Former Lab Members
Research Highlights
Group Event
The He Group Publications

Mayman, N.; Wei, J.; Cai, S.; Soman, R.; Raynes, H.; La Vega-Talbott, M.; He, C.; Naidich, T.; Raju, G. P.*; Kathiresu Nageshwaran S.* Case report: A novel biallelic FTO variant causing multisystem anomalies with severe epilepsy, widening the spectrum of FTO syndrome. SAGE Open Med. Case Rep. 2023, online. [pdf]



Zhang, J.; Wei, J.; Sun, R.; Sheng, H.; Yin, K.; Pan, Y.; Jimenez, R.; Chen, S.; Cui, X. L.; Zou, Z.; Yue, Z.; Emch, M. J.; Hawse, J. R.; Wang, L.; He, H. H.; Xia, S.; Han, B.; He, C.*; Huang, H.* A lncRNA from the FTO locus acts as a suppressor of the m6A writer complex and p53 tumor suppression signaling. Mol. Cell 2023, 84, 2692-2708. [pdf]



Cai, Q.; Zhang, Z.*; Cui, X.; Zeng, C.; Cai, J.; Cai, J.; Wu, K.; Zhang, X.; Shi, Y.; Arvanitakis, Z.; Bissonnette, M. A.; Chiu, B. C.; Cheng, S. Y.; He, C.; Zhang, W.* PETCH-DB: a portal for exploring tissue-specific and complex disease-associated 5-hydroxymethylcytosines. Database 2023, online. [pdf]



Shao, J.; Shah, S.; Ganguly, S.; Zu, Y.; He, C.; Li, Z. Classification of acute myeloid leukemia by cell-free DNA 5-hydroxymethylcytosine. Genes 2023, 14, 1180. [pdf]



Li, Y.; Dou, X.; Liu, J.; Xiao, Y.; Zhang, Z.; Hayes, L.; Wu, R.; Fu, X.; Ye, Y.; Yang, B.; Ostrow, L. W.; He, C.; Sun, S. Globally reduced N6-methyladenosine (m6A) in C9ORF72-ALS/FTD dysregulates RNA metabolism and contributes to neurodegeneration. Nat. Neurosci. 2023, 26, 1328-1338. [pdf]



Zhang, L.; Dou, X.; Zheng, Z.; Ye, C.; Lu, T. X.; Liang, H. L.; Wang, L.; Weichselbaum, R. R.; He, C. YTHDF2/m6A/NF-kB axis controls anti-tumor immunity by regulating intratumoral Tregs. EMBO J. 2023, 42, e113126. [pdf]



Wu, T.; He, C. 6mA-METL-9 axis regulates innate immunity in C. elegans. Cell Res. 2023, 33, 581-582.[pdf]



Chen, L.; Zhang, L. S.; Ye, C.; Zhou, H.; Liu, B.; Gao, B.; Deng, Z.; Zhao, C.; He, C.*; Dickinson B. C.* Nm-Mut-seq: a base-resolution quantitative method for mapping transcriptome-wide 2'-O-methylation. Cell Res. 2023, online. [pdf]



Liang, G.; Wang, L.; You, Q.; Cahill, K.; Chen, C.; Zhang, W.; Fulton, N.; Stock, W.; Odenike, O.*; He, C.*; Han, D.* Cellular composition and 5hmC signature predict the treatment response of AML patients to azacitidine combined with chemotherapy. Adv. Sci. 2023, online. [pdf]



Yu, F.; Zhu, A. C.; Liu, S.; Gao, B.; Wang, Y.; Khudaverdyan, N.; Yu, C.; Wu, Q.; Jiang, Y.; Song, J.; Jin, L.; He, C.*; Qian, Z.* RBM33 is a unique m6A RNA-binding protein that regulates ALKBH5 demethylase activity and substrate selectivity. Mol. Cell 2023, 83, 2003-2019. [pdf]



Wang, L.; Dou, X.; Chen, S.; Yu, X.; Huang, X.; Zhang, L.; Chen, Y.; Wang, J.; Yang, K.; Bugno, J.; Pitroda, S.; Ding, X.; Piffko, A.; Si, W.; Chen, C.; Jiang, H.; Zhou, B.; Chmura, S. J.; Luo, C.*; Liang, H. L.*; He, C.*; Weichselbaum, R. R.* YTHDF2 inhibition potentiates radiotherapy antitumor efficacy. Cancer Cell 2023, 41, 1294-1308. [pdf]



Beadell, A. V.; Zhang, Z.; Capuano, A. W.; Bennett, D. A.; He, C.; Zhang, W.*; Arvanitakis, Z.* Genome-wide mapping implicates 5-hydroxymethylcytosines in diabetes mellitus and Alzheimer's disease. J. Alzheimers Dis. 2023, 93, 1135-1151. [pdf]



Pomaville, M. M.*; He, C. Advances in targeting RNA modifications for anticancer therapy. Trends Cancer 2023, 9, 528-542. [pdf]



Marinov, G. K.*; Kim, S. H.; Bagdatli, S. T.; Higashino, S. I.; Trevino, A. E.; Tycko, J.; Wu, T.; Bintu, L.; Bassik, M. C.; He, C.; Kundaje, A.; Greenleaf, W. J.* CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping. Genome Biol. 2023, 24, 85. [pdf]



Li, Y.; Zhi, S.; Wu, T.; Chen, H. X.; Kang, R.; Ma, D. Z.; Songyang, Z.; He, C.*; Liang, P.*; Luo, G. Z.* Systematic identification of CRISPR off-target effects by CROss-seq. Protein Cell 2023, 14, 299-303. [pdf]



Dou, X.; Huang, L.; Xiao, Y.; Liu, C.; Li, Y.; Zhang, X.; Yu, L.; Zhao, R.; Yang, L.; Chen, C.; Yu, X.; Gao, B.; Qi, M.; Gao, Y.; Shen, B.; Sun, S.; He, C.*; Liu, J.* METTL14 is a chromatin regulator independent of its RNA N6-methyladenosine methyltransferase activity. Protein Cell 2023, online. [pdf]



Zou, Z.; He, C. Splice epitranscriptomics and DNA damage repair together: ALKBH5-m6A-SF3B1 regulation in leukemic transformation. Mol. Cell 2023, 83, 1022-23. [pdf]



Xie, J.; Zheng, Z.; Liu, X.; Zhang, N.; Choi, S.; He, C.; Dong, G. Asymmetric total synthesis of (+)-phainanoid A and biological evaluation of the natural product and its synthetic analogues. J. Am. Chem. Soc. 2023, 145, 4828-4852. [pdf]



Feng, X.; He, C. Mammalian DNA N6-methyladenosine: Challenges and new insights. Mol. Cell 2023, 83, 343-351. [pdf]



He, P. C.; Wei, J.; Dou, X.; Harada, B. T.; Zhang, Z.; Ge, R.; Liu, C.; Zhang, L. S.; Yu, X.; Wang, S.; Lyu, R.; Zou, Z.; Chen, M.; He, C. Exon architecture controls mRNA m6A suppression and gene expression. Science 2023, 379, 677-682. [pdf]



Zou, Z.; Sepich-Poore, C.; Zhou, X.; Wei, J.; He, C. The mechanism underlying redundant functions of the YTHDF proteins. Genome Biol. 2023, 24, 17. [pdf]



Ma, S.; Sun, B.; Duan, S.; Han, J.; Barr, T.; Zhang, J.; Bissonnette, M. B.; Kortylewski, M.; He, C.; Chen, J.; Caligiuri, M. A.*; Yu, J.* YTHDF2 orchestrates tumor-associated macrophage reprogramming and controls antitumor immunity through CD8+ T cells. Nat. Immunol. 2023, 24, 255-266. [pdf]



Xiao, Y. L.; Liu, S.; Ge, R.; Wu, Y.; He, C.*; Chen, M.*; Tang, W.* Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination. Nat. Biotechnol. 2023, 41, 993-1003. [pdf]



Ge, R.; Ye, C.; Peng, Y.; Dai, Q.; Zhao, Y.; Liu, S.; Wang, P.; Hu, L.*; He C.* m6A-SAC-seq for quantitative whole transcriptome m6A profiling. Nat. Protoc. 2023, 18, 626-657. [pdf]



Zhang, L. S.; Dai, Q.; He, C. BID-seq: the quantitative and base-resolution sequencing method for RNA pseudouridine. ACS Chem. Biol. 2023, 18, 4-6. [pdf]



Beadell, A. ythdf2(ch200) and its role in development of the early zebrafish embryo. bioRxiv 2022, online. [pdf]



Garg, R.; Melstrom, L.; Chen, J.; He, C.; Goel, A. Targeting FTO suppresses pancreatic carcinogenesis via regulating stem cell maintenance and EMT pathway. Cancers 2022, 14, 5919. [pdf]



Hsu, K. W.; Lai, J. C.; Chang, J.S.; Peng, P. H.; Huang, C. H.; Lee, D. Y.; Tsai, Y. C.; Chung, C. J.; Chang, H.; Chang, C. H.; Chen, J. L.; Pang, S. T.; Hao, Z.; Cui, X. L.; He, C.; Wu, K. J. METTL4-mediated nuclear N6-deoxyadenosine methylation promotes metastasis through activating multiple metastasis-inducing targets. Genome Biol. 2022, 23, 249. [pdf]



Wu, T.; Lyu, R.; He, C. spKAS-seq reveals R-loop dynamics using low-input materials by detecting single-stranded DNA with strand specificity. Sci. Adv. 2022, 8, eabq2166. [pdf]



Zhang, L. S.*; Ju, C. W.; Liu, C.; Wei, J.; Dai, Q.; Chen, L.; Ye, C.; He, C.* m7G-quant-seq: quantitative Detection of RNA internal N7-methylguanosine. ACS Chem. Biol. 2022, 17, 3306-3312. [pdf]



Sjöström, M.; Zhao, S. G.; Levy, S.; Zhang, M.; Ning, Y.; Shrestha, R.; Lundberg, A.; Herberts, C.; Foye, A.; Aggarwal, R.; Hua, J. T.; Li, H.; Bergamaschi, A.; Maurice-Dror, C.; Maheshwari, A.; Chen, S.; Ng, S. W. S.; Ye, W.; Petricca, J.; Fraser, M.; Chesner, L.; Perry, M. D.; Moreno-Rodriguez, T.; Chen, W. S.; Alumkal, J. J.; Chou, J.; Morgans, A. K.; Beer, T. M.; Thomas, G. V.; Gleave, M.; Lloyd, P.; Phillips, T.; McCarthy, E.; Haffner, M. C.; Zoubeidi, A.; Annala, M.; Reiter, R. E.; Rettig, M. B.; Witte, O. N.; Fong, L.; Bose, R.; Huang, F. W.; Luo, J.; Bjartell, A.; Lang, J. M.; Mahajan, N. P.; Lara, P. N.; Evans, C. P.; Tran, P. T.; Posadas, E. M.; He, C.; Cui, X. L.; Huang, J.; Zwart, W.; Gilbert, L. A.; Maher, C. A.; Boutros, P. C.; Chi, K. N.; Ashworth, A.; Small, E. J.; He, H. H.; Wyatt, A. W.; Quigley, D. A.; Feng, F. Y. The 5-hydroxymethylcytosine landscape of prostate cancer. Cancer Res. 2022, 82, 3888-3902. [pdf]



Dai, Q.*; Zhang, L. S.*; Sun, H. L.; Pajdzik, K.; Yang, L.; Ye, C.; Ju, C. W.; Liu, S.; Wang, Y.; Zheng, Z.; Zhang, L.; Harada, B. T.; Dou, X.; Irkliyenko, I.; Feng, X.; Zhang, W.; Pan, T.; He, C.* Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution. Nat. Biotechnol. 2022, 41, 344-354. [pdf]



Zhang, Y.; Zhang, L. S.; Dai, Q.; Chen, P.; Lu, M.; Kairis, E. L.; Murugaiah, V.; Xu, J.; Shukla, R. K.; Liang, X.; Zou, Z.; Cormet-Boyaka, E.; Qiu, J.; Peeples, M. E.; Sharma, A.; He, C.*; Li, J*. 5-methylcytosine (m5C) RNA modification controls the innate immune response to virus infection by regulating type I interferons. Proc. Natl. Acad. Sci. 2022, 119, e2123338119. [pdf]



Peng, Y.; Meng, H.; Ge, R.; Liu, S.; Chen, M.; He, C.*; Hu, L.* Detection of m6A RNA modifications at single-nucleotide resolution using m6A-selective allyl chemical labeling and sequencing. STAR Protoc. 2022, 3, 101677. [pdf]



Du, J.; Sarkar, R.; Li, Y.; He, L.; Kang, W.; Liao, W.; Liu, W.; Nguyen, T.; Zhang, L.; Deng, Z.; Dougherty, U.; Kupfer, S. S.; Chen, M.; Pekow, J.; Bissonnette, M.; He, C.; Li, Y. C. N6-adenomethylation of GsdmC is essential for Lgr5+ stem cell survival to maintain normal colonic epithelial morphogenesis. Dev. Cell 2022, 57, 1976-1994.e8. [pdf]



Chiu, B. C.*; Zhang, Z.; Derman, B. A.; Karpus, J.; Luo, L.; Zhang, S.; Langerman, S. S.; Sukhanova, M.; Bhatti, P.; Jakubowiak, A.; He, C.; Zhang, W.* Genome-wide profiling of 5-hydroxymethylcytosines in circulating cell-free DNA reveals population-specific pathways in the development of multiple myeloma. J. Hematol. Oncol. 2022, 15, 106. [pdf]



Shao, J.; Wang, S.; West-Szymanski, D.; Karpus, J.; Shah, S.; Ganguly, S.; Smith, J.; Zu, Y.; He, C.; Li, Z. Cell-free DNA 5-hydroxymethylcytosine is an emerging marker of acute myeloid leukemia. Sci. Rep. 2022, 12, 12410. [pdf]



Mu, Y.; Zhang, L.*; Hu, J.; Zhou, J.; Lin, H. W.; He, C.; Chen, H. Z.*; Zhang, L.* A fungal dioxygenase CcTet serves as a eukaryotic 6mA demethylase on duplex DNA. Nat. Chem. Biol. 2022, 18, 733-741. [pdf]



Liu, H.; Zeng, T.; He, C.; Rawal, V. H.; Zhou, H.*; Dickinson, B. C.* Development of mild chemical catalysis conditions for m1A-to-m6A rearrangement on RNA. ACS Chem. Biol. 2022, 17, 1334-1342. [pdf]



Wei, J.; Yu, X.; Yang, L.; Liu, X.; Gao, B.; Huang, B.; Dou, X.; Liu, J.; Zou, Z.; Cui, X. L.; Zhang, L. S.; Zhao, X.; Liu, Q.; He, PC.; Sepich-Poore, C.; Zhong, N.; Liu, W.; Li, Y.; Kou, X.; Zhao, Y.; Wu, Y.; Cheng, X.; Chen, C.; An, Y.; Dong, X.; Wang, H.; Shu, Q.; Hao, Z.; Duan, T.; He, Y. Y.; Li, X.; Gao, S.*; Gao, Y.*; He, C.* FTO mediates LINE1 m6A demethylation and chromatin regulation in mESCs and mouse development. Science 2022, 376, 968-973. [pdf]



Cerneckis, J.; Cui, Q.; He, C.; Yi, C.; Shi, Y. Decoding pseudouridine: an emerging target for therapeutic development. Trends Pharmacol. Sci. 2022, 43, 522-535. [pdf]



Yang, Y.; Zeng, C.; Yang, K.; Xu, S.; Zhang, Z.; Cai, Q.; He, C.; Zhang, W.*; Liu, S. M.* Genome-wide analysis reflects novel 5-hydroxymethylcytosines implicated in diabetic nephropathy and the biomarker potential. Extracell. Vesicles Circ. Nucl. Acids 2022, 3, 49-60. [pdf]



Hu, L.*; Liu, S.; Peng, Y.; Ge, R.; Su, R.; Senevirathne, C.; Harada, B. T.; Dai, Q.; Wei, J.; Zhang, L.; Hao, Z.; Luo, L.; Wang, H.; Wang, Y.; Luo, M.; Chen, M.*; Chen, J.*; He C.* m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome. Nat. Biotechnol. 2022, 40, 1210-1219.[pdf]



Marinov, G. K.*; Chen, X.; Wu, T.; He, C.; Grossman, A. R.; Kundaje, A.; Greenleaf, W. J.* The chromatin organization of a chlorarachniophyte nucleomorph genome. Genome Biol. 2022, 23, 65.[pdf]



Hsu, P. J.; Singh, K.; Dhiman, A.; Witmer, H. D. D.; He, C.; Eng, O. S.; Catenacci, D. V. T.; Posner, M. C.; Turaga, K. K. Utility of perioperative measurement of cell-free DNA and circulating tumor DNA in informing the prognosis of GI cancers: a systematic review. JCO Precis. Oncol. 2022, 6, e2100337.[pdf]



Su, R.*; Dong, L.; Li, Y.; Gao, M.; He, P. C.; Liu, W.; Wei, J.; Zhao, Z.; Gao, L.; Han, L.; Deng, X.; Li, C.; Prince, E.; Tan, B.; Qing, Y.; Qin, X.; Shen, C.; Xue, M.; Zhou, K.; Chen, Z.; Xue, J.; Li, W.; Qin, H.; Wu, X.; Sun, M.; Nam, Y.; Chen, C. W.; Huang, W.; Horne, D.; Rosen, S. T.; He, C.*; Chen J.* METTL16 exerts an m6A-independent function to facilitate translation and tumorigenesis. Nat. Cell Biol. 2022, 24, 205-216.[pdf]



Chen, H. Y.; Li, X. X.; Li, C.; Zhu, H. C.; Hou, H. Y.; Zhang, B.; Cheng, L. M.; Hu, H.; Lu, Z. X.; Liu, J. X.; Yang, Z. R.; Zhang, L.; Xu, N.; Chen, L.; He, C.; Dong, C. R.*; Ge, Q. G.*; Lin, J.* 5-hydroxymethylcytosine signatures in circulating cell-free DNA as early warning biomarkers for COVID-19 progression and myocardial injury. Front. Cell. Dev. Biol. 2022, 9, 781267.[pdf]



He, C. ACS Chemical Biology. 2022 Editorial Statement. ACS Chem. Biol. 2022, 17, 1.[pdf]



Sepich-Poore, C.; Zheng, Z.; Schmitt, E.; Wen, K.; Zhang, Z. S.; Cui, X. L.; Dai, Q.; Zhu, A. C.; Zhang, L.; Sanchez Castillo A.; Tan, H.; Peng, J.; Zhuang, X.; He, C.*; Nachtergaele, S.* The METTL5-TRMT112 N6-methyladenosine methyltransferase complex regulates mRNA translation via 18S rRNA methylation. J. Biol. Chem. 2022, 298, 101590.[pdf]



Lyu, R.; Wu, T.; Zhu, A. C.; West-Szymanski, D. C.; Weng, X.; Chen, M.; He, C. KAS-seq: genome-wide sequencing of single-stranded DNA by N3-kethoxal-assisted labeling. Nat. Protoc. 2022, 17, 402-420.[pdf]



Petrosino, J. M.; Hinger, S. A.; Golubeva, V. A.; Barajas, J. M.; Dorn, L. E.; Iyer, C. C.; Sun, H. L.; Arnold, W. D.; He, C.; Accornero, F. The m6A methyltransferase METTL3 regulates muscle maintenance and growth in mice. Nat. Commun. 2022, 13, 168.[pdf]



Barajas, J. M.; Lin, C. H.; Sun, H. L.; Alencastro, F.; Zhu, A. C.; Aljuhani, M.; Navari, L.; Yilmaz, S. A.; Yu, L.; Corps, K.; He, C.; Duncan, A. W.*; Ghoshal, K.* METTL3 regulates liver homeostasis, hepatocyte ploidy, and circadian rhythm-controlled gene expression in mice. Am. J. Pathol. 2022, 92, 56-71.[pdf]



Olazagoitia-Garmendia, A.; Zhang, L.; Mera, P.; Godbout, J. K.; Sebastian-DelaCruz, M.; Garcia-Santisteban, I.; Mendoza, L. M.; Huerta, A.; Irastorza, I.; Bhagat, G.; Green, P. H.; Herrero, L.; Serra, D.; Rodriguez, J. A.; Verdu, E. F.; He, C.; Bilbao, J. R.; Castellanos-Rubio, A. Gluten-induced RNA methylation changes regulate intestinal inflammation via allele-specific XPO1 translation in epithelial cells. Gut 2022, 71, 68-76.[pdf]



Shimura, T.; Kandimalla, R.; Okugawa, Y.; Ohi, M.; Toiyama, Y.; He, C.; Goel, A. Novel evidence for m6A methylation regulators as prognostic biomarkers and FTO as a potential therapeutic target in gastric cancer. Br. J. Cancer. 2022, 126, 228-237. [pdf]



Cui, Q.; Yin, K.; Zhang, X.; Ye, P.; Chen, X.; Chao, J.; Meng, H.; Wei, J.; Roeth, D.; Li, L.; Qin, Y.; Sun, G.; Zhang, M.; Klein, J.; Huynhle, M.; Wang, C.; Zhang, L.; Badie, B.; Kalkum, M.; He, C.; Yi, C.*; Shi, Y.* Targeting PUS7 suppresses tRNA pseudouridylation and glioblastoma tumorigenesis. Nat. Cancer. 2021, 2, 932-949. [pdf]



Sheng, Y.; Wei, J.; Yu, F.; Xu, H.; Yu, C.; Wu, Q.; Liu, Y.; Li, L.; Cui, X. L.; Gu, X.; Shen, B.; Li, W.; Huang, Y.; Bhaduri-McIntosh, S.; He, C.*; Qian, Z.* A critical role of nuclear m6A reader YTHDC1 in leukemogenesis by regulating MCM complex-mediated DNA replication. Blood 2021, 138, 2838-2852.[pdf]



Xue, M.; Zhang, Y.; Wang, H.; Kairis, E. L.; Lu, M.; Ahmad, S.; Attia, Z.; Harder, O.; Zhang, Z.; Wei, J.; Chen, P.; Gao, Y.; Peeples, M. E.; Sharma, A.; Boyaka, P.; He, C.; Hur, S.; Niewiesk, S.; Li, J. Viral RNA N6-methyladenosine modification modulates both innate and adaptive immune responses of human respiratory syncytial virus. PLoS Pathog. 2021, 17, e1010142.[pdf]



Wei, J.*; Harada, B. T.; Lu, D.; Ma, R.; Gao, B.; Xu, Y.; Montauti, E.; Mani, N.; Chaudhuri, S. M.; Gregory, S.; Weinberg, S. E.; Zhang, D. D.; Green, R.; He, C.; Fang, D.* HRD1-mediated METTL14 degradation regulates m6A mRNA modification to suppress ER proteotoxic liver disease. Mol. Cell 2021, 81, 5052-5065, e6.[pdf]



Paul, D.; Mu, H.; Tavakoli, A.; Dai, Q.; Chakraborty, S.; He, C.; Ansari, A.; Broyde, S.*; Min, J. H.* Impact of DNA sequences on DNA 'opening' by the Rad4/XPC nucleotide excision repair complex. DNA Repair 2021, 107, 103194.[pdf]



Tsao, N.; Brickner, J. R.; Rodell, R.; Ganguly, A.; Wood, M.; Oyeniran, C.; Ahmad, T.; Sun, H.; Bacolla, A.; Zhang, L.; Lukinovic, V.; Soll, J. M.; Townley, B. A.; Casanova, A. G.; Tainer, J. A.; He, C.; Vindigni, A.; Reynoird, N.; Mosammaparast, N. Aberrant RNA methylation triggers recruitment of an alkylation repair complex. Mol. Cell 2021, 81, 4228-4242, e8.[pdf]



Zhao, F.; Xu, Y.; Gao, S.; Qin, L.; Austria, Q.; Siedlak, S. L.; Pajdzik, K.; Dai, Q.; He, C.; Wang, W.; O'Donnell, J. M.; Tang, B.; Zhu, X. METTL3-dependent RNA m6A dysregulation contributes to neurodegeneration in Alzheimer's disease through aberrant cell cycle events. Mol. Neurodegener. 2021, 16, 70. [pdf]



Yang, Z.; Yang, S.; Cui, Y. H.; Wei, J.; Shah, P.; Park, G.; Cui, X.; He, C.; He, Y. Y. METTL14 facilitates global genome repair and suppresses skin tumorigenesis. Proc. Natl. Acad. Sci. 2021, 118, e2025948118. [pdf]



Yu, F.; Wei, J.; Cui, X.; Yu, C.; Ni, W.; Bungert, J.; Wu, L.; He, C.*; Qian, Z.* Post-translational modification of RNA m6A demethylase ALKBH5 regulates ROS-induced DNA damage response. Nucleic Acids Res. 2021, 49, 5779-5797. [pdf]



Terajima, H.; Lu, M.; Zhang, L.; Cui, Q.; Shi, Y.; Li, J.; He, C. N6-methyladenosine promotes induction of ADAR1-mediated A-to-I RNA editing to suppress aberrant antiviral innate immune responses. PLoS Biol. 2021, 19, e3001292. [pdf]



Yu, Q.; Liu, S.; Yu, L.; Xiao, Y.; Zhang, S.; Wang, X.; Xu, Y.; Yu, H.; Li, Y.; Yang, J.; Tang, J.; Duan, H. C.; Wei, L. H.; Zhang, H.; Wei, J.; Tang, Q.; Wang, C.; Zhang, W.; Wang, Y.; Song, P.; Lu, Q.; Zhang, W.; Dong, S.; Song, B.*; He, C.*; Jia, G.* RNA demethylation increases the yield and biomass of rice and potato plants in field trials. Nat. Biotechnol. 2021, 39, 1581-1588. [pdf]



Chen, D.; Xia, S.; Zhang, R.; Li, Y.; Famulare, C. A.; Fan, H.; Wu, R.; Wang, M.; Zhu, A. C.; Elf, S. E.; Su, R.; Dong, L.; Arellano, M.; Blum, W. G.; Mao, H.; Lonial, S.; Stock, W.; Odenike, O.; Le Beau, M.; Boggon, T. J.; He, C.; Chen, J.; Gao, X.*; Levine, R. L.*; Chen, J.* Lysine acetylation restricts mutant IDH2 activity to optimize transformation in AML cells. Mol. Cell 2021, 81, 1-15. [pdf]



Zhang, L. S.; Xiong, Q. P.; Peña Perez, S.; Liu, C.; Wei, J.; Le, C.; Zhang, L.; Harada, B. T.; Dai, Q.; Feng, X.; Hao, Z.; Wang, Y.; Dong, X.; Hu, L.; Wang, E. D.; Pan,T.; Klungland, A.; Liu, R. J.*; He, C.* ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing. Nat. Cell Biol. 2021, 23, 684-691. [pdf]



Cai, J.; Zeng, C.; Hua, W.; Qi, Z.; Song, Y.; Lu, X.; Li, D.; Zhang, Z.; Cui, X.; Zhang, X.; Yang, Z.; Zhang, J.; Quan, K.; Zhu, W.; Cai, J.; He, C.; Cheng, S. Y.; Zhang, W.*; Mao, Y.* An integrative analysis of genome-wide 5-hydroxymethylcytosines in circulating cell-free DNA detects noninvasive diagnostic markers for gliomas. Neurooncol. Adv. 2021, 3, vdab049. [pdf]



Zhang, L. S.; Liu, C.; He, C. Transcriptome-Wide detection of internal N7-methylguanosine. Methods Mol. Biol. 2021, 2298, 97-104. [pdf]



Yu, F.; Wei, J.; Cui, X.; Yu, C.; Ni, W.; Bungert, J.; Wu, L.; He, C.*; Qian, Z.* Post-translational modification of RNA m6A demethylase ALKBH5 regulates ROS-induced DNA damage response. Nucleic Acids Res. 2021, 49, 5779-5797. [pdf]



Cui, Y. H.; Yang, S.; Wei, J.; Shea, C. R.; Zhong, W.; Wang, F.; Shah, P.; Kibriya, M. G.; Cui, X.; Ahsan, H.; He, C.; He, Y. Y. Autophagy of the m6A mRNA demethylase FTO is impaired by low-level arsenic exposure to promote tumorigenesis. Nat. Commun. 2021, 12, 2183. [pdf]



Dixon, G.; Pan, H.; Yang, D.; Rosen, B. P.; Jashari, T.; Verma, N.; Pulecio, J.; Caspi, I.; Lee, K.; Stransky, S.; Glezer, A.; Liu, C.; Rivas, M.; Kumar, R.; Lan, Y.; Torregroza, I.; He, C.; Sidoli, S.; Evans, T.; Elemento, O.*; Huangfu, D.* QSER1 protects DNA methylation valleys from de novo methylation. Science 2021, 372, eabd0875. [pdf]



Lee, J.; Wu, Y.; Harada, B. T.; Li, Y.; Zhao, J.; He, C.*; Ma, Y.*; Wu, X.* N6-methyladenosine modification of lncRNA Pvt1 governs epidermal stemness. EMBO J. 2021, 40, e106276. [pdf]



Wei, J.; He, C. Chromatin and transcriptional regulation by reversible RNA methylation. Curr. Opin. Cell Biol. 2021, 70, 109-115. [pdf]



Chen, S.; Kumar, S.; Espada, C. E.; Tirumuru, N.; Cahill, M. P.; Hu, L.; He, C.; Wu, L. N6-methyladenosine modification of HIV-1 RNA suppresses type-I interferon induction in differentiated monocytic cells and primary macrophages. PLoS Pathog. 2021, 17, e1009421. [pdf]



Chiu, B. C.*; Chen, C.; You, Q.; Chiu, R.; Venkataraman, G.; Zeng, C.; Zhang, Z.; Cui, X.; Smith, S. M.; He, C.; Zhang, W.* Alterations of 5-hydroxymethylation in circulating cell-free DNA reflect molecular distinctions of subtypes of non-Hodgkin lymphoma. NPJ Genom. Med. 2021, 6, 11. [pdf]



Chen, H. Y.; Zhang, W. L.; Zhang, L.; Yang, P.; Li, F.; Yang, Z. R.; Wang, J.; Pang, M.; Hong, Y.; Yan, C.; Li, W.; Liu, J.; Xu, N.; Chen, L.; Xiao, X. B.; Qin, Y.; He, X. H.; Liu, H.; Zhu, H. C.; He, C.; Lin, J.*; Jing, H. M.* 5-Hydroxymethylcytosine profiles of cfDNA are highly predictive of R-CHOP treatment response in diffuse large B cell lymphoma patients. Clin. Epigenetics 2021, 13, 33. [pdf]



Lu, M.; Xue, M.; Wang, H. T.; Kairis, E. L.; Ahmad, S.; Wei, J.; Zhang, Z.; Liu, Q.; Zhang, Y.; Gao, Y.; Garcin, D.; Peeples, M. E.; Sharma, A.; Hur, S.; He, C.; Li, J. Nonsegmented negative-sense RNA viruses utilize N6-methyladenosine (m6A) as a common strategy to evade host innate immunity. J. Virol. 2021, 95, e01939-20. [pdf]



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62. Yi, C.; Yang, C.-G.; He, C. A Non-Heme Iron-Mediated Chemical Demethylation in DNA and RNA. Acc. Chem. Res. 2009, 42, 519-529. [pdf]
61. Yang, C.-G.; Garcia, K.; He, C. Damage Detection and Base Flipping in Direct DNA Alkylation Repair. ChemBioChem 2009, 10, 417-423. [pdf]
60. Richter, S; Anderson, V. J.; Garufi, G.; Lu, L.; Budzik, J. M.; Joachimiak, A.; He, C.; Schneewind, O.; Missiakas, D. Capsule anchoring in Bacillus anthracis occurs by a transpeptidation reaction that is inhibited by capsidin. Mol. Microbiol. 2009, 71, 404-420. [pdf]
59. Chen, P. R.; Nishida, S.; Poor, C. B.; Cheng, A.; Bae, T.; Kuechenmeister, L.; Dunman, P. M.; Missiakas, D.; He, C. A new oxidative sensing and regulation pathway mediated by the MgrA homologue SarZ in Staphylococcus aureus. Mol. Microbiol. 2009, 71, 198-211. [pdf]
58. 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, 130, 17634-17635. [pdf]
57. Qiu, Z.; Lu, L.; Jian, X.; He, C. A Diazirine-Based Nucleoside Analogue for Efficient DNA Interstrand Photocross-Linking. J. Am. Chem. Soc. 2008, 130, 14398-14399. [pdf]
56. 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, 3313-3319. [pdf]
55. 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, 13586-13591. [pdf]
54. Li, X.; Ye, S.; He, C.; Yu, Z.-X. Mechanisms of Brønsted Acid Catalyzed Additions of Phenols and Protected Amines to Olefins: A DFT Study. Eur. J. Org. Chem. 2008, 25, 4296-4303. [pdf]
53. 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. [pdf] [C&EN]
52. Li, Z.; Brouwer, C.; He, C. Gold-Catalyzed Organic Transformations Chem. Rev. 2008, 108, 3239-3265. [pdf]
51. 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. [pdf] [U. Chicago Press] [C&EN] [AAAS] [Argonne Lab Press] (For additional news links, go to "Research Highlights"
50.  Chen, P. R. and He, C.  Selective recognition of metal ions by metalloregulatory proteins. Curr. Opin. Chem. Biol. 2008, 12, 214-221. [pdf]
49.  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. [pdf]
48.  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. [pdf]
47.  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. [pdf] [J. Proteome Res. press]
46.  Durek, T.; Zhang, J.; He, C.; Kent, S. B.H . Synthesis of Photoactive Analogues of a Cysteine Knot Trypsin Inhibitor Protein Org. Lett. 2007, 9, 5497-5500.   [pdf]
45. 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, 12461-12467.  [pdf]

44. 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, 12350-12351. [pdf]

43. 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, 12058-12059. [pdf]

42. Brouwer, C.; Rahatrian, R.; He, C. Gold(I)-Mediated Hydrothiolation of Conjugated Olefins. Synlett 2007, 11, 1785-1789. [pdf]

41. Li, Z.; Capretto, D. A.; Rahaman, R. O.; He, C. Silver-Catalyzed Intermolecular Amination of C-H Groups. Angew. Chem. Intl. Ed. 2007, 46, 5184-5186. [pdf] [C&EN]

40. 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, 3474-3475. [pdf]

39. 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. [pdf] [C&EN] [IDBD Listing]


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.  [pdf]


37. Li, Z.; Ding, X. and He, C. Nitrene Transfer Reactions Catalyzed by Gold Complexes. J. Org. Chem. 2006, 71:5876-80.  [pdf]
36. Li, Z. and He, C. Recent Advances in Silver-Catalyzed Nitrene, Carbene, and Silylene-Transfer Reactions. Euro. J. Org. Chem. 2006, 4313-4322.[pdf]
Mishina, Y. and He, C. Oxidative Dealkylation DNA Repair Mediated by the Mononuclear Non-Heme
 Iron AlkB Proteins. J. Inorg. Biochem. 2006, 100, 670-678. [pdf] 
Reich, N. W.; Yang, C.-G.; Shi, Z. and He, C. Gold(I)-Catalyzed Synthesis of Dihydrobenzofurans from
 Aryl Allyl Ethers. Synlett. 2006, 8, 1278-1280. [pdf] 


Brouwer, C. and He, C. Efficient Gold-Catalyzed Hydroamination of 1,3-Dienes. Angew Chem. Int. Ed. 2006, 45, 1744-1747. [pdf]



Zhang, J.; Yang, C.-G. and He, C. Gold(I)-Catalyzed Intra- and Intermolecular Hydroamination of Unactivated Olefins. J. Am. Chem. Soc. 2006, 128, 1798-1799. [pdf]



Mishina, Y.; Duguid, M. E. and He, C. Direct Reversal of DNA Alkylation Damage. Chem. Rev. 2006, 106, 215-232.  [pdf]




Yang, C.-G.; Reich, N. W. and He, C. Intramolecular Additions of Alcohols and Carboxylic Acids to Inert Olefins Catalyzed by Silver(I) Triflate. Org. Lett. 2005, 7, 4553-4556. [pdf]



Mishina, Y.; Yang, C.-G. and He, C. Direct Repair of the Exocyclic DNA Adduct 1,N6-Ethenoadenine by E. coli AlkB and Human ABH3. J. Am. Chem. Soc. 2005, 127, 14594-14595. [pdf]



Li, Z.; Shi, Z. and He, C. Addition of Heterocycles to Electron Deficient Olefins and Alkynes Catalyzed by Gold(III). J. Organom. Chem. 2005, 690, 5049-5054. [pdf]



Yang, C.-G. and He, C. Gold(I)-Catalyzed Intermolecular Addition of Phenols and Carboxylic Acids to Olefins. J. Am. Chem. Soc. 2005, 127, 6966-6967. [pdf]



Duguid, M. E.; Rice, P. A. and He, C. Implications for How the Human DNA Repair Protein AGT Locates Damage as Revealed from A Unique X-ray Structure of Its DNA Bound Form. J. Mol. Biol. 2005, 350, 657-666. [pdf]



Chen, P.; Greenberg, B.; Taghavi, S.; Romano, C.; van der Lelie, D. and He, C. An Exceptionally Selective Lead(II)-Regulatory Protein from Ralstonia Metallidurans: Development of A Fluorescent Lead(II) Probe. Angew Chem. Int. Ed. 2005, 44, 2715-2719.  [pdf]   C&EN, News1 News2 News3 News4  News5 News6



He, C.; Sun, L. J.; Zhou, P.; Norman, D. P. G.; Dötsch, V.; Gross, J. D.; Lane, W. S.; Wagner, G.; Verdine, G. L. A Zinc-Mediated Electrostatic Switch Controls the Adaptive Response of E. coli to Methylating Agents. Mol. Cell. 2005, 20, 117-129. [pdf]



Mishina, Y.; Chen, L. X. and He, C. Preparation and Characterization of the Native Iron(II)-Containing AlkB Protein Directly from Escherichia coli. J. Am. Chem. Soc. 2004,  126, 16930-16936. [pdf]



Shi, Z. and He, C. Direct Functionalization of Arenes by Primary Alcohol Sulfonate Esters Catalyzed by Gold(III). J. Am. Chem. Soc. 2004, 126, 13596-13597. [pdf]



Cui, Y. and He, C. A Silver-Catalyzed Intramolecular Amidation of Saturated C–H bonds. Angew Chem. Int. Ed. 2004, 43, 4210-4212. [pdf]



Shi, Z. and He, C. Efficient Functionalization of Aromatic C–H Bonds Catalyzed by Gold(III) under Mild and Solvent Free Conditions. J. Org. Chem. 2004, 69, 3669-3671. [pdf]



Shi, Z. and He, C. An Au-Catalyzed Cyclialkylation of Electron Rich Arenes with Epoxides to Prepare 3-Chromanols. J. Am. Chem. Soc. 2004, 126, 5964-5965. [pdf]



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, 1548-1554.  [pdf]



He, C. and Mishina, Y. Modeling non-heme iron proteins. Curr. Opin. Chem. Biol. 2004, 8, 201-208. [pdf]



Chen, P. and He, C. A General Strategy to Convert the MeR Family Proteins Into Highly Sensitive and Selective Fluorescent Biosensors for Metal Ions. J. Am. Chem. Soc. 2004, 126, 728-729. [pdf], C&EN  Analytical Chemistry




Cui, Y. and He, C. Efficient Aziridination of Olefins Catalyzed by A Unique Disilver(I) Compound. J. Am. Chem. Soc. 2003, 125, 16202-16203. [pdf]



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. [pdf]



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, 8730-8731. [pdf]


Other Publications

12.  He, C.; Wei, H.; Verdine, G. L. Converting the Sacrificial DNA Repair Protein N-Ada into a Catalytic Methyl Phosphotriester Repair Enzyme. J. Am. Chem. Soc. 2003, 125, 1450-1451.

11.  He, C.; Verdine, G. L. Trapping Distinct Structural States of a Protein/DNA Interaction through Disulfide Cross-linking. Chem. & Biol. 2002, 9, 1297-1303.

10.  He, C.; DuBois, J. L.; Hedman, B.; Hodgson, K. O.; Lippard, S. J. A short Copper-Copper Distance in a (m-1,2-Peroxo)dicopper(II) Complex Having 1,8-Naphthyridine Unit as an Additional Bridge. Angew. Chem. Int. Ed. 2001, 40, 1484-1487.

9.  He, C.; 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. 2001, 40, 1414-1420 (cover story).

8.  He, C.; Barrios, A. M.; Lee, D.; Kuzelka, J.; Davydov, R. M.; Lippard, S. J. Diiron Complexes of 1,8-Naphthyridine-Based Dinucleating Ligands as Models for Hemerythrin. J. Am. Chem. Soc. 2000, 122, 12683-12690.

7.   He, C.; 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, 5225-5231.

6.  He, C.; Lippard, S. J. Design and Synthesis of Multidentate Dinucleating Ligands Based on 1,8-Naphthyridine. Tetrahedron 2000, 56, 8245-8252.

5.  He, C.; Gomez, V.; Spingler, B.; 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, 4188-4189.

4.  Kaminskaia, N. V.; He, C.; Lippard, S. J. Reactivity of m-Hydroxodizinc(II) Centers in Enzymatic Catalysis through Model Studies. Inorg. Chem. 2000, 39, 3365-3373.

3.  He, C.; 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.; Lippard, S. J. Aminoguanidinium Hydrolysis Effected by a Hydroxo-Bridged Dicobalt(II) Complexes. J. Am. Chem. Soc. 1998, 120, 105-113.

1.  Qian, Y.; Xie, Y.; He, C.; Li, J.; Chen, Z. Hydrothermal Preparation and Characterization of Ultrafine Magnetite Powders. Material Research Bulletin 1994, 29, 953-957.