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Publications

Pfeifer Laboratory

Selected Publications

For a full list of Dr. Pfeifer’s publications, please visit PubMed.

Jin SG, Zhang ZM, Dunwell TL, Harter MR, Wu X, Johnson J, Li Z, Liu J, Szabó PE, Lu Q, Xu GL, Song J, Pfeifer GP. In press. Tet3 reads 5-carboxylcytosine through its CXXC domain and is a potential guardian against neurodegeneration. Cell Rep.    Article

Jin SG, Xiong W, Wu X, Yang L, Pfeifer GP. In press. The DNA methylation landscape of human melanoma. Genomics.      PubMed

Jung M, Kadam S, Xiong W, Rauch TA, Jin SG, Pfeifer GP. 2015. MIRA-seq for DNA methylation analysis of CpG islands. Epigenomics 7(5):695–706       PubMed

Jung M, Pfeifer GP. 2015 Aging and DNA methylation. BMC Biol 13:7      PubMed

Jung M, Jin SG, Zhang X, Xiong W, Gogoshin G, Rodin AS, Pfeifer GP. 2015. Longitudinal epigenetic and gene expression profiles analyzed by three-component analysis reveal down-regulation of genes involved in protein translation in human aging. Nucleic Acids Res 43(15):e100     PubMed

Iqbal K, Tran DA, Li AX, Warden C, Bai AY, Singh P, Wu X, Pfeifer GP, Szabó PE. 2015. Deleterious effects of endocrine disruptors are corrected in the mammalian germline by epigenome reprogramming. Genome Biol 16:59.     PubMed

Pfeifer GP. 2015. How the environment shapes cancer genomes. Current Opin Oncol 27(1):71–77.     PubMed

Hahn MA, Li AX, Wu X, Pfeifer GP. 2015. Single base resolution analysis of 5-methylcytosine and 5-hydroxymethylcytosine by RRBS and TAB-RRBS. Methods Mol Biol 1238:273–287.     PubMed

Mezzanotte J, Hill V, Schmidt ML, Shinawi T, Tommasi S, Krex D, Schackert G, Pfeifer GP, Latif F, Clark GJ. 2014. RASSF6 exhibits promoter hypermethylation in metastatic melanoma and inhibits invasion in melanoma cells. Epigenetics 9(11):1496–1503.     PubMed

Hahn MA, Szabó PE, Pfeifer GP. 2014. 5-hydroxymethylcytosine: a stable or transient DNA modification? Genomics 104(5):314-323.     PubMed

Dunwell TL, Pfeifer GP. 2014. Drosophila genomic methylation: new evidence and new questions. Epigenomics 6(5):459–461.     PubMed

Fu L, Guerrero C, Zhong N, Amato N, Liu Y, Liu S, Cai Q, Jin SG, Ji D, Niedernhofer L, Pfeifer GP, Xu GL, Wang Y. Tet-mediated formation of 5-hydroxymethylcytosine in RNA. J Am Chem Soc 136(33):11582–1585.     PubMed

Hahn MA, Li AX, Wu X, Yang R, Drew DA, Rosenberg DW, Pfeifer GP. 2014. Loss of the polycomb mark from bivalent promoters leads to activation of numerous cancer-promoting genes in colorectal tumors. Cancer Res 74(13):3617–3629.     PubMed

Dunwell TL, McGuffin LJ, Dunwell JM, Pfeifer GP. 2013. The mysterious presence of a 5-methylcytosine oxidase in the Drosophila genome: possible explanations. Cell Cycle 12(21):3357–3365.     PubMed

Kalari S, Jung M, Kernstine KH, Takahashi T, Pfeifer GP. 2013. The DNA methylation landscape of small cell lung cancer suggests a differentiation defect of neuroendocrine cells. Oncogene 32(30):3559–3568.      PubMed

Pfeifer GP, Kadam S, Jin SG. 2013. 5-hydroxymethylcytosine and its potential roles in development and cancer. Epigenetics Chromatin 6(1):10.      PubMed

Hahn MA, Qiu R, Wu X, Li AX, Wang J, Zhang H, Jui J, Jin SG, Jiang Y, Pfeifer GP*, Lu Q*. 2013. Dynamics of 5-hydroxymethylcytosine and chromatin marks in mammalian neurogenesis. Cell Reports 3(2):291–300.      PubMed
*Contributing authors, equal contributions

Lomniczi A, Loche A, Castellano JM, Ronnekleiv OK, Bosch M, Kaidar G, Knoll JG, Wright H, Pfeifer GP, Ojeda SR. 2013. Epigenetic control of female puberty. Nat Neurosci 16(3):281–289.      PubMed

Zheng L, Dai H, Zhou M, Li X, Liu C, Guo Z, Wu Z, Wu J, Wang C, Zhong J, Huang Q, Garcia-Aguilar J, Pfeifer GP, Shen B. 2012. Polyploid cells rewire DNA damage response networks to overcome replication stress-induced barriers for tumor progression. Nat Commun 3:815.      PubMed

Jin SG, Jiang Y, Qiu R, Rauch TA, Wang Y, Schackert G, Krex D, Lu Q, Pfeifer GP. 2011. 5-hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutations. Cancer Res 71(24):7360–7365 (Priority Report).      PubMed

Gu TP, Guo F, Yang H, Wu HP, Xu GF, Liu W, Xie ZG, Shi L, He X, Jin SG, Iqbal K, Shi YG, Deng Z, Szabo PE, Pfeifer GP, Li J, Xu GL. 2011. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 477(7366):606–610.     PubMed

Jin SG, Wu X, Li AX, Pfeifer GP. 2011. Genomic mapping of 5-hydroxymethylcytosine in the human brain. Nucleic Acids Res 39(12):5015–5024.     PubMed

Iqbal K, Jin SG, Pfeifer GP*, Szabó PE*. 2011. Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc Natl Acad Sci USA 108(9):3642–3647.     PubMed  
*Equally contributing authors

Guo C, Zhang X, Pfeifer GP. 2011. The tumor suppressor RASSF1A prevents dephosphorylation of the mammalian STE20-like kinases MST1 and MST2. J Biol Chem 286(8):6253–6261.     PubMed

Pfeifer GP, Hainaut P. 2011. Next-generation sequencing: emerging lessons on the origins of human cancer. Curr Opin Oncol 23(1):62–68.      PubMed

Kalari S, Pfeifer GP. 2010. Identification of driver and passenger DNA methylation in cancer by epigenomic analysis. Adv Genet 70:277–308.      PubMed

Jin SG, Kadam S, Pfeifer GP. 2010. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res 38(11):e125.     PubMed

Pfeifer GP, Dammann R, Tommasi S. 2010. RASSF proteins. Curr Biol 20(8):R344-R345.     PubMed

Wu X, Rauch TA, Zhong X, Bennett WP, Latif F, Krex D, Pfeifer GP. 2010. CpG island hypermethylation in human astrocytomas. Cancer Res 70(7):2718–2727.     PubMed

Rauch TA, Wu X, Zhong X, Riggs AD, Pfeifer GP. 2009. A human B cell methylome at 100-base pair resolution. Proc Natl Acad Sci USA 106(3):671–678.      PubMed

Hahn MA, Hahn T, Lee DH, Esworthy RS, Kim BW, Riggs AD, Chu FF, Pfeifer GP. 2008. Methylation of polycomb target genes in intestinal cancer is mediated by inflammation. Cancer Res 68(24):10280–10289.      PubMed

Jin SG, Guo C, Pfeifer GP. 2008. GADD45A does not promote DNA demethylation. PLoS Genet 4(3):e1000013.      PubMed

Rauch TA, Zhong X, Wu X, Wang M, Kernstine KH, Wang Z, Riggs AD, Pfeifer GP. 2008. High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer. Proc Natl Acad Sci USA 105(1):252–257.      PubMed

Guo C, Tommasi S, Liu L, Yee JK, Dammann R, Pfeifer GP. 2007. The RASSF1A tumor suppressor protein is a component of a mammalian complex analogous to the Drosophila Hippo/Salvador/Lats tumor suppressor network. Curr Biol 17(8):700–705.      PubMed

Rauch T, Wang Z, Zhang X, Zhong X, Wu X, Lau S, Kernstine K, Riggs AD, Pfeifer GP. 2007. Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay. Proc Natl Acad Sci USA 104(13):5527–5532.     PubMed

Rauch T, Li H, Wu X, Pfeifer GP. 2006. MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res 66(16):7939–7947.     PubMed

Liu L, Tommasi S, Lee DH, Dammann R, Pfeifer GP. 2003. Control of microtubule stability by the RASSF1A tumor suppressor. Oncogene 22(50):8125–8136.     PubMed

Pfeifer GP, Denissenko MF, Olivier M, Tretyakova N, Hecht SS, Hainaut P. 2002. Tobacco smoke carcinogens, DNA damage and p53 mutations in smoking-associated cancers. Oncogene 21(48):7435–7451.     PubMed

Dammann R, Li C, Yoon JH, Chin PL, Bates S, Pfeifer GP. 2000. Epigenetic inactivation of a RAS association domain family protein from the lung tumour suppressor locus 3p21.3. Nat Genet 25(3):315–319.     PubMed

Denissenko MF, Chen JX, Tang MS, Pfeifer GP. 1997. Cytosine methylation determines hotspots of DNA damage in the human P53 gene. Proc Natl Acad Sci USA 94(8):3893–3898.     PubMed

Denissenko MF, Pao A, Tang MS, Pfeifer GP. 1996. Preferential formation of benzo[a]pyrene adducts at lung cancer mutational hotspots in P53Science 274(5286):430–432.     PubMed

Tornaletti S, Pfeifer GP. 1994. Slow repair of pyrimidine dimers at p53 mutation hot spots in skin cancer. Science 263(5152):1436–1438.     PubMed

Pfeifer GP, Steigerwald SD, Mueller PR, Wold B, Riggs AD. 1989. Genomic sequencing and methylation analysis by ligation mediated PCR. Science 246(4931):810–813.     PubMed