He, Chuan - University of Chicago - Department of Biochemistry & Molecular Biology

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Mishra, T.; Phillips, S.; Zhao, Y.; Wilms, B.; He, C.; Wu, L. Epitranscriptomic m6A modifications during reactivation of HIV-1 latency in CD4+T cells. mBio 2024, e0221424. Zou, Z.; Dou, X.; Li, Y.; Zhang, Z.; Wang, J.; Gao, B.; Xiao, Y.; Wang, Y.; Zhao, L.; Sun, C.; Liu, Q.; Yu, X.; Wang, H.; Hong, J.; Dai, Q.; Yang, F. C.; Xu, M.*; He, C.* RNA m5C oxidation by TET2 regulates chromatin state and leukaemogenesis. Nature 2024, online. Wen, C.; Wang, L.; Piffko, A.; Chen, D.; Yu, X.; Zawieracz, K.; Bugno, J.; Yang, K.; Naccasha, E. Z.; Ji, F.; Wang, J.; Huang, X.; Luo, S. Y.; Tan, L.; Shen, B.; Luo, C.; McNerney, M. E.; Chmura, S. J.; Arina, A.; Pitroda, S. P.; He, C.*; Liang, H.*; Weichselbaum, R. R.* YTHDF1 loss in dendritic cells potentiates radiation-induced antitumor immunity via STING-dependent type I IFN production. J. Clin. Invest. 2024, e181612. Kahraman, S.; De Jesus, D. F.; Wei, J.; Brown, N. K.; Zou, Z.; Hu, J.; Pirouz, M.; Gregory, R. I.; He, C.; Kulkarni, R. N. m6A mRNA methylation by METTL14 regulates early pancreatic cell differentiation. EMBO J. 2024, online. Xiao, L.; De Jesus, D. F.; Ju, C. W.; Wei, J. B.; Hu, J.; DiStefano-Forti, A.; Tsuji, T.; Cero, C.; Mannisto, V.; Manninen, S. M.; Wei, S.; Ijaduola, O.; Bluher, M.; Cypess, A. M.; Pihlajamaki, J.; Tseng, Y. H.; He, C.; Kulkarni R. N. m6A mRNA methylation in brown fat regulates systemic insulin sensitivity via an inter-organ prostaglandin signaling axis independent of UCP1. Cell Metab. 2024, 36, 2207-2227. Malovic, E.; Ealy, A.; Miller, C.; Jang, A.; Hsu, P. J.; Sarkar, S.; Rokad, D.; Goeser, C.; Hartman, A. K.; Zhu, A.; Palanisamy, B.; Zenitsky, G.; Jin, H.; Anantharam, V.; Kanthasamy, A.; He, C.; Kanthasamy, A.G. Epitranscriptomic reader YTHDF2 regulates SEK1(MAP2K4)-JNK-cJUN inflammatory signaling in astrocytes during neurotoxic stress. iScience 2024, 27, 110619. Liu, C.; Dou, X.; Zhao, Y.; Zhang, L.; Zhang, L.; Dai, Q.; Liu, J.; Wu, T.; Xiao, Y.; He, C. IGF2BP3 promotes mRNA degradation through internal m7G modification. Nat. Commun. 2024, 15, 7421. Bhola M.; Abe K.; Orozco P.; Rahnamoun H.; Avila-Lopez, P.; Taylor, E.; Muhammad, N.; Liu, B.; Patel, P.; Marko, J. F.; Starner, A. C.; He, C.; Van Nostrand, E. L.; Mondragon, A.; Lauberth, S. M. RNA interacts with topoisomerase I to adjust DNA topology. Mol. Cell 2024, 84, 3192-3208. Ross, M. O.*; Xie, Y.; Owyang, R. C.; Ye, C.; Zbihley, O.N. P.; Lyu, R.; Wu, T.; Wang, P.; Karginova, O.; Olopade, O. I.; Zhao, M.; He, C.* PTPN2 copper-sensing relays copper level fluctuations into EGFR/CREB activation and associated CTR1 transcriptional repression. Nat. Commun. 2024, 15, 6947. Lyu, R.; Gao, Y.; Wu, T.; Ye, C.; Wang, P.; He, C. Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq. Nat. Commun. 2024, 15, 6582. Chen T.; Greene G. H.; Motley J.; Mwimba M.; Luo G. Z.; Xu G.; Karapetyan S.; Xiang Y.; Liu C.; He C.; Dong X. m6A modification plays an integral role in mRNA stability and translation during pattern-triggered immunity. Proc. Natl. Acad. Sci. 2024, 121, e2411100121. Kaufman, M. E.; Vayani, O. R.; Moore, K.; Chlenski, A.; Wu, T.; Lee, S. M.; Desai, A. V.; He, C.; Cohn, S. L.; Applebaum, M. A. Characterizing relationships between T-cell inflammation and outcomes in patients with high-risk neuroblastoma according to mesenchymal and adrenergic signatures. Cancer Res. Commun. 2024, 4, 2255-2266. Zhao, Y.; Ma, X.; Ye, C.; Li, W.; Pajdzik, K.; Dai, Q.; Sun, H. L.; He, C. Pseudouridine detection and quantification using bisulfite incorporation hindered ligation. ACS Chem. Biol. 2024, 19, 1813-1819. Cui, X. L.; Nie, J.; Zhu, H.; Kowitwanich, K.; Beadell, A. V.; West-Szymanski, D. C.; Zhang, Z.; Dougherty, U.; Kwesi, A.; Deng, Z.; Li ,Y.; Meng, D.; Roggin, K.; Barry, T.; Owyang, R.; Fefferman, B.; Zeng, C.; Gao, L.; Zhao, C. W. T.; Malina, Y.; Wei, J.; Weigert, M.; Kang, W.; Goel, A.; Chiu ,B. C.; Bissonnette, M.; Zhang, W.*; Chen, M.*; He, C.* LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA. Genome Biol. 2024, 25, 157. Wang, G.; Li, H.; Ye, C.; He, K.; Liu, S.; Jiang, B.; Ge, R.; Gao, B.; Wei, J.; Zhao, Y.; Li, A.; Zhang, D.; Zhang, J.; He, C. Quantitative profiling of m6A at single base resolution across the life cycle of rice and Arabidopsis. Nat. Commun. 2024, 15, 4881. Xiao, S.; Ma, S.; Sun, B.; Pu, W.; Duan, S.; Han, J.; Hong, Y.; Zhang, J.; Peng, Y.; He, C.; Yi, P.*; Caligiuri, M. A.*; Yu, J.* The tumor-intrinsic role of the m6A reader YTHDF2 in regulating immune evasion. Sci. Immunol. 2024, 9, eadl2171. Chang, W.; Zhang, Z.; Jia, B.; Ding, K.; Pan, Z.; Su, G.; Zhang, W.; Liu, T.; Zhong, Y.; He, G.; Ren, L.; Wei, Y.; Li, D.; Cui, X.; Yang, J.; Shi, Y.; Bissonnette, M.; He, C.; Zhang, W.*; Fan, J.*; Xu, J.* A 5-hydroxymethylcytosine-based noninvasive model for early detection of colorectal carcinomas and advanced adenomas: The METHOD-2 Study. Clin. Cancer Res. 2024, 30, 3337-3348. Olazagoitia-Garmendia, A.; Rojas-M�rquez, H.; Romero, M. D. M.; Ruiz, P.; Agirre-Lizaso, A.; Chen, Y.; Perugorria, M. J.; Herrero, L.; Serra, D.; Luo, C.; Bujanda, L.; He C.; Castellanos-Rubio, A. Inhibition of YTHDF1 by salvianolic acid overcomes gluten-induced intestinal inflammation. Gut 2024, 73, 1590-1592. Bugno, J.; Wang, L.; Yu, X.; Cao, X.; Wang, J.; Huang, X.; Yang, K.; Piffko, A.; Chen, K.; Luo, S. Y.; Naccasha, E.; Hou, Y.; Fu, S.; He, C.; Fu, Y. X.; Liang, H. L.; Weichselbaum. R. R. Targeting the dendritic cell-secreted immunoregulatory cytokine CCL22 alleviates radioresistance. Clin. Cancer Res. 2024, 30, 4450-4463. Pomaville, M.; Chennakesavalu, M.; Wang, P.; Jiang, Z.; Sun, H. L.; Ren, P.; Borchert, R.; Gupta, V.; Ye, C.; Ge, R.; Zhu, Z.; Brodnik, M.; Zhong, Y.; Moore, K.; Salwen, H.; George, R. E.; Krajewska, M.; Chlenski, A.; Applebaum, M. A.; He, C.; Cohn, S. L. Small-molecule inhibition of the METTL3/METTL14 complex suppresses neuroblastoma tumor growth and promotes differentiation. Cell Rep. 2024, 43, 114165. Shen, W.; Hou, Y.; Yi, Y.; Li, F.; He, C.; Wang, J. G-Clamp heterocycle modification containing interstrand photo-cross-linker to capture intracellular microRNA targets. J. Am. Chem. Soc. 2024, 146, 12778-12789. Zou, Z.; He, C. The YTHDF proteins display distinct cellular functions on m6A-modified RNA. Trends Biochem. Sci. 2024, 49, 611-621. Shao, J.; Xu, Y.; Olsen, RJ.; Kasparian, S.; Sun, K.; Mathur, S.; Zhang, J.; He, C.; Chen, S. H.; Bernicker, E. H.; Li, Z. 5-Hydroxymethylcytosine in cell-free DNA predicts immunotherapy response in lung cancer. Cells 2024, 13, 715. Xue, Q.; Yu, W.; Li, J. P.*; He, C.; Guo, Z.* Revealing the nature of Pt-based immunotherapy through the lens of neoantigens in cancer. Sci. Bull. 2024, 69, 2314-2318. Zhang, Y.; Dong, Q.; Wang, Z.; Liu, Q.; Yu, H.; Sun, W.; Cheema, J.; You, Q.; Ding, L.; Cao, X.; He, C.; Ding, Y.*; Zhang, H.* A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics. Nat. Commun. 2024, 15, 3253. Pajdzik, K.; Lyu, R.; Dou, X.; Ye, C.; Zhang, L. S.; Dai, Q.*; He, C.* Chemical manipulation of m1A mediates its detection in human tRNA. RNA 2024, 30, 548-559. Yu, F.; Liu, S.; Zhu, A. C.; He, C.*; Qian, Z.* Protocol for detecting RBM33-binding sites in HEK293T cells using PAR-CLIP-seq. STAR Protoc. 2024, 5, 102855. Kahl, M.; Xu, Z.; Arumugam, S.; Edens, B.; Fischietti, M.; Zhu, A. C.; Platanias, L. C.; He, C.; Zhuang, X.; Ma, Y. C. m6A RNA methylation regulates mitochondrial function. Hum. Mol. Genet. 2024, 33, 969-980. De Jesus, D. F.; Zhang, Z.; Brown, N. K.; Li, X.; Xiao, L.; Hu, J.; Gaffrey, M. J.; Fogarty, G.; Kahraman, S.; Wei J.; Basile G.; Rana T. M.; Mathews, C.; Powers, A. C.; Parent, A. V.; Atkinson, M. A.; Dhe-Paganon, S.; Eizirik, D. L.; Qian, W. J.; He, C.*; Kulkarni, R. N.* Redox regulation of m6A methyltransferase METTL3 in β-cells controls the innate immune response in type 1 diabetes. Nat. Cell Biol. 2024, 26, 421-437. Weigert, M.; Cui, X. L.; West-Szymanski, D.; Yu, X.; Bilecz, A. J.; Zhang, Z.; Dhir, R.; Kehoe, M.; Zhang, W.; He, C.; Lengyel, E. 5-Hydroxymethylcytosine signals in serum are a predictor of chemoresistance in high-grade serous ovarian cancer. Gynecol. Oncol. 2024, 182, 82-90. He, P. C.; He, C. mRNA accessibility within mRNPs as a determinant of gene expression. Trends Biochem. Sci. 2024, 49, 199-207. Ren, Y.; Zhang, Z.; She, Y.; He, Y.; Li, D.; Shi, Y.; He, C.; Yang, Y.*; Zhang, W.*; Chen, C.* A highly sensitive and specific non-invasive test through genome-wide 5-hydroxymethylation mapping for early detection of lung cancer. Small Methods 2024, 8, e2300747. Guo, J.; Zou, Z.; Dou, X.; Zhao, X.; Wang, Y.; Wei, L.; Pi, Y.; Wang, Y.; He, C.; Guo, S. Zebrafish Mbd5 binds to RNA m5C and regulates histone deubiquitylation and gene expression in development metabolism and behavior. Nucleic Acids Res. 2024, 52, 4257-4275. Zhang, L.; Duan, H. C.; Paduch, M.; Hu, J.; Zhang, C.; Mu, Y.; Lin, H.; He, C.; Kossiakoff, A. A.; Jia, G.*; Zhang, L.* The molecular basis of human ALKBH3 mediated RNA N1-methyladenosine (m1A) demethylation. Angew. Chem. Int. Ed. 2024, 63, e202313900. Li, Y.; Liu, H.*; He, C.; Ma, L.* Comparison of transcriptome-wide N6-methyladenosine profiles from healthy trio families reveals regulator-mediated methylation alterations. Genetics 2024, 226, iyad206. Shao, J.; Olsen, R. J.; Kasparian, S.; He, C.; Bernicker, E. H.; Li, Z. Cell-free DNA 5-hydroxymethylcytosine signatures for lung cancer prognosis. Cells 2024, 13, 298. Feng, X.; Cui, X.; Zhang, L. S.; Ye, C.; Wang, P.; Zhong, Y.; Wu, T.; Zheng, Z.; He, C. Sequencing of N6-methyl-deoxyadenosine at single-base resolution across the mammalian genome. Mol. Cell 2024, 84, 596-610. Xiao, Y.; Chen, Y. M.; Zou, Z.; Ye, C.; Dou, X.; Wu, J.; Liu, C.; Liu, S.; Yan, H.; Wang, P.; Zeng, T. B.; Liu, Q.; Fei, J.; Tang, W.; He, C. Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing. Nat. Methods 2024, 21, 247-258. Zhang, L. S.; Ye, C.; Ju, C. W.; Gao, B.; Feng, X.; Sun, H. L.; Wei, J.; Yang, F.; Dai, Q.*; He, C.* BID-seq for transcriptome-wide quantitative sequencing of mRNA pseudouridine at base resolution. Nat. Protoc. 2024, 19, 517-538. Yang, Q.*; Vafaei, S.; Falahati, A.; Khosh, A.; Bariani, M. V.; Omran, M. M.; Bai, T.; Siblini, H.; Ali, M.; He, C.; Boyer, T. G.; Al-Hendy, A. Bromodomain-containing protein 9 regulates signaling pathways and reprograms the epigenome in immortalized human uterine fibroid cells. Int. J. Mol. Sci. 2024, 25, 905. Wu, T.; Cheng, A. Y.; Zhang, Y.; Xu, J.; Wu, J.; Wen, L.; Li X.; Liu, B.; Dou, X.; Wang, P.; Zhang, L.; Fei, J.; Li, J.; Ouyang, Z.*; He, C.* KARR-seq reveals cellular higher-order RNA structures and RNA-RNA interactions. Nat. Biotechnol. 2024, online. Chennakesavalu, M.; Moore, K.; Chaves, G.; Veeravalli, S.; TerHaar, R.; Wu, T.; Lyu, R.; Chlenski, A.; He, C.; Piunti, A.; Applebaum, M. A. 5-hydroxymethylcytosine profiling of cell-free DNA identifies bivalent genes that are prognostic of survival in high-risk neuroblastoma. JCO Precis. Oncol. 2024, 8. e2300297. Dai, Q.*; Ye, C.; Irkliyenko, I.; Wang, Y.; Sun, H. L.; Gao, Y.; Liu, Y.; Beadell, A.; Perea, J.; Goel, A.; He, C.* Ultrafast bisulfite sequencing detection of 5-methylcytosine in DNA and RNA. Nat. Biotechnol. 2024, online. Zhang, L. S.; Dai, Q.; He, C. Base-resolution sequencing methods for whole-transcriptome quantification of mRNA modifications. Acc. Chem. Res. 2024, 57, 47-58. Cerneckis, J.; Ming, G. L.; Song, H.*; He, C.; Shi, Y.* The rise of epitranscriptomics: recent developments and future directions. Trends Pharmacol. Sci. 2024, 45, 24-38. Vayani, O. R.; Kaufman, M. E.; Moore, K.; Chennakesavalu, M.; TerHaar, R.; Chaves, G.; Chlenski, A.; He, C.; Cohn, S. L.; Applebaum, M. A. Adrenergic and mesenchymal signatures are identifiable in cell-free DNA and correlate with metastatic disease burden in children with neuroblastoma. Pediatr. Blood Cancer 2024, 71, 30735. Zhang, L.S; Dai, Q.; He, C. Quantitative base-resolution sequencing technology for mapping pseudouridines in mammalian mRNA. Acc. Chem. Res.2024, 57, 47-58. Tao, Y.; Felber, J. G.; Zou, Z.; Njomen, E.; Remsberg, J. R.; Ogasawara, D.; Ye, C.; Melillo, B.; Schreiber, S. L.; He, C.*; Remillard, D.*; Cravatt, B. F.* Chemical proteomic discovery of isotype-selective covalent inhibitors of the RNA methyltransferase NSUN2. Angew. Chem. Int. Ed.2023, 62, e202311924. Wang, L.*; Si, W.; Yu, X.; Piffko, A.; Dou, X.; Ding, X.; Bugno, J.; Yang, K.; Wen, C.; Zhang, L.; Chen, D.; Huang, X.; Wang, J.; Arina, A.; Pitroda, S.; Chmura, S. J.; He, C.; Liang, H. L.; Weichselbaum, R.* Epitranscriptional regulation of TGF-β pseudoreceptor BAMBI by m6A/YTHDF2 drives extrinsic radioresistance. J. Clin. Invest. 2023, 133, e172919. Wang, L.*; Katipally, R. R.; Liang, H. L.; Yang, K.; Pitroda, S. P.; He, C.; Weichselbaum, R. R.* RNA m6A methylation and MDSCs: Roles and therapeutic implications for radiotherapy. Med. 2023, 4, 863-874. Lv, D.; Zhong, C.; Dixit, D.; Yang, K.; Wu, Q.; Godugu, B.; Prager, B. C.; Zhao, G.; Wang, X.; Xie, Q.; Bao, S.; He, C.; Heiland, D. H.; Rosenfeld, M. G.; Rich, J. N. EGFR promotes ALKBH5 nuclear retention to attenuate N6-methyladenosine and protect against ferroptosis in glioblastoma. Mol. Cell 2023, 83, 4334-4351. Zou, Z.; Wei, J.; Chen, Y.; Kang, Y.; Shi, H.; Yang, F.; Shi, Z.; Chen, S.; Zhou, Y.; Sepich-Poore, C.; Zhuang, X.; Zhou, X.; Jiang, H.; Wen, Z.; Jin, P.*; Luo, C.*; He, C.* FMRP phosphorylation modulates neuronal translation through YTHDF1. Mol. Cell 2023, 83, 4304-4317. Jiang, B.*; Zhong, Z.; Gu, L.; Zhang, X.; Wei, J.; Ye, C.; Lin, G.; Qu, G.; Xiang, X.; Wen, C.; Hummel, M.; Bailey-Serres, J.; Wang, Q.; He, C.; Wang, X.*; Lin, C.* Light-induced LLPS of the CRY2/SPA1/FIO1 complex regulating mRNA methylation and chlorophyll homeostasis in Arabidopsis. Nat. Plants 2023, 9, 2042-2058. Gao, L.; Zhang, Z.; Cui, X. L.; West-Szymanski, D.; Ye, C.; He, C.; Zhang, W.*; Bissonnette, M.* Analysis of genome-wide 5-hydroxymethylation of blood samples stored in different anticoagulants: opportunities for the expansion of clinical resources for epigenetic research. Epigenetics 2023, 18, 2271692. Liau, W. S.*; Zhao, Q.; Bademosi, A.; Gormal, R. S.; Gong, H.; Marshall, P. R.; Periyakaruppiah, A.; Madugalle, S. U.; Zajaczkowski, E. L.; Leighton, L. J.; Ren, H.; Musgrove, M.; Davies, J.; Rauch, S.; He, C.; Dickinson, B. C.; Li, X.; Wei, W.; Meunier, F. A.; Fern�ndez-Moya, S. M.; Kiebler, M. A.; Srinivasan, B.; Banerjee, S.; Clark, M.; Spitale, R. C.; Bredy, T. W.* Fear extinction is regulated by the activity of long noncoding RNAs at the synapse. Nat. Commun. 2023, 14, 7616. Marinov, G. K.*; Bagdatli, S. T.; Wu, T.; He, C.; Kundaje, A.; Greenleaf, W. J. The chromatin landscape of the euryarchaeon Haloferax volcanii. Genome Biol. 2023, 24, 253. Fan, H.; Xia, S.; Xiang, J.; Li, Y.; Ross, M. O.; Lim, S. A.; Yang, F.; Tu, J.; Xie, L.; Dougherty, U.; Zhang, F. Q.; Zheng, Z.; Zhang, R.; Wu, R.; Dong, L.; Su, R.; Chen, X.; Althaus, T.; Riedell, P. A.; Jonker, P. B.; Muir, A.; Lesinski, G. B.; Rafiq, S.; Dhodapkar, M. V.; Stock, W.; Odenike, O.; Patel, A. A.; Opferman, J.; Tsuji, T.; Matsuzaki, J.; Shah, H.; Faubert, B.; Elf, S. E.; Layden, B.; Bissonnette, B. M.; He, Y. Y.; Kline, J.; Mao, H.; Odunsi, K.; Gao, X.; Chi, H.*; He, C.*; Chen, J.* Trans-vaccenic acid reprograms CD8+ T cells and anti-tumour immunity. Nature 2023, 623, 1034-1043. Chen, Y.; Wan, R.; Zou, Z.; Lao, L.; Shao, G.; Zheng, Y.; Tang, L.; Yuan, Y.; Ge, Y.*; He, C.*; Lin, S*. O-GlcNAcylation determines the translational regulation and phase separation of YTHDF proteins. Nat. Cell Biol. 2023, 25, 1676-1690. Olazagoitia-Garmendia, A.; Rojas-M�rquez, H.; Romero, M. D. M.; Ruiz, P.; Agirre-Lizaso, A.; Chen, Y.; Perugorria, M. J.; Herrero, L.; Serra, D.; Luo, C.; Bujanda, L.; He, C.; Castellanos-Rubio, A. Inhibition of YTHDF1 by salvianolic acid overcomes gluten-induced intestinal inflammation. Gut 2023, 0, 1-3. Madugalle, S. U.; Liau, W. S.; Zhao, Q.; Li, X.; Gong, H.; Marshall, P. R.; Periyakaruppiah, A.; Zajaczkowski, E. L.; Leighton, L. J.; Ren, H.; Musgrove, M. R. B.; Davies, J. W. A.; Kim, G.; Rauch, S.; He, C.; Dickinson, B. C.; Fulopova, B.; Fletcher, L. N.; Williams, S. R.; Spitale, R. C.; Bredy, T. W. Synapse-enriched m6A-modified Malat1 interacts with the novel m6A reader, DPYSL2, and is required for fear-extinction memory. J. Neurosci. 2023, 43, 7084-7100. Lee, S. M.; Koo, B.; Carr�, C.; Fischer, A.; He, C.; Kumar, A.; Liu, K.; Meyer, K. D.; Ming, G. L.; Peng, J.; Roignant, J. Y.; Storkebaum, E.; Sun, S.; De Pietri Tonelli, D.; Wang, Y.; Weng, Y. L.; Pulvirenti, L.; Shi, Y.; Yoon, K. J.; Song, H. Exploring the brain epitranscriptome: perspectives from the NSAS summit. Front. Neurosci. 2023, 17, 1291446. Zheng, Y.; Li, X.; Deng, S.; Zhao, H.; Ye, Y.; Zhang, S.; Huang, X.; Bai, R.; Zhuang, L.; Zhou, Q.; Li, M.; Su, J.; Li, R.; Bao, X.; Zeng, L.; Chen, R.; Zheng, J.; Lin, D.*; He, C.*; Zhang, J* Zuo, Z.* CSTF2 mediated mRNA N6-methyladenosine modification drives pancreatic ductal adenocarcinoma m6A subtypes. Nat. Commun. 2023, 14, 6334. Lyu, R.; Wu, T.; Park, G.; He, Y. Y.; Chen, M.*; He, C.* KAS-Analyzer: a novel computational framework for exploring KAS-seq data. Bioinform. Adv. 2023, 3, vbad121. Dou, X.; Xiao, Y.; Shen, C.; Wang, K.; Wu, T.; Liu, C.; Li, Y.; Yu, X.; Liu, J.; Dai, Q.; Pajdzik, K.; Ye, C.; Ge, R.; Gao, B.; Yu, J.; Sun, S.; Chen, M.*; Chen, J.*; He, C.* RBFOX2 recognizes N6-methyladenosine to suppress transcription and block myeloid leukaemia differentiation. Nat. Cell Biol. 2023, 25, 1359-1368. Shao, J.; Shah, S.; Ganguly, S.; Zu, Y.; He, C.; Li, Z. Cell-free DNA 5-hydroxymethylcytosine is highly sensitive for MRD assessment in acute myeloid leukemia. Clin. Epigenetics 2023, 15, 134. 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, 11, 2050313X231188883. 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. 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, 2023, baad042. 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. 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. 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. Wu, T.; He, C. 6mA-METL-9 axis regulates innate immunity in C. elegans. Cell Res. 2023, 33, 581-582. 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, 33, 727-730. 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, 10, e2300445. 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. 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. Zhang, L.S; Ju, C.W.; Jiang, B.; He, C. Base-resolution quantitative DAMM-seq for mapping RNA methylations in tRNA and mitochondrial polycistronic RNA. Methods Enzymol 2023, 692, 39-54. Zhang, L.S; He, C. Ex vivo gliadin stimulation of intestinal cells. Methods Cell Biol. 2023, 179, 13-20. 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. Pomaville, M. M.*; He, C. Advances in targeting RNA modifications for anticancer therapy. Trends Cancer 2023, 9, 528-542. 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. 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. 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, 14, 683-697. Zou, Z.; He, C. Splice epitranscriptomics and DNA damage repair together: ALKBH5-m6A-SF3B1 regulation in leukemic transformation. Mol. Cell 2023, 83, 1022-23. 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. Feng, X.; He, C. Mammalian DNA N6-methyladenosine: Challenges and new insights. Mol. Cell 2023, 83, 343-351. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. He, C. ACS Chemical Biology. 2022 Editorial Statement. ACS Chem. Biol. 2022, 17, 1. 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. 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. 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. 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. 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. 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.

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