The He Group - University of Chicago
Hohos, N. M.; Lee, K.; Ji, L.; Yu, M.; Kandasamy, M. M.; Phillips, B. G.; Baile, C. A.; He, C.; Schmitz, R. J.; Meagher, R. B. DNA cytosine hydroxymethylation levels are distinct among non-overlapping classes of peripheral blood leukocytes. J. Immunol. Methods 2016, [Epub ahead of print]
Yu, P.; Ji, L.; Lee, K. J.; Yu, M.; He, C.; Ambati, S.; McKinney, E. C.; Jackson, C.; Baile, C. A.; Schmitz, R. J.; Meagher, R. B. Subsets of Visceral Adipose Tissue Nuclei with Distinct Levels of 5-Hydroxymethylcytosine. PLoS One 2016, 11, e0154949.
Yang, Y. A.; Zhao, J. C.; Fong, K. W.; Kim, J.; Li, S.; Song, C.; Song, B.; Zheng, B.; He, C.; Yu, J. FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function. Nucleic Acids Res. 2016, [Epub ahead of print]
von Meyenn, F.; Iurlaro, M.; Habibi, E.; Liu, N. Q.; Salehzadeh-Yazdi, A.; Santos, F.;
Petrini, E.; Milagre, I.; Yu, M.; Xie, Z.; Kroeze, L. I.; Nesterova, T. B.; Jansen, J. H.;
Xie, H.; He, C.; Reik, W.; Stunnenberg, H. G. Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells. Mol. Cell 2016,[Epub ahead of print]
Luo, G. Z.; Wang, F.; Weng, X.; Chen, K.; Hao, Z.; Yu, M.; Deng, X.; Liu, J.; He, C. Characterization of eukaryotic DNA N6-methyladenine by a highly sensitive restriction enzyme-assisted sequencing. Nat. Commun. 2016, 7, 11301.
Bernstein, A. I.; Lin, Y.; Street, R. C.; Lin, L.; Dai, Q.; Yu, L.; Bao, H.; Gearing, M.;
Lah, J. J.; Nelson, P. T.; He, C. Levey AI, Mull& JG, Duan R, Jin P. 5-hydroxymethylation-associated epigenetic modifiers of Alzheimer's disease modulate Tau-induced neurotoxicity. Hum. Mol. Genet. 2016, [Epub ahead of print]
Roundtree, I. A.; He, C. Nuclear m6A Reader YTHDC1 Regulates mRNA Splicing. Hum. Mol. Genet. 2016, 32, 320-321.
Sun, M.; Song, M. M.; Wei, B.; Gao, Q.; Li, L.; Yao, B.; Chen, L.; Lin, L.; Dai, Q.; Zhou, X.; Tao, J.; Chen, J.; He, C.; Jin, P.; Xu, Z. 5-hydroxymethylcytosine-mediated alteration of transposon activity associated with the exposure to adverse in utero environments in human. Hum. Mol. Genet. 2016, [Epub ahead of print]
Ji, Q.; Chen, P. J.; Qin, G.; Deng, X.; Hao, Z.; Wawrzak, Z.; Yeo, W. S.; Quang, J. W.; Cho, H.; Luo, G. Z.; Weng, X.; You, Q.; Luan, C. H.; Yang, X.; Bae, T.; Yu, K.; Jiang, H.; He, C. Structure and mechanism of the essential two-component signal-transduction system WalKR in Staphylococcus aureus. Nat. Commun. 2016, 7, 11000.
Chen, K.; Zhao, B. S.; He, C. Nucleic Acid Modifications in Regulation of Gene Expression. Cell Chem. Biol. 2016, 74-85.
Ngo, T. T.; Yoo, J.; Dai, Q.; Zhang, Q.; He, C.; Aksimentiev, A.; Ha, T. Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability. Nat. Commun. 2016, 7, 10813.
Huang, H.; Jiang, X.; Wang, J.; Li, Y.; Song, C. X.; Chen, P.; Li, S.; Gurbuxani, S.; Arnovitz, S.; Wang, Y.; Weng, H.; Neilly, M. B.; He, C.; Li, Z.; Chen, J. Identification of MLL-fusion/MYC┫miR-26┫TET1 signaling circuit in MLL-rearranged leukemia. Cancer Lett. 2016, 372, 157-165.
Dominissini, D.; Nachtergaele, S.; Moshitch-Moshkovitz, S.; Peer, E.; Kol, N.;
Ben-Haim, M. S.; Dai, Q.; Di Segni, A.; Salmon-Divon, M.; Clark, W. C.; Zheng, G.; Pan,
T.; Solomon, O.; Eyal, E.; Hershkovitz, V.; Han, D.; Dor&, L. C.; Amariglio, N.;
Rechavi, G.; He, C. The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA. Nature 2016, 530, 441-446.
Dominissini, D.; He, C.; Rechavi, G. RNA epigenetics. The Scientist 2016, 30, 35-39.
Roundtree, I. A.; He, C. RNA epigenetics & chemical messages for posttranscriptional gene regulation. Curr. Opin. Chem. Bio. 2016, 30, 46-51.
Chen, K.; Zhang, J.; Guo, Z.; Ma, Q.; Xu, Z.; Zhou, Y.; Xu, Z.; Li, Z.; Liu, Y.; Ye, X.; Li, X.; Yuan, B.; Ke, Y.; He, C.; Zhou, L.; Liu, J.; Ci, W. Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer. Cell Res. 2016, 26, 103-118.
Dai, Q.; Sanstead, P. J.; Peng, C. S.; Han, D.; He, C.;* Tokmakoff, A.* Weakened N3 Hydrogen Bonding by 5-Formylcytosine and 5-Carboxylcytosine Reduces Their Base-Pairing Stability. ACS Chem. Bio. 2016, 11, 470-477.
Hu, L.; He, C. Detecting hepatocellular carcinoma in blood. Cell Res. 2015, 25, .
Wang, J.; Luo, C.; Shan, C.; You, Q.; Lu, J.;
Vinkenborg, J. L.; Fan, J.; Kang, H.;
Xie, Y.; Karpus, J.; Chen, S.;
Ouyang, S.;
Zhang, N.; Ding, H.; Merkx, M.;
Chen, J.*;
Jiang H.*; He, C.* Inhibition of human copper trafficking by a small molecule significantly attenuates cancer cell proliferation. Nat. Chem. 2015, 7, 968-979.
Hu, L.; Lu, J.; Cheng, J.; Rao, Q.; Li, Z.; Hou, H.; Lou, Z.; Zhang, L.; Li, W.; Gong, W.; Liu, M.; Sun, C.; Yin, X.; Li, J.; Tan, X.; Wang, P.; Wang, Y.; Fang, D.; Cui, Q.; Yang, P.; He, C.; Jiang, H.; Luo, C.; Xu, Y. Structural insight into substrate preference for TET-mediated oxidation. Nature
2015, 527, 118-122.
Luo, G.-Z.; Blanco, M. A.; Greer, E. L.; He, C.*; Shi, Y.* DNA N6-methyladenine: a new epigenetic mark in eukaryotes? Nat. Rev. Mol. Cell Biol. 2015, 16, 705-710.
Lin, R.; Elf, S.; Shan, C.; Kang, H. B.; Ji, Q.; Zhou, L.; Hitosugi, T.; Zhang, L.; Zhang, S.; Seo, J. H.; Xie, J.; Tucker, M.; Gu, T. L.; Sudderth, J.; Jiang, L.; Mitsche, M.; DeBerardinis, R. J.; Wu, S.; Li, Y.; Mao, H.; Chen, P. R.; Wang, D.; Chen, G. Z.; Hurwitz, S. J.; Lonial, S.; Arellano, M. L.; Khoury, H. J.; Khuri, F. R.; Lee, B. H.; Lei, Q.; Brat, D. J.; Ye, K.; Boggon, T. J.; He, C.; Kang, S.; Fan, J.; Chen, J. 6-Phosphogluconate dehydrogenase links oxidative PPP, lipogenesis and tumour growth by inhibiting LKB1-AMPK signalling. Nat. Cell Biol. 2015, 17, .
He, C. Chemical decaging in living systems. Natl. Sci. Rev. 2015, 2, 250-251.
Pacis, A.; Tailleux, L.; Morin, A. M.; Lambourne, J.; Maclsaac, J. L.; Yotova, V.; Dumaine, A.; Danckaert, A.; Luca, F.; Grenier, J. C.; Hansen, K. D.; Gicquel, B.; Yu, M.; Pai, A.; He, C.; Tung, J.; Pastinen, T.; Kobor, M. S.; Pique-Regi, R.; Gilad, Y.; Barreiro, L. B. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Res. 2015, 25, .
Xia, B.; Han, D.; Lu, X.; Sun, Z.; Zhou, A.; Yin, Q.; Zeng, H.; Liu, M.; Jiang, X.; Xie, W.; He, C.*; Yi, C.* Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale. Nat. Methods 2015, 12, .
Yu, M.; Ji, L.; Neumann, D. A.; Chung, D. H.; Groom, J.; Westpheling, J.; He, C.*; Schmitz, R. J.* Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite-sequencing. Nucleic Acids Res. 2015, 43, e148.
Kang, H. B.; Fan, J.; Lin, R.; Elf, S.; Ji, Q.; Zhao, L.; Jin, L.; Seo, J. H.; Shan, C.; Arbiser, J. L.; Cohen, C.;, Brat, D.; Miziorko, H. M.; Kim, E.; Abdel-Wahab, O.; Merghoub, T.; Fr&hling, S.; Scholl, C.; Tamayo, P.; Barbie, D. A.; Zhou, L.; Pollack, B. P.; Fisher, K.; Kudchadkar, R. R.; Lawson, D. H.; Sica, G.; Rossi, M.; Lonial, S.; Khoury, H. J.; Khuri, F. R.; Lee, B. H.; Boggon, T. J.; He, C.; Kang, S.; Chen, J. Metabolic Rewiring by Oncogenic BRAF V600E Links Ketogenesis Pathway to BRAF-MEK1 Signaling. Mol. Cell 2015, 59, 345-358.
Wang, L.; Zhou, Y.; Xu, L.; Xiao, R.; Lu, X.; Chen, L.; Chong, J.; Li, H.; He, C.; Fu, X. D.; Wang, D. Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex. Nature 2015, 523, 621-625.
Zheng, G.; Qin, Y.; Clark, W. C.; Dai, Q.; Yi, C.; He, C.; Lambowitz, A. M.; Pan, T. Efficient and quantitative high-throughput tRNA sequencing. Nat. Methods 2015, 12, 835-837.
Yue, Y.; Liu, J.; He, C.
RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation. Genes Dev. 2015, 29, .
Deng, X.; Chen, K.; Luo, G. Z.; Weng, X.; Ji, Q.; Zhou, T.; He, C. Widespread occurrence of N6-methyladenosine in bacterial mRNA. Nucleic Acids Res. 2015, 43, .
He, C. Decoding the transcriptome and DNA methylome of human primordial germ cells. Sci. China Life Sci. 2015, 58, 729-730.
Wang, X.; Zhao, B. S.; Roundtree, I. A.; Lu, Z.; Han, D.; Ma, H.; Weng, X.; Chen, K.; Shi, H.; He, C. N6-methyladenosine Modulates Messenger RNA Translation Efficiency. Cell 2015, 161, .
Greer, E. L.; Blanco, M. A.; Gu, L.; Sendinc, E.; Liu, J.; Aristiz&bal-Corrales, D.; Hsu, C. H.; Aravind, L.; He, C.; Shi, Y. DNA Methylation on N6-Adenine in C. elegans. Cell 2015, 161, 868-878.
Fu, Y.; Luo, G. Z.; Chen, K.; Deng, X.; Yu, M.; Han, D.; Hao, Z.; Liu, J.; Lu, X.; Dor&, L. C.; Weng, X.; Ji, Q.; Mets, L.; He, C. N6-methyldeoxyadenosine marks active transcription start sites in chlamydomonas. Cell 2015, 161, 879-892.
Zhang, G.; Huang, H.; Liu, D.; Cheng, Y.; Liu, X.; Zhang, W.; Yin, R.; Zhang, D.; Zhang, P.; Liu, J.; Li, C.; Liu, B.; Luo, Y.; Zhu, Y.; Zhang, N.; He, S.; He, C.; Wang, H.; Chen, D. N6-methyladenine DNA modification in Drosophila. Cell 2015, 161, 893-906.
Cheglakov, Z.; Cronin, T. M.; He, C.; Weizmann, Y. Live Cell MicroRNA Imaging Using Cascade Hybridization Reaction. J. Am. Chem. Soc. 2015, 137, .
Song, Y.; Yang, M.; Wegner, S. V.; Zhao, J.; Zhu, R.; Wu, Y.; He, C.; Chen, P. R. A Genetically Encoded FRET Sensor for Intracellular Heme. ACS Chem. Biol. 2015. 17, .
He, C.; Cole, P. Introduction: epigenetics. Chem. Rev. 2015, 115, .
Zhao, B. S.; He, C. Fate by RNA methylation: m6A steers stem cell pluripotency. Genome Biol. 2015, 16, 43.
Liu, N.; Dai, Q.; Zheng, G.; He, C.; Parisien, M.; Pan, T. N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature 2015, 518, 560-564.
Lu, X.; Zhao, B. S.; He, C. TET family proteins: oxidation activity, interacting molecules, and functions in diseases. Chem. Rev. 2015, 115, .
Jin, L.; Li, D.; Alesi, G. N.; Fan, J.; Kang, H. B.; Lu, Z.; Boggon, T. J.; Jin, P.; Yi, H.; Wright, E. R.; Duong, D.; Seyfried, N. T.; Egnatchik, R.; DeBerardinis, R. J.; Magliocca, K. R.; He, C.; Arellano, M. L.; Khoury, H. J.; Shin, D. M.; Khuri, F. R.; Kang, S. Glutamate dehydrogenase 1 signals through antioxidant glutathione peroxidase 1 to regulate redox homeostasis and tumor growth. Cancer Cell 2015, 27, 257-270.
Lu, X.; Han, D.; Zhao, B. S.; Song, C. X.; Zhang, L. S.; Dore, L. C.; He, C. Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics. Cell Res.2015, 25, 386-389.
Chen, X.; Velmurugu, Y.; Zheng, G.; Park, B.; Shim, Y.; Kim, Y.; Liu, L.; Van Houten, B.; He, C.; Ansari, A.; Min, J. H. Kinetic gating mechanism of DNA damage recognition by Rad4/XPC. Nat. Commun. 2015, 6, 5849.
Chen, K.; Lu, Z.; Wang, X.; Fu, Y.; Luo, G. Z.; Liu, N.; Han, D.; Dominissini, D.; Dai, Q.; Pan, T.; He, C. High-Resolution N(6) -Methyladenosine (m(6) A) Map Using Photo-Crosslinking-Assisted m(6) A Sequencing. Angew. Chem. Int. Ed. 2015, 54, .
Yu, M.; Song, C. X.; He, C. Detection of mismatched 5-hydroxymethyluracil in DNA by selective chemical labeling. Methods
2015, 72, 16-20.
Zhao, B. S.; He, C. Pseudouridine in a new era of RNA modifications. Cell Res. 2015, 25, 153-154.
He, C. Visualizing a protein's sugars. Natl. Sci. Rev. 2014, 1, 480-481.
Tsai, Y. P.; Chen, H. F.; Chen, S. Y.; Cheng, W. C.; Wang, H. W.; Shen, Z. J.; Song, C.; Teng, S. C.; He, C.; Wu, K. J. TET1 regulates hypoxia-induced epithelial-mesenchymal transition by acting as a co-activator. Genome Biol. 2014, 15, 513.
Rampal, R.; Alkalin, A.; Madzo, J.; Vasanthakumar, A.; Pronier, E.; Patel, J.; Li, Y.; Ahn, J.; Abdel-Wahab, O.; Shih, A.; Lu, C.; Ward, P. S.; Tsai, J. J.; Hricik, T.; Tosello, V.; Tallman, J. E.; Zhao, X.; Daniels, D.; Dai, Q.; Ciminio, L.; Aifantis, I.; He, C.; Fuks, F.; Tallman, M. S.; Ferrando, A.; Nimer, S.; Paietta, E.; Thompson, C. B.; Licht, J. D.; Mason, C. E.; Godley, L. A.; Melnick, A.; Figueroa, M. E.; Levine, R. L. DNA Hydroxymethylation Profiling Reveals that WT1 Mutations Result in Loss of TET2 Function in Acute Myeloid Leukemia. Cell Rep. 2014, 9, .
Luo, G. Z.; MacQueen, A.; Zheng, G.; Duan, H.; Dore, L. C.; Lu, Z.; Liu, J.; Chen, K.; Jia, G.; Bergelson, J.; He, C. Unique features of the m(6)A methylome in Arabidopsis thaliana. Nat. Commun. 2014, 5, 5630.
Zhao, X.; Yang, Y.; Sun, B. F.; Shi, Y.; Yang, X.; Xiao, W.; Hao, Y. J.; Ping, X. L.; Chen, Y. S.; Wang, W. J.; Jin, K. X.; Wang, X.; Huang, C. M.; Fu, Y.; Ge, X. M.; Song, S. H.; Jeong, H. S.; Yanagisawa, H.; Niu, Y.; Jia, G. F.; Wu, W.; Tong, W. M.; Okamoto, A.; He, C.; Rendtlew Danielsen, J. M.; Wang, X. J.; Yang, Y. G. FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Res. 2014, 24, .
Zhu, T.; Roundtree, I. A.; Wang, P.; Wang, X.; Wang, L.; Sun, C.; Tian, Y.; Li, J.; He, C.; Xu, Y. Crystal structure of the YTH domain of YTHDF2 reveals mechanism for recognition of N6-methyladenosine. Cell Res. 2014, 24, .
Odoh, S. O.; Bondarevsky, G. D.; Karpus, J.; Cui, Q.; He, C.; Spezia, R.; Gagliardi, L. UO Uptake by Proteins: Understanding the Binding Features of the Super Uranyl Binding Protein and Design of a Protein with Higher Affinity. J. Am. Chem. Soc. 2014, 136, .
Wang, X.; He, C. Dynamic RNA modifications in posttranscriptional regulation. Mol. Cell 2014, 56, 5-12.
Deng, X.; Liang, H.; Chen, K.; He, C.; Lan, L.; Tang, X. Molecular mechanisms of two-component system RhpRS regulating type III secretion system in Pseudomonas syringae. Nucleic Acids Res. 2014, 42, .
Hon, G. C.; Song, C. X.; Du, T.; Jin, F.; Selvaraj, S.; Lee, A. Y.; Yen, C. A.; Ye, Z.; Mao, S. Q.; Wang, B. A.; Kuan, S.; Edsall, L. E.; Zhao, B. S.; Xu, G. L.; He, C.; Ren, B. 5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation. Mol. Cell. 2014, 56, 286-297.
Xu, C.; Wang, X.; Liu, K.; Roundtree, I. A.; Tempel, W.; Li, Y.; Lu, Z.; He, C.; Min, J. Structural basis for selective binding of m(6)A RNA by the YTHDC1 YTH domain. Nat. Chem. Biol. 2014, 10, 927-929.
Nazor, K. L.; Boland, M. J.; Bibikova, M.; Klotzle, B.; Yu, M.; Glenn-Pratola, V. L.; Schell, J. P.; Coleman, R. L.; Cabral-da-Silva, M. C.; Schmidt, U.; Peterson, S. E.; He, C.; Loring, J. F.; Fan, J. B. Application of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution in human pluripotent stem cells. Genomics 2014, 104, 358-367.
Cheng, Y.; Dai, Q.; Morshed, R. A.; Fan, X.; Wegscheid, M. L.; Wainwright, D. A.; Han, Y.; Zhang, L.; Auffinger, B.; Tobias, A. L.; Rincon, E.; Thaci, B.; Ahmed, A. U.; Warnke, P. C.; He, C.; Lesniak, M. S. Blood-Brain Barrier Permeable Gold Nanoparticles: An Efficient Delivery Platform for Enhanced Malignant Glioma Therapy and Imaging. Small 2014, 10, .
Shan, C.; Elf, S.; Ji, Q.; Kang, H. B.; Zhou, L.; Hitosugi, T.; Jin, L.; Lin, R.; Zhang, L.; Seo, J. H.; Xie, J.; Tucker, M.; Gu, T. L.; Sudderth, J.; Jiang, L.; DeBerardinis, R. J.; Wu, S.; Li, Y.; Mao, H.; Chen, P. R.; Wang, D.; Chen, G. Z.; Lonial, S.; Arellano, M. L.; Khoury, H. J.; Khuri, F. R.; Lee, B. H.; Brat, D. J.; Ye, K.; Boggon, T. J.; He, C.; Kang, S.; Fan, J.; Chen, J. Lysine acetylation activates 6-phosphogluconate dehydrogenase to promote tumor growth. Mol. Cell 2014, 55, 552-565.
Zhao, L.; Sun, M. A.; Li, Z.; Bai, X.; Yu, M.; Wang, M.; Liang, L.; Shao, X.; Arnovitz, S.; Wang, Q.; He, C.; Lu, X.; Chen, J.; Xie, H. The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation. Genome Res. 2014, 24, .
Zheng, G.; Cox, T.; Tribbey, L.; Wang, G. Z.; Iacoban, P.; Booher, M. E.; Gabriel, G. J.; Zhou, L.; Bae, N.; Rowles, J.; He, C.; Olsen, M. J. Synthesis of a FTO inhibitor with anticonvulsant activity. ACS Chem. Neurosci. 2014, 5, 658-665.
Wen, L.; Li, X.; Yan, L.; Tan, Y.; Li, R.; Zhao, Y.; Wang, Y.; Xie, J.; Zhang, Y.; Song, C.; Yu, M.; Liu, X.; Zhu, P.; Hou, Y.; Guo, H.; Wu, X.; He, C.; Tang, F.; Qiao, J. Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain. Genome Biol. 2014, 15, R49.
Yin, Y.; Yang, L.; Zheng, G.; Gu, C.; Yi, C.; He, C.; Gao, Y. Q.; Zhao, X. S. Dynamics of spontaneous flipping of a mismatched base in DNA duplex. Proc. Natl. Acad. Sci. 2014, 111, .
Zhao, L.; Sun, M. A.; Li, Z.; Bai, X.; Yu, M.; Wang, M.; Liang, L.; Shao, X.; Arnovitz, S.; Wang, Q.; He, C.; Lu, X.; Chen, J.; Xie, H. The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation. Genome Res. 2014, 24, .
Wang, X.; He, C. Reading RNA methylation codes through methyl-specific binding proteins. RNA Biol. 2014, 11, 669-672.
Wang, L.; Zhang, J.; Duan, J.; Gao, X.; Zhu, W.; Lu, X.; Yang, L.; Li, G.; Ci, W.; Li, W.; Zhou, Q.; Aluru, N.; Tang, F.; He, C.; Huang, X.; Liu, J. Programming and inheritance of parental DNA methylomes in mammals. Cell 2014, 157, 979-991.
Deng, X.; Liang, H.; Ulanovskaya, O. A.; Ji, Q.; Zhou, T.; Sun, F.; Lu, Z.; Hutchison, A. L.; Lan, L.; Wu, M.; Cravatt, B. F.; He, C. Steady-state hydrogen peroxide induces glycolysis in Staphylococcus aureus and Pseudomonas aeruginosa. J. Bacteriol 2014, 196, .
Dominissini, D.; He, C. Cancer: Damage prevention targeted. Nature. 2014, 508, 191-192.
Fu, Y.; Dominissini, D.; Rechavi, G.; He, C. Gene expression regulation mediated through reversible m(6)A RNA methylation. Nat. Rev. Genet. 2014, 15, 293-306.
Zhang, L.; Chen, W.; Iyer, L. M.; Hu, J.; Wang, G.; Fu, Y.; Yu, M.; Dai, Q.; Aravind, L.; He, C. A TET Homologue Protein from Coprinopsis cinerea (CcTET) That Biochemically Converts 5-Methylcytosine to 5-Hydroxymethylcytosine, 5-Formylcytosine, and 5-Carboxylcytosine. J. Am. Chem. Soc. 2014, 136, .
Poor, C. B.; Wegner, S. V.; Li, H.; Dlouhy, A. C.; Schuermann, J. P.; Sanishvili, R.; Hinshaw, J. R.; Riggs-Gelasco, P. J.; Outten, C. E.; He, C. Molecular mechanism and structure of the Saccharomyces cerevisiae iron regulator Aft2. Proc. Natl. Acad. Sci. 2014, 111, .
Zheng, G.; Fu, Y.; He, C. Nucleic acid oxidation in DNA damage repair and epigenetics. Chem. Rev. 2014, 114, .
Chen, W.; Zhang, L.; Zheng, G.; Fu, Y.; Ji, Q.; Liu, F.; Chen, H.; He, C. Crystal structure of the RNA demethylase ALKBH5 from zebrafish. FEBS Lett. 2014, 588, 892-898.
Zhou, L.; Bosscher, M.; Zhang, C.; Ozcubukcu, S.; Zhang, L.; Zhang, W.; Li, C. J.; Liu, J.; Jensen, M. P.; Lai, L.; He, C. A protein engineered to bind uranyl selectively and with femtomolar affinity. Nat. Chem. 2014, 6, 236-241.
Madzo, J.; Liu, H.; Rodriguez, A.; Vasanthakumar, A.; Sundaravel, S.; Caces, D. B.; Looney, T. J.; Zhang, L.; Lepore, J. B.; Macrae, T.; Duszynski, R.; Shih, A. H.; Song, C. X.; Yu, M.; Yu, Y.; Grossman, R.; Raumann, B.; Verma, A.; He, C.; Levine, R. L.; Lavelle, D.; Lahn, B. T.; Wickrema, A.; Godley, L. A. Hydroxymethylation at Gene Regulatory Regions Directs Stem/Early Progenitor Cell Commitment during Erythropoiesis. Cell Rep.. 2014, 6, 231-244.
Liu, J.; Yue, Y.; Han, D.; Wang, X.; Fu, Y.; Zhang, L.; Jia, G.; Yu, M.; Lu, Z.; Deng, X.; Dai, Q.; Chen, W.; He, C. A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat. Chem. Biol. 2014, 10, 93-95.
Wang, X.; Lu, Z.; Gomez, A.; Hon, G. C.; Yue, Y.; Han, D.; Fu, Y.; Parisien, M.; Dai, Q.; Jia, G.; Ren, B.; Pan, T.; He, C. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 2014, 505, 117-120.
Hao, Z.; Lou, H.; Zhu, R.; Zhu, J.; Zhang, D.; Zhao, B. S.; Zeng, S.; Chen, X.; Chan, J.; He, C.; Chen, P. R. The multiple antibiotic resistance regulator MarR is a copper sensor in Escherichia coli. Nat. Chem. Biol. 2014, 10, 21-28.
Chen, C. C.; Xiao, S.; Xie, D.; Cao, X.; Song, C. X.; Wang, T.; He, C.; Zhong, S. Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions. PLoS Comput. Biol.. 2013, 9, e1003367.
Zhao, B. S.; Zhang, G.; Zeng, S.; He, C.; Chen, P. R. Probing subcellular organic hydroperoxide formation via a genetically encoded ratiometric and reversible fluorescent indicator. Integrative Biology. 2013, 5, .
Liu, N.; Parisien, M.; Dai, Q.; Zheng, G.; He, C.; Pan, T. Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA. RNA. 2013, 19, .
Song, C. X.; He, C. Trends Biochem. Sci. Potential functional roles of DNA demethylation intermediates. 2013, 38, 480-484.
Ji, Q.; Zhao, B. S.; He, C. A highly sensitive and genetically encoded fluorescent reporter for ratiometric monitoring of quinones in living cells. Chem. Commun. 2013, 49, .
Lister, R.; Mukamel, E. A.; Nery, J. R.; Urich, M.; Puddifoot, C. A.; Johnson, N. D.; Lucero, J.; Huang, Y.; Dwork, A. J.; Schultz, M. D.; Yu, M.; Tonti-Filippini, J.; Heyn, H.; Hu, S.; Wu, J. C.; Rao, A.; Esteller, M.; He, C.; Haghighi, F. G.; Sejnowski, T. J.; Behrens, M. M.; Ecker, J. R. Global epigenomic reconfiguration during mammalian brain development. Science. 2013, 341, 1237905.
Huang, H.; Jiang, X.; Li, Z.; Li, Y.; Song, C. X.; He, C.; Sun, M.; Chen, P.; Gurbuxani, S.; Wang, J.; Hong, G. M.; Elkahloun, A. G.; Arnovitz, S.; Szulwach, K.; Lin, L.; Street, C.; Wunderlich, M.; Dawlaty, M.; Neilly, M. B.; Jaenisch, R.; Yang, F. C.; Mulloy, J. C.; Jin, P.; Liu, P. P.; Rowley, J. D.; Xu, M.; Chen, J. TET1 plays an essential oncogenic role in MLL-rearranged leukemia. Proc. Natl. Acad. Sci. 2013, 110, .
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2009, 71, 198-211.
Shigdel, U.K. and He, C. "A New 1'-Methylenedisulfide
Deoxyribose that Forms an Efficient Cross-Link to DNA Cytosine-5 Methyltransferase (DNMT) J. Am. Chem. Soc. 2008,
Qiu, Z.; Lu, L.; Jian, X.;
He, C. "A Diazirine-Based Nucleoside Analogue for Efficient DNA
Interstrand Photocross-Linking" J. Am. Chem. Soc. 2008,
Jia, G.; Yang, C.-G.; Yang, S.; Jian, X.;
Yi, C.; Zhou, Z.; He, C. "Oxidative demethylation of 3-methylthymine and
3-methyluracil in single-stranded DNA and RNA by mouse and human FTO"
FEBS Letters 2008, 582, .
Chen, H.; Hu, J.; Chen, P.R.; Lan, L.; Li,
Z.; Hicks, L.M.; Dinner, A.R; He, C. "The Pseudomonas aeruginosa
multidrug efflux regulator MexR uses an oxidation-sensing mechanism"
Proc. Natl. Acad. Sci. 2008, 105, .
Li, X.; Ye, S.; He, C.; Yu, Z.-X.
"Mechanisms of Br&nsted Acid Catalyzed Additions of
Phenols and Protected Amines to Olefins: A DFT Study" Eur. J. Org.
Chem. 2008, 25, .
Shan, G.; Li, Y.; Zhang, J.; Li, W.;
Szulwach, K.E.; Duan, R.; Faghihi, M.A.; Khalil, A.M.; Lu, L.; Paroo,
Z.; Chan, A.W.S.; Shi, Z.; Liu, Q.; Wahlestedt, C.; He, C.; Jin, P. "A
small molecule enhances RNA interference and promotes microRNA
processing"& Nature Biotechnology 2008,
26, 933-940.
Li, Z.; Brouwer, C.; He, C. "Gold-Catalyzed
Organic Transformations" Chem. Rev. 2008, 108,
Submitted for publication in the special issue:
Coinage Metals in Organic Synthesis
Yang, C.-G.; Yi, C.; Duguid, E. M.;
Sullivan, C. T.; Jian, X.; Rice, P. A.; He, C. "Crystal structures of
DNA-RNA repair enzymes AlkB and ABH2 bound to dsDNA" Nature
2008, 452, 961-965.
additional news links, go to ""
&Chen, P.R. and He, C.& "Selective
recognition of metal ions by metalloregulatory proteins"
Curr. Opin. Chem. Biol. 2008,
12, 214-221.
&Chang, S.; Bray, S.M.;
Li, Z.; Zarnescu, D.C.; He, C.; Jin, P.; Warren, S.T.& "Identification
of small molecules rescuing fragile X syndrome phenotypes in
Drosophila"
Nat. Chem. Biol. 2008,
&4, 256-263.
&Shigdel, U. K.; Zhang,
J.; He, C. "Diazirine-Based DNA
Photo-Cross-Linking Probes for the Study of Protein-DNA Interactions"
Angew. Chem. Intl. Ed. 2008,
47, 90-93.
&Chen, C.-S.; Korobkova,
E.; Chen, H.; Zhu, J.; Jian, X.; Tao, S.-C.; He, C.*; Zhu, H.* "A
proteome chip approach reveals new DNA damage recognition activities in
Escherichia Coli" Nat. Methods,
2008, 5, 69-74.
"Synthesis of Photoactive Analogues of a Cysteine Knot Trypsin Inhibitor
Protein" Org. Lett. 2007,
Sarkar, S.K.; Andoy, N.M.; Benitez, J.J.;
Chen, P.R.; Kong, J.S.; He,&C.; Chen, P. "Engineered Holliday Junctions
as Single-Molecule Reporters for Protein-DNA Interactions with
Application to a MerR-Family Regulator"
J. Am. Chem. Soc. 2007, 129, . &
Chen, P.R.; Wasinger, E. C.; Zhao, J.; van
der Lelie, D.; Chen, L.X. ; He,&C. "Spectroscopic
Insights into Lead(II) Coordination by the Selective Lead(II)-Binding
Protein PbrR691"
J. Am. Chem. Soc. 2007, 129, .
Li, Z.; Capretto, D.A.; Rahaman, R.O.; He,
C. "Gold(III)-Catalyzed Nitrene
Insertion into Aromatic and Benzylic C-H Groups" J. Am. Chem. Soc.
&2007, 129,
Brouwer,&C.; Rahaman,&R O..; He,&C.
"Gold(I)-Mediated Hydrothiolation of Conjugated
Olefins" Synlett 2007, 11, .
(Invited Contribution)
Li, Z.; Capretto, D.A.; Rahaman, R.O.; He,
C. "Silver-Catalyzed Intermolecular Amination of C-H Groups"
Angew. Chem. Intl. Ed. 2007, 46, .
Wegner, S. V.; Okesli, A.;
Chen, P.; He, C. "Design of an Emission Ratiometric Biosensor from
MerR Family Proteins: A Sensitive and Selective Sensor for Hg2+" J.
Am. Chem. Soc. 2007, 129, .
Chen, P.; Bae, T.; Williams, W. A.; Duguid,
E. M.; Rice, P. A.; Schneewind, O. and He, C. "An Oxidation Sensing
Mechanism is Used by A Global Regulator of Staphylococcus aureus"
Nature Chem. Biol. 2006, 2, 591-595.
Li, Z.; Zhang, J.; Brouwer, C.; Yang,
C.-G.; Reich, N. W. and He, C. "Bronsted Acid Catalyzed Addition of
Phenols, Carboxylic Acids and Tosylamides to Simple Olefin" Org. Lett.
2006, 8:4175-8.
Li, Z.; Ding, X. and He, C. "Nitrene
Transfer Reactions Catalyzed by Gold Complexes" J. Org. Chem.
2006, 71:5876-80.
Recent Advances
in Silver-Catalyzed Nitrene, Carbene, and Silylene-Transfer Reactions
Euro. J. Org. Chem.,
(an invited review).
BrouwerEfficient Gold-Catalyzed Hydroamination of
1,3-Dienes
Gold(I)-Catalyzed
Intra- and Intermolecular Hydroamination of Unactivated Olefins
J. Am. Chem. Soc.
Mishina, Y.; Duguid, M. E. and He, C. "Direct
Reversal of DNA Alkylation
Damage", Chem. Rev.
J. Am. Chem. Soc.
J. Am. Chem. Soc.
Duguid, M. E.; Rice, P. A. and He,
C. &Implications for How the Human DNA Repair Protein AGT
Angew Chem. Int. Ed 2005, 44, .
Y.; Chen, L. X. and He, C. &Preparation and Characterization of the
Native Iron(II)-Containing AlkB Protein Directly from Escherichia
Chem. Soc 2004, &126,
Shi, Z. and He, C. &Direct
Functionalization of Arenes by Primary Alcohol Sulfonate Esters
Catalyzed by Gold(III)&,
J. Am. Chem. Soc. 2004, 126, .
Cui, Y. and He, C. &A
Silver-Catalyzed Intramolecular Amidation of Saturated C&H bonds&,
Angew Chem. Int. Ed. 2004, 43, .
Shi, Z. and He, C.
&Efficient Functionalization of Aromatic C&H Bonds Catalyzed by
under Mild and Solvent Free Conditions&, J. Org. Chem.
Shi, Z. and He, C. &An
Au-Catalyzed Cyclialkylation of Electron Rich Arenes with Epoxides to
Prepare 3-Chromanols&,
Chem. Soc. 2004, 126,
Mishina, Y., Lee, C.-H.
J. and He, C. &Potential DNA Preferences of Human and Bacterial AlkB
Proteins as Revealed from Chemical Crosslink Studies&, Nucleic Acids
Res. 2004, 32,
He, C. and Mishina, Y.
&Modeling non-heme iron proteins&, Curr. Opin. Chem. Biol.
2004, 8, 201-208.
and He, C. &Constructing Highly Sensitive and Selective Fluorescent
Biosensors for Metal Ions by Using the MerR Family Proteins&, J. Am.
Chem. Soc. 2004, 126, 728-729.
Cui, Y. and He, C.
&Efficient Aziridination of Olefins Catalyzed by A Unique Disilver(I)
Compound&, J. Am. Chem. Soc. 2003, 125, .
Duguid, E. M.; Mishina,
Y. and He, C. &A Chemical Disulfide Crosslinking Method to Investigate the
Damage-Searching Mechanism of O6-Alkylguanine-DNA
Alkyltransferases&, Chem. & Biol. 2003, 10, 827-835
Mishina, Y. and He, C.
&Probing the Structure and Function of E. coli DNA Alkylation
Repair AlkB Protein through Chemical Crosslinking&, J. Am. Chem. Soc.
&2003, 125, .
Other Publications:
C.; Sun, L. J.; Zhou, P.; Norman, D. P. G.; D&tsch, V.; Gross, J. D.;
Lane, W. S.; Wagner, G. and Verdine, G. L. &A Zinc-Mediated Electrostatic
Switch Controls the Adaptive Response of E. coli to Methylating
Agents&, Mol. Cell. 2005, 20, 117-129.
C.; Wei, H. and Verdine, G. L. &Converting the Sacrificial DNA Repair
Protein N-Ada into a Catalytic Methyl Phosphotriester Repair Enzyme&,
J. Am. Chem. Soc. 2003, 125, .
11.& He, C.
and Verdine, G. L. &Trapping Distinct Structural States of a Protein/DNA
Interaction through Disulfide Cross-linking&, Chem. & Biol. 2002,
C.; DuBois, J. L.; Hedman, B.; Hodgson, K. O. and Lippard, S. J. &A short
Copper-Copper Distance in a (-1,2-Peroxo)dicopper(II) Complex Having 1,8-Naphthyridine Unit
as an Additional Bridge&, Angew. Chem. Int. Ed. Engl. 2001,
9.& He, C.
and Lippard, S. J. &Synthesis and Electrochemical Studies of Diiron
Complexes of 1,8-Naphthyridine-Based Dinucleating Ligands to Model
Features of the Active Sites of Non-Heme Diiron Enzymes&, Inorg. Chem.
(cover story).
C.; Barrios, A. M.; Lee, D.; Kuzelka, J.; Davydov, R. M. and Lippard, S.
J. &Diiron Complexes of 1,8-Naphthyridine-Based Dinucleating Ligands as
Models for Hemerythrin&, J. Am. Chem. Soc. 2000, 122,
C. and Lippard, S. J. &Synthesis and Characterization of Several
Dicopper(I) Complexes and a Spin-Delocalized Dicopper(I,II) Mixed-Valence
Complex Using a 1,8-Naphthyridine-Based Dinucleating Ligand&, Inorg.
Chem. 2000, 39, .
6.& He, C.
and Lippard, S. J. &Design and Synthesis of Multidentate Dinucleating
Ligands Based on 1,8-Naphthyridine&, Tetrahedron 2000, 56,
C.; Gomez, V.; Spingler, B. and Lippard, S. J. &Monodentate-Bridged
Phosphodiester and Sulfate Complexes: Structural Insight into the
Biological Activation of Phosphodiesters, Sulfate, and Sulfate Esters&,
Inorg. Chem. 2000, 39, .
4.& Kaminskaia, N. V.; He, C. and Lippard, S. J. &Reactivity of
-Hydroxodizinc(II) Centers in
Enzymatic Catalysis through Model Studies&, Inorg. Chem. 2000,
3.& He, C.
and Lippard, S. J. &Modeling Carboxylate-Bridged Dinuclear Active Sites in
Metalloenzymes Using a Novel Naphthyridine-Based Dinucleating Ligand&,
J. Am. Chem. Soc. 2000, 122, 184-185.
2.& He, C.
and Lippard, S. J. &Aminoguanidinium Hydrolysis Effected by a Hydroxo-Bridged
Dicobalt(II) Complexes&, J. Am. Chem. Soc. 1998, 120,
Y.; Xie, Y.; He, C.; Li, J. and Chen, Z. &Hydrothermal Preparation and
Characterization of Ultrafine Magnetite Powders&, Material Research
Bulletin 1994, 29, 953-957.}