Penn Program in Epigenetics
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Welcome to the Penn Epigenetics Program

The mission of the UPenn Epigenetics Program is to advance epigenetics research at the Perelman School of Medicine by bringing together diverse programs performing epigenetics research or that wish to perform epigenetic research so that synergies, new insights, and therapeutic approaches can emerge towards the ultimate goal of improving human health.

New and Upcoming Events


Penn Epigenetics Monthly Meeting
Thursday, June 5, 2014, 4:00PM
9-146 Smilow Center for Translational Research



Roberto Bonasio, Ph.D.  Assistant Professor of Cell and Developmental Biology

Jennifer E. Phillips-Cremins, Ph.D.  Assistant Professor of Bioengineering

Ronen Marmorstein, Ph.D.  Professor of Biochemistry and Biophysics, Investigator, Abramson Family Cancer Research Institute


The Sequence-Specific Transcription Factor c-Jun Targets Cockayne Syndrome Protein B to Regulate Transcription and Chromatin Structure. Robert J. Lake, Erica L. Boetefuer, Pei-Fang Tsai, Jieun Jeong, Inchan Choi, Kyoung-Jae Won and Hua-Ying Fan: PLoS Genetics 10(4): e1004284, April 2014 Notes: doi:10.1371/journal.pgen.100428.

Ted Abel, Ph.D. and Benjamin Garcia, Ph.D. were recently awarded an R21 grant entitled “Cell-Type Specific Epigenomics in the Brain” to develop novel tools to purify chromatin from specific populations of neurons.

DNA methylation is required for the control of stem cell differentiation in the small intestine. Karyn L. Sheaffer, Rinho Kim, Reina Aoki, Ellen N. Elliott, Jonathan Schug, Lykas Burger, Dirk Schubeler, and Klaus H. Kaestner. Genes Dev. 2014 March 15; 28(6):652-664. doi: 10.1101/gad.230318.113.

RBPJ, the Major Transcriptional Effector of Notch Signaling, Remains Associated with Chromatin Throughout Mitosis, Suggesting a Role in Mitotic Bookmarking. Lake, R. J., Tsai, P. F., Choi, I., Won, K. J., and Fan, H.-Y. (2014) PLoS Genet 10(3): e1004204. doi:10.1371/journal.pgen.1004204

Maya Capelson, Ph.D. Awarded March of Dimes Basil O’Connor Starter Scholar Award (for proposed work on spatial genome organization in gene regulation and development)

Shelley Berger, Ph.D., Ronen Marmorstein, Ph.D., Brad Johnson, M.D., Ph.D., Peter Adams, Ph.D., Dave Schultz, Ph.D., Li-San Wang, Ph.D., and Benjamin Garcia, Ph.D. , Renewal of NIH NIA-sponsored Program Project "Epigenetics of Aging and Aging-associated Disease"

Gerd A. Blobel, MD, Ph.D. Awarded RO1 entitled, "Functions, mechanisms, and therapeutic potential of chromatin looping” (HL119479)"

Doris Wagner, Ph.D. Awarded NSF grant entitled, "Plant Polycomb Response Elements (PREs) and Polycomb Complex recruitment"

Roger A. Greenberg, M.D., Ph.D. Awarded RO1 entitled, "Roles of Chromatin Modification in BRCA1 Dependent DNA Repair"

Roger A. Greenberg, M.D., Ph.D. Awarded RO1 entitled, "DNA Double Strand Break Chromatin Alterations and Genome Integrity"

Roger A. Greenberg, M.D., Ph.D. Awarded Harrington Scholar-Innovator Grant entitled, "Targeting DNA damage induced ubiquitin regulation for cancer chemotherapy"

Roger A. Greenberg, M.D., Ph.D. Awarded PA Breast Cancer Foundation Grant entitled, "Ubiquitin regulated DNA repair and breast cancer biology"

Benjamin Garcia, Ph.D. Awarded shared instrumentation S10 grant entitled, "Orbitrap Elite Mass Spectrometer for Chromatin Biology and Epigenetics Research"

Benjamin Garcia, Ph.D. Renewal of Eli Lilly industrial-academic grant entitled "Proteomic and genomic investigation of histone lysine methyltransferases as novel targets for the treatment of cancer"

Yibin Kang, Ph.D. and Benjamin Garcia, Ph.D. Awarded Department of Defense Breast Cancer Collaborative Scholars and Innovators Award grant entitled, "Organ-tropic metastatic secretomes and exosomes in breast cancer"

Johannes Dapprich, Ph.D. and Benjamin Garcia, Ph.D. Awarded NIH R43 entitled "Reverse ChIP: Sequence-specific extraction of DNA-bound histones for analysis of post-translational modification"

Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape.  Shah PP, Donahue G, Otte GL, Capell BC, Nelson DM, Cao K, Aggarwala V, Cruickshanks HA, Rai TS, McBryan T, Gregory BD, Adams PD, Berger SL.
Genes Dev. 2013 Aug 15;27(16):1787-99. doi: 10.1101/gad.223834.113. Epub 2013 Aug 9.

ATP-dependent chromatin remodeling by Cockayne syndrome protein B and NAP1-like histone chaperones is required for efficient transcription-coupled DNA repair.
Cho I, Tsai PF, Lake RJ, Basheer A, Fan HY. PLoS Genet. 2013 Apr;9(4):e1003407. doi: 10.1371/journal.pgen.1003407. Epub 2013 Apr 18.

Maternal imprinting at the H19-Igf2 locus maintains adult haematopoietic stem cell quiescence.
Venkatraman Aparna, He Xi C, Thorvaldsen Joanne L, Sugimura Ryohichi, Perry John M, Tao Fang, Zhao Meng, Christenson Matthew K, Sanchez Rebeca, Yu Jaclyn Y, Peng Lai, Haug Jeffrey S, Paulson Ariel, Li Hua, Zhong Xiao-Bo, Clemens Thomas L, Bartolomei Marisa S, Li Linheng.Nature. 2013 Aug 15;500(7462):345-9. doi: 10.1038/nature12303. Epub 2013 Jul 17.

Regulation of leaf maturation by chromatin-mediated modulation of hormonal responses. Efroni, I., Han, S.K., Kim, H.Y., Wu, M.F., Sang, Y., Hong, J.C., Eshed, Y*, and Wagner, D*. Developmental Cell. (2013) 24, 438-445. *Corresponding authors 

Bookmarking by specific and nonspecific binding of FoxA pioneer factor to mitotic chromosomes.  Caravaca, J.M., Donahue, G., Becker, J.S., and Zaret, K.S. (2013) Genes and Development 27, 251-260.

An iPS cell line from human pancreatic ductal adenocarcinoma undergoes early to invasive stages of pancreatic cancer progression. Kim, J., Hoffman, J.P., Alpaugh, K.R., Reichert, M., Furth, E.E., Sepulveda, A.R., Yuan, C.-X., Won, K-J., Donahue, G., Sands, J., Gumbs, A. and Zaret, K.S.  (2013) Cell Reports 3, 1-12.  NIHMS 494266.

The octamer is the major form of CENP-A nucleosomes at human centromeres. Hasson, D. †, T. Panchenko†, K.J. Salimian†, M.U. Salman, N. Sekulic, A. Alonso, P.E. Warburton, and B.E. Black*. 2013. Nat. Struct. Mol. Biol., 20:687-695. (*corresponding author; †contributed equally and listed in alphabetical order)

Post-translational modification of CENP-A influences the conformation of centromeric chromatin. Bailey, A.O.†, T. Panchenko†, S.K. Matadda, J.J. Petkowski, P. Pai, D.L. Bai, D.H. Russell, I.G. Macara, J. Shabanowitz, D.F. Hunt, B.E. Black*, and D.R. Foltz*. 2013. Proc. Natl. Acad. Sci. U. S. A., 110:11827-11832. (*corresponding authors; †contributed equally)

A BRISC-SHMT complex deubiquitinates IFNAR1 and regulates interferon responses.  Zheng H, Gupta V, Patterson-Fortin J, Bhattacharya S, Katlinski K, Wu J, Varghese B, Carbone CJ, Aressy B, Fuch SY, and Greenberg RA. Cell Reports S2211-1247(13)00466-X 2013.

Acetylation limits 53BP1 association with damaged chromatin to promote homologous recombination.  Tang J, Cho NW, Cui G, Manion EM, Shanbhag NM, Botuyan MV, Mer G, Greenberg RA. Nat Struct Mol Biol 20:317-25 2013.

Biallelic deleterious BRCA1 mutations in a woman with early-onset ovarian cancer. Domchek SM, Tang J, Jill Stopfer, Lilli DR, Tischkowitz M, Foulkes WD, Monteiro ANA, Messick TE, Powers J, Yonker A, Couch FJ, Goldgar D, Nathanson KL, Greenberg RA. Cancer Discovery 3: 399-405 2013

Initial characterization of histone H3 serine 10 O-acetylation.  Britton LM, Newhart A, Bhanu NV, Sridharan R, Gonzales-Cope M, Plath K, Janicki SM, Garcia BA. Epigenetics. 2013, 8(10).

A quantitative atlas of histone modification signatures from human cancer cells.  Leroy G, Dimaggio PA, Chan EY, Zee BM, Blanco MA, Bryant B, Flaniken IZ, Liu S, Kang Y, Trojer P, Garcia BA. Epigenetics Chromatin. 2013, 6(1):20.

Proteomic and genomic approaches reveal critical functions of the H3K9 methylation pathway and Heterochromatin Protein-1γ in reprogramming to pluripotency.  Sridharan, R., Gonzales-Cope, M., Bonora, G., Chronis, C., McKee, R., Mishra, N., Garcia, B.A.*, Plath, K.* Nature Cell Biology, 2013, 15(7):872-82. *co-corresponding authors

Quantitative dynamics of the link between cellular metabolism and histone acetylation. Evertts AG, Zee BM, Dimaggio PA, Gonzales-Cope M, Coller HA, Garcia BA. J Biol Chem. 2013, 288(17):12142-51.

Large-scale global identification of protein lysine methylation in vivo. Cao, X.J., Arnaudo, A.M., Garcia, B.A. Epigenetics, 2013, 8(5):477-85.


The Roadmap Project, sponsored by NIH, provides convergence of epigenomic data on this website:  More info can be found in our research section.