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Publications

Pfeifer Laboratory

Selected Publications

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

Liu J, Wu X, Zhang H, Pfeifer GP, Lu Q. 2017. Dynamics of RNA polymerase II pausing and bivalent histone H3 methylation during neuronal differentiation in brain development. Cell Rep 20(6)1307–1318.

Hanley MP, Hahn MA, Li AX, Wu X, Lin J, Wang J, Choi A, Ouyang Z, Fong Y, Pfeifer GP, Devers TJ, Rosenberg DW. 2017. Genome-wide DNA methylation profiling reveals cancer-associated changes within early colonic neoplasia. Oncogene 36(35):5035–5044.

Weng YL, An R, Cassin J, Joseph J, Mi R, Wang C, Zhong C, Jin SG, Pfeifer GP, Bellacosa A, Dong X, Hoke A, He Z, Song H, Ming GL. 2017. An intrinsic epigenetic barrier for functional axon regeneration. Neuron 94(2):337–346.

Pfeifer GP. 2017. DNA methylation and mutation 2.0. Encyclopedia of Life Sciences. John Wiley & Sons, Ltd, Chichester.

Rauch TA, Pfeifer GP. 2017. Methods for assessing DNA cytosine modifications genome-wide. Handbook of Epigenetics, 2nd Edition, edited by T. Tollefsbol, Elsevier. Waltham, MA. pp. 125–134. 

Pfeifer GP, Kernstine KH. 2017. DNA methylation biomarkers in lung cancer diagnosis: closer to practical use? Transl Cancer Res 6(Suppl. 1):S122–S126.

Pfeifer GP. 2016. How tobacco smoke changes the (epi)genome. Science 354(6312):549–550.

Song J, Pfeifer GP. 2016. Are there specific readers of oxidized 5-methylcytosine bases? BioEssays 38(10):1038–1047.

Iqbal K, Tran DA, Li AX, Warden C, Bai AY, Singh P, Madaj ZB, Winn ME, Wu X, Pfeifer GP, Szabó PE. 2016. High type I error and misrepresentations in search for transgenerational epigenetic inheritance: response to Guerrero-Bosagna. Genome Biol 17:154.

Pfeifer GP. 2016. Switching enhancer methylation in metastatic melanoma. Pigm Cell Melanoma Res 29(5):491 –493.

Pfeifer GP. 2016. Epigenetics: An elusive DNA base in mammals. Nature 532:319–320.

Zhang X, Guo C, Wu X, Li AX, Liu L, Tsark W, Dammann R, Shen H, Vonderfecht SL, Pfeifer GP. 2016. Analysis of liver tumor-prone mouse models of the Hippo kinase scaffold proteins RASSF1A and SAV1. Cancer Res 76:2824–2835.

Pfeifer GP. 2016. Properly dividing with YAP. Sci Signal 9(417):fs3.

Hainaut P, Pfeifer GP. 2016. Somatic TP53 mutations in the era of genome sequencing. Cold Spring Harb Perspect Med 6(11).

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. 2016. Tet3 reads 5-carboxylcytosine through its CXXC domain and is a potential guardian against neurodegenerationCell Rep 14(3):493–505.  

Jin SG, Xiong W, Wu X, Yang L, Pfeifer GP. 2015. The DNA methylation landscape of human melanomaGenomics 106(6):322–330.       

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

Jung M, Pfeifer GP. 2015. Aging and DNA methylationBMC Biol 13:7.

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 agingNucleic Acids Res 43(15):e100.     

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 reprogrammingGenome Biol 16:59.    

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

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

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 cellsEpigenetics 9(11):1496–1503.    

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

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

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. 2014. Tet-mediated formation of 5-hydroxymethylcytosine in RNAJ Am Chem Soc 136(33):11582–1585.     

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 tumorsCancer Res 74(13):3617–3629.     

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

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 cellsOncogene 32(30):3559–3568.      

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

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 neurogenesisCell Reports 3(2):291–300.     
*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 pubertyNat Neurosci 16(3):281–289.      

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 progressionNat Commun 3:815.      

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 mutationsCancer Res 71(24):7360–7365 (Priority Report).     

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 oocytesNature 477(7366):606–610.     

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.     

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

Guo C, Zhang X, Pfeifer GP. 2011. The tumor suppressor RASSF1A prevents dephosphorylation of the mammalian STE20-like kinases MST1 and MST2J Biol Chem 286(8):6253–6261.     

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

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

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

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

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

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

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 inflammationCancer Res 68(24):10280–10289.      

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

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 cancerProc Natl Acad Sci USA 105(1):252–257.      

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 networkCurr Biol 17(8):700–705.      

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 assayProc Natl Acad Sci USA 104(13):5527–5532.     

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 cellsCancer Res 66(16):7939–7947.     

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

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

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 3p21.3Nat Genet 25(3):315–319.     

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

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.     

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

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