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Patrick J. Murphy, Ph.D.

Patrick J. Murphy, Ph.D.

Contact

Office (585) 275-0113

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About Me

Faculty Appointments

Associate Professor - Department of Biomedical Genetics (SMD)

Associate Professor - Department of Biology RC (RC) - Joint

Research

The Murphy lab investigates the mechanisms that activate or silence genes as cells transition from one state to another. In very early embryos, stem cells begin to divide and change. Through this process, called differentiation, tissues start to form, and all the cell types of the organism begin to ...
The Murphy lab investigates the mechanisms that activate or silence genes as cells transition from one state to another. In very early embryos, stem cells begin to divide and change. Through this process, called differentiation, tissues start to form, and all the cell types of the organism begin to arise. Differentiation relies on a highly coordinated series of gene activation and silencing events. As cells divide during differentiation, changes in gene expression provide each cell type with a specific identity and function. In a similar sense, when the gene expression patterns of normal adult cells change inappropriately, the cell identity also changes, and this can lead to carcinogenesis. Presently, it is unknown what molecular machinery allows a cell to transition from one gene expression state to another.

Publications

Journal Articles

CUT&Tag applied to zebrafish adult tail fins reveals a return of embryonic H3K4me3 patterns during regeneration.

Duong P, Rodriguez-Parks A, Kang J, Murphy PJ

Epigenetics & chromatin.. 2024 July 2017 (1):22. Epub 07/20/2024.

Role of the histone variant H2A.Z.1 in memory, transcription, and alternative splicing is mediated by lysine modification.

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

Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology.. 2024 July 49 (8):1285-1295. Epub 02/16/2024.

Smad4 restricts injury-provoked biliary proliferation and carcinogenesis.

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

Disease models & mechanisms.. 2024 June 117 (6)Epub 02/28/2024.

CUT&Tag Applied to Zebrafish Adult Tail Fins Reveals a Return of Embryonic H3K4me3 Patterns During Regeneration.

Duong P, Rodriguez-Parks A, Kang J, Murphy PJ

Research square.. 2024 April 3 Epub 04/03/2024.

Epigenetic erosion of H4K20me1 induced by inflammation drives aged stem cell ferroptosis.

Blanc R, Shah N, Salama N, Meng F, Mousaei A, Chakkalakal J, Onukwufor J, Murphy P, Calvi L, Dirksen R

Research square.. 2024 March 15 Epub 03/15/2024.

Anp32e protects against accumulation of H2A.Z at Sox motif containing promoters during zebrafish gastrulation.

Halblander FN, Meng FW, Murphy PJ

Developmental biology.. 2024 March 507 :34-43. Epub 12/28/2023.

The chromatin source-sink hypothesis: a shared mode of chromatin-mediated regulations.

Murphy PJ, Berger F

Development.. 2023 November 1150 (21)Epub 11/03/2023.

Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression.

Meng FW, Murphy KE, Makowski CE, Delatte B, Murphy PJ

Development.. 2023 November 1150 (21)Epub 11/08/2023.

NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization.

Chen S, Rosin LF, Pegoraro G, Moshkovich N, Murphy PJ, Yu G, Lei EP

Nucleic acids research.. 2022 August 1250 (14):7906-7924. Epub 1900 01 01.

Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag.

Akdogan-Ozdilek B, Duval KL, Meng FW, Murphy PJ, Goll MG

Developmental dynamics : an official publication of the American Association of Anatomists.. 2022 April 251 (4):729-742. Epub 10/23/2021.

Establishment of developmental gene silencing by ordered polycomb complex recruitment in early zebrafish embryos.

Hickey GJ, Wike CL, Nie X, Guo Y, Tan M, Murphy PJ, Cairns BR

eLife.. 2022 January 411 Epub 01/04/2022.

Subtype-Independent ANP32E Reduction During Breast Cancer Progression in Accordance with Chromatin Relaxation.

Ruff GL, Murphy KE, Smith ZR, Vertino PM, Murphy PJ

BMC cancer.. 2021 December 1821 (1):1342. Epub 12/18/2021.

The histone chaperone Anp32e regulates memory formation, transcription, and dendritic morphology by regulating steady-state H2A.Z binding in neurons.

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

Cell reports.. 2021 August 1736 (7):109551. Epub 1900 01 01.

Rolling uphill: in vivo reacquisition of pluripotency during cranial neural crest differentiation.

Meng FW, Murphy PJ

Communications biology.. 2021 May 204 (1):626. Epub 05/20/2021.

Genome-wide chromatin accessibility is restricted by ANP32E.

Murphy KE, Meng FW, Makowski CE, Murphy PJ

Nature communications.. 2020 October 811 (1):5063. Epub 10/08/2020.

NRF2 loss recapitulates heritable impacts of paternal cigarette smoke exposure.

Murphy PJ, Guo J, Jenkins TG, James ER, Hoidal JR, Huecksteadt T, Broberg DS, Hotaling JM, Alonso DF, Carrell DT, Cairns BR, Aston KI

PLoS genetics.. 2020 June 16 (6):e1008756. Epub 06/10/2020.

Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan.

Rougeot J, Chrispijn ND, Aben M, Elurbe DM, Andralojc KM, Murphy PJ, Jansen PWTC, Vermeulen M, Cairns BR, Kamminga LM

Development.. 2019 September 30146 (19)Epub 09/30/2019.

Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming.

Murphy PJ, Wu SF, James CR, Wike CL, Cairns BR

Cell.. 2018 February 22172 (5):993-1006.e13. Epub 02/15/2018.

Cigarette smoking significantly alters sperm DNA methylation patterns.

Jenkins TG, James ER, Alonso DF, Hoidal JR, Murphy PJ, Hotaling JM, Cairns BR, Carrell DT, Aston KI

Andrology.. 2017 November 5 (6):1089-1099. Epub 09/26/2017.

Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development.

Guo J, Grow EJ, Yi C, Mlcochova H, Maher GJ, Lindskog C, Murphy PJ, Wike CL, Carrell DT, Goriely A, Hotaling JM, Cairns BR

Cell stem cell.. 2017 October 521 (4):533-546.e6. Epub 1900 01 01.

Genome-wide DNA methylation profiling in zebrafish.

Murphy PJ, Cairns BR

Methods in cell biology.. 2016 135 :345-59. Epub 06/21/2016.

Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells.

Murphy PJ, Cipriany BR, Wallin CB, Ju CY, Szeto K, Hagarman JA, Benitez JJ, Craighead HG, Soloway PD

Proceedings of the National Academy of Sciences of the United States of America.. 2013 May 7110 (19):7772-7. Epub 04/22/2013.

Microfluidic extraction, stretching and analysis of human chromosomal DNA from single cells.

Benítez JJ, Topolancik J, Tian HC, Wallin CB, Latulippe DR, Szeto K, Murphy PJ, Cipriany BR, Levy SL, Soloway PD, Craighead HG

Lab on a chip.. 2012 November 2112 (22):4848-54. Epub 1900 01 01.

Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel.

Cipriany BR, Murphy PJ, Hagarman JA, Cerf A, Latulippe D, Levy SL, Benítez JJ, Tan CP, Topolancik J, Soloway PD, Craighead HG

Proceedings of the National Academy of Sciences of the United States of America.. 2012 May 29109 (22):8477-82. Epub 05/14/2012.

Sequences sufficient for programming imprinted germline DNA methylation defined.

Park YJ, Herman H, Gao Y, Lindroth AM, Hu BY, Murphy PJ, Putnam JR, Soloway PD

PloS one.. 2012 7 (3):e33024. Epub 03/05/2012.

Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus.

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

Science.. 2011 May 13332 (6031):848-52. Epub 1900 01 01.

Single molecule epigenetic analysis in a nanofluidic channel.

Cipriany BR, Zhao R, Murphy PJ, Levy SL, Tan CP, Craighead HG, Soloway PD

Analytical chemistry.. 2010 March 1582 (6):2480-7. Epub 1900 01 01.

Books

Transgenerational Epigenetics : Evidence and Debate (2014)

Chapter: Epigenetic Changes in the Paternal Germline

Authors: Murphy KE, Murphy PJ, and Carrell DT

Publisher: Oxford: Academic Press 2014