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A cross-divisional department spanning

The Wang Laboratory of Human Environmental Epigenomes

Selected Publications

Li W, Shang L, Huang K, Li J, Wang Z, Yao H. (2017) Identification of critical base pairs required for CTCF binding in motif M1 and M2. Protein & Cell. doi: 10.1007/s13238-017-0387-5. PMID: 28315159

An C°, Zhu G°, Martos SN°, Feng X, Zhang H°, Jia Y, and Wang, Z. (2017) TALEN-mediated FLAG-tagging of endogenous histone methyltransferase DOT1L. Advances in Biosciences and Biotechnology 8, 311-323

Martos SN°, Li T°, Bossardi R°, Lou D°, Dai H°,  Xu J, Gao G°, Wang Q°, An C°, Zhang X, Jia Y, Dawson V, Dawson TM, Ji HK, and Wang Z. (2017) Two approaches revealed a new paradigm of ‘switchable or genetics-influenced allele-specific DNA methylation (ASM)’ with potential in human disease. Cell Discovery 3, 17038: doi:10.1038/celldisc.2017.38

Wang T, Pehrsson EC, Purushotham D, Li D, Zhang B, Lawson HA, Province MA, Krapp C, Lan Y, Coarfa C, Katz TA, Tang, WY, Wang Z, Biswal S, Rajagopalan S, Colacino J, Sartor M, Neier K, Dolinoy D, Pinto J, Hamanaka R, Mutlu G, Patisaul HB, Aylor DL, Crawford GE, Chadwick LH, Duncan CG, Garton AE, McAllister KA, TaRGET II Consortium, Bartolomei MS, Walker CL, Tyson FL. (2018) The NIEHS TaRGET II Consortium and environmental epigenomes. Nature Biotechnology 36, 225-227

Li W, Shang L, Huang K, Li J, Wang Z, Yao H. (2017) Identification of critical base pairs required for CTCF binding in motif M1 and M2. Protein & Cell. doi: 10.1007/s13238-017-0387-5. PMID: 28315159

Siyu Wu, Lili Lei, Mengting Liu, Yang Song, Shibo Lu, Dan Lou°, Yonghong Shi, Zhibin Wang, and Defu He.Caenorhabditis elegans is mediated through mitochondria-associated membrane proteins Hop-1 and PINK1. Experimental Neurology (co-correspondence author) (in revision)

Fengji Liang, Ke Lyu, Yue Wang, Yanhong Yuan, Liang Lu, Qiang Feng, Xiaolu Jing, Honghui Wang, Changning Liu, Simon Rayner, Shukuan Ling, Hailong Chen, Yumin Wan, Wanlong Zhou, Li He, Bin Wu, Lina Qu, Zhibin Wang, Shanguang Chen, Jianghui Xiong, Yinghui Li. Personalized epigenome remodeling under biochemical and psychological changes during Mars500 simulated mission to Mars. Clinical Epigenetics (IF 4.987)

Lina Zhao, Mengling Yan, Xinjin Wang, Guiya Xiong, Chunhua Wu, Zhibin Wang, Zhijun Zhou, Xiuli Chang. Modification of Wnt signaling pathway on Paraquat-induced inhibition of neural progenitor cells proliferation. Toxicological and Applied Pharmacology (in revision)

Dan Lou, Wang Z. Vulnerable genetic variants-shaped allele-specific DNA methylation for complex disease risk. Frontiers in Genetics (in revision)

Guoyin Yin; Juan Liu; Yaoyan Li; Deqing Cao; Liwen Zhang; Qiaoyun Yang; Guifan Sun; Zhibin Wang; Qiang Zhang; Naijun Tang. Transgenerational inheritance of male reproductive toxicity with Igf2/H19 epigenetic alteration in CD1 mouse induced by in utero arsenic exposure. Archives of Toxicology (submitted)

*Li Z, *Dai H, Martos SN, Xu B, Gao Y, Li T, Zhu G, Schones DE, and Wang Z. (2015) Distinct roles of DNMT1-dependent and –independent methylation patterns in the genome of mouse embryonic stem cells. Genome Biol DOI: 10.1186/s13059-015-0685-2

Martos SN, Tang W, Wang Z. (2015) Elusive inheritance: Transgenerational effects and epigenetic inheritance in human environmental disease. Prog Biophys Mol Biol DOI:10.1016/j.pbiomolbio. 2015.02.011 

*Li, T., *Li, Z., Dai, H., Martos, S., Xu, J., Gao, G., An, C., Schones, D.E., Zhang, X., Dawson, VL., Dawson, TM., and Wang, Z. Novel approaches identified 17 novel candidate imprinted loci with potential in adult diseases (submitted)

Singh, A., Venkannagari, S., Oh, K., Zhang, YQ., Rhode, J., Liu, L, Nimmagadda, S., Sudini, K., Brimacombe, K., Gajghate, S., Ma, J., Wang, A., Xu, X., Shahane, S., Xia, M., Mensah, G., Wang, Z., Ferrer, M., Gabrielson, E., Li, Z., Rastinejad, F., She, M., Boxer, M., and Biswal, S. Specific small molecule inhibitor of NRF2 selectively intervenes therapeutic resistance of KEAP1 deficient NSCLC tumors. (Submitted to Nature Chemical Biology).

Martos, S.N., Tang, W., and Wang, Z. (2014) Transgenerational elusive inheritance: transgenerational effects and epigenetic inheritance in human environmental disease. Progress in Biophysics and Molecular Biology (Invited review)

*Li, Z., *Dai, H., Xu, B., Zhu, G., Li, T., Schones, D.E., and Wang, Z. (2014) Distinct roles of DNMT1-dependent and –independent methylation patterns in the genome of mouse ES cells. (*Contribute equally) (revised back for Genome Biology) (Impact factor 10.5)

Jin, Q., Zhuang, L., Lai, B., Wang, C., Li, W., Dolan, B., Wang, Z., Zhao, K., Peng, W., Dent, S., and Ge, K. (2014) Gcn5 and PCAF negatively regulate interferon b production through HAT-independent inhibition. EMBO Report DOI: 10.15252/embr.201438990

Dai, H., and Wang, Z. (2014) Histone modification patterns and their responses to environment. Current Environmental Health Reports 1:11-21 (Invited review) First published review of this new journal (1 citation already)

Wu, H., D'Alessio, A.C.D., Ito, S., Wang, Z., Cui, K., Zhao, K., Sun, Y.E., and Zhang, Y. (2011) Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual regulation in mouse embryonic stem cells. Genes Dev. 25:679-684

*Wu, H., *D'Alessio, A.C.D., Ito, S., Xia, K., Wang, Z., Cui, K., Zhao, K., Sun, Y.E., and Zhang, Y. (2011) Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature doi: 10.1038/nature 09934 (Brand New)(*Contribute equally)......................... DNA 5mC-5hmC

Daniel, J.A., *Santos, M.A., *Wang, Z., *Zang, C., Jankovic, M., Gazumyan, A., Kristopher R. Schwab, K.R.,Yamane, A., Filsuf, D., Cho, Y-W., Ge, K., Nussenzweig, M.C., Casellas, R., Dressler, G.R., Zhao, K., and Nussenzweig, A. (2010) PTIP promotes chromatin changes critical for immunoglobulin switch recombination. Science 329, 917-923 (*Contribute equally)

#Qi, H.H., #Sarkissian, M., *Hu, G-q., *Wang, Z., Bhattacharjee, A., Gordon, D.B., Lan, F., Ongusaha, P.P., Huarte, M., Yaghi, N.K., Lim, H., Garcia, B.A., Brizuela, L., Zhao, K., Roberts, T.M., and Shi, Y. (2010) Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Nature 466, 503-507  (# These authors contribute equally; * These authors contribute equally to ChIP-Seq)

Zhou, J., Wang, C., Wang, Z., Dampier, W., Wu, K., Casimiro, M.C., Yu, Z., Wang, M., Liang, B., Chepelev,L., Popov, V.M., Sune, C., Quong, A., Lisanti, M.P., Tozeren, A., Zhao, K., and Pestell, R.G. (2010) Attenuation of forkhead signaling by the retinal determination factor DACH1. Proc Natl Acad Sci USA 107,6864-6869

*Wang, Z., *Zang, C., *Cui, K., Schones, D.E., Barski, A., Peng, W., Zhao, K. (2009) Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 138,1019-1031 (*Contribute equally)(over 330 citations).............................Establishment Mechanism of Histone Acetylation Codes; Co-repressor HDACs associate with expressed genes

Comments on changing concepts in textbooks based on our discoveries. 1) HDACs binding to active genes instead of broadly accepted silent genes. Perissi, V., Jepsen, K., Glass, C.K., and Rosenfeld, M.G. (2010) Deconstructing repression: evolving models of co-repressor action. Nature Review Genetics 11,109-123; 2)histone language’ as an alternative to ‘histone code’: Lee, J-S., Smith, E., and Shilatifard, A. (2010) The language of histone crosstalk. Cell 142,682-685

*Araki, Y., *Wang, Z., Zang, C., Wood, W. III., Schones, D. E., Lhotsky, B., Westo, R., Peng, W., Becker, K.,Zhao, K., and Weng, N-p. (2009) Genome-wide analysis of histone methylation reveals chromatin state-based complex regulation of gene transcription and function of memory CD8+ T cells. Immunity 30,912-925 (* Contribute equally)

Wang Z., Schones, D.E., and Zhao, K. (2009) Characterization of human epigenomes. Current Opinion in Genetics and Development. 19,127-134

*Schones, D.E., *Cui, K., Cuddapah, S., Roh, T-y, Barski, A., Wang, Z., Wei, G., Zhao, K. (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132,887-898 (*Contribute equally)...............Human Nucleosome Map

*Wang, Z., *Zang, C., *Rosenfeld, J.A., Schones, D.E., Barski, A., Cuddapah, S., Cui, K., Roh, T-y., Peng, W., Zhang, M., Zhao, K. (2008). Combinatorial patterns of histone acetylations and methylations in the human genome.  Nature Genetics 40, 897-903 (*Contribute equally) (over 744 citations).........Human Acetylome and Identification of Histone Codes/Patterns

Comments/Debates on combinatorial patterns as histone code (a) or not (b): a, Campos, E.I. and Reinberg, D. (2009) Histones: annotating chromatin. Annu. Rev. Genet. 43,559-99; b, Rando, O.J. and Chang, H.Y. (2009) Genome-wide views of chromatin structure. Annu. Rev. Biochem. 78,245-71

Barski, A., Cuddapah, S., Cui, K., Roh, T-y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I., Zhao, K. (2007) Response: Mapping nucleosome positions using ChIP-Seq data.  Cell 131, 832-833

*Barski, A., *Cuddapah, S., *Cui, K., *Roh, T-y., *Schones, D.E., *Wang, Z., *Wei, G., Chepelev, I.,  Zhao, K.(2007) High-resolution profiling of histone methylations in the human genome. Cell 129, 823-837     (*Contribute equally and are listed alphabetically; Addressed 10 out of the published 20 histone methylations)(The No.3 hottest biology papers of 2009 by TheScientiest; over 2576 citations)..........................Human Methylome

Wu, H., D'Alessio, A.C.D., Ito, S., Wang, Z., Cui, K., Zhao, K., Sun, Y.E., and Zhang, Y. (2011) Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual regulation in mouse embryonic stem cells. Genes Dev. 25:679-684

Wu, H., D'Alessio, A.C.D., Ito, S., Wang, Z., Cui, K., Zhao, K., Sun, Y.E., and Zhang, Y. (2011) Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual regulation in mouse embryonic stem cells. Genes Dev. 25:679-684

Selected comments in journals:

Baylin, S.B and Schuebel, K.E. (2007) Genomic biology: The epigenomic era opens. Nature 448, 548-9

Goymer, P (2007) Epigenetics: Mapping the methylome without chips. Nature Review Genetics 8,489

Mardis, E.R. (2007) ChIP-seq: Welcome to the new frontier. Nature Methods 4,613-614