ, Putnam JR, Soloway PD. Sequences sufficient for programming imprinted germline DNA methylation defined. PLoS One. 2012;7(3):e33024. doi: 10.1371/journal.pone.0033024. Epub 2012 Mar 5. PubMed PMID: 22403732; PubMed Central PMCID: PMC3293921.

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Watanabe T, Tomizawa S, Mitsuya K, Totoki Y, Yamamoto Y, Kuramochi-Miyagawa S, Iida N, Hoki Y, Murphy PJ, Toyoda A, Gotoh K, Hiura H, Arima T, Fujiyama A, Sado T, Shibata T, Nakano T, Lin H, Ichiyanagi K, Soloway PD, Sasaki H. Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus. Science. 2011 May 13;332(6031):848-52. doi: 10.1126/science.1203919. PubMed PMID: 21566194; PubMed Central PMCID: PMC3368507.

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Cipriany BR, Zhao R, Murphy PJ, Levy SL, Tan CP, Craighead HG, Soloway PD. Single molecule epigenetic analysis in a nanofluidic channel. Anal Chem. 2010 Mar 15;82(6):2480-7. doi: 10.1021/ac9028642. PubMed PMID: 20184350; PubMed Central PMCID: PMC2839087.