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Chuan He

Professor
chuanhe@uchicago.edu
Research Summary
Chuan He is the John T. Wilson Distinguished Service Professor in the Department of Chemistry and Department of Biochemistry and Molecular Biology at the University of Chicago.He received his B.S. (1994) from the University of Science and Technology of China. He received his Ph. D. degree from Massachusetts Institute of Technology in chemistry in 2000. After being trained as a Damon-Runyon postdoctoral fellow at Harvard University from 2000-2002, he joined the University of Chicago as an Assistant Professor, and was promoted to Associate Professor in 2008, Professor in 2010 and John T. Wilson Distinguished Service Professor in 2014. He is also a member of the Cancer Research Center at the University of Chicago. His research spans a broad range of chemical biology, RNA biology, epigenetics, biochemistry, molecular biology, and genomics. His recent research concerns reversible RNA and DNA methylation in biological regulation. His research group discovered the first RNA demethylase and showed that reversible RNA methylation significantly affects gene expression regulation.
Keywords
RNA modification, DNA methylation, Epigenetics, Chemical biology
Education
  • University of Sci. & Tech. China, Hefei/China, B.S. Chemistry 1994
  • MIT, Cambridge, Ph.D. Chemistry 2000
  • Harvard, Cambridge, Postdoc Chemical Biology 2002
Biosciences Graduate Program Association
Awards & Honors
  • 2013 - HHMI Investigator
  • 2017 - Paul Marks Prize in Cancer Research
  • 2019 - ACS Chemical Biology Lectureship
Publications

  1. Asymmetric Total Synthesis of (+)-Phainanoid A and Biological Evaluation of the Natural Product and Its Synthetic Analogues. J Am Chem Soc. 2023 03 01; 145(8):4828-4852. View in: PubMed

  2. Mammalian DNA N6-methyladenosine: Challenges and new insights. Mol Cell. 2023 02 02; 83(3):343-351. View in: PubMed

  3. Exon architecture controls mRNA m6A suppression and gene expression. Science. 2023 02 17; 379(6633):677-682. View in: PubMed

  4. The mechanism underlying redundant functions of the YTHDF proteins. Genome Biol. 2023 01 24; 24(1):17. View in: PubMed

  5. Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination. Nat Biotechnol. 2023 Jan 02. View in: PubMed

  6. BID-seq: The Quantitative and Base-Resolution Sequencing Method for RNA Pseudouridine. ACS Chem Biol. 2023 01 20; 18(1):4-6. View in: PubMed

  7. Author Correction: m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome. Nat Biotechnol. 2022 Nov 30. View in: PubMed

  8. spKAS-seq reveals R-loop dynamics using low-input materials by detecting single-stranded DNA with strand specificity. Sci Adv. 2022 12 02; 8(48):eabq2166. View in: PubMed

  9. m6A-SAC-seq for quantitative whole transcriptome m6A profiling. Nat Protoc. 2023 02; 18(2):626-657. View in: PubMed

  10. m7G-quant-seq: Quantitative Detection of RNA Internal N7-Methylguanosine. ACS Chem Biol. 2022 Nov 18. View in: PubMed

  11. Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution. Nat Biotechnol. 2023 03; 41(3):344-354. View in: PubMed

  12. Detection of m6A RNA modifications at single-nucleotide resolution using m6A-selective allyl chemical labeling and sequencing. STAR Protoc. 2022 Sep 14; 3(4):101677. View in: PubMed

  13. 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 08 16; 15(1):106. View in: PubMed

  14. N6-adenomethylation of GsdmC is essential for Lgr5+ stem cell survival to maintain normal colonic epithelial morphogenesis. Dev Cell. 2022 08 22; 57(16):1976-1994.e8. View in: PubMed

  15. Development of Mild Chemical Catalysis Conditions for m1A-to-m6A Rearrangement on RNA. ACS Chem Biol. 2022 06 17; 17(6):1334-1342. View in: PubMed

  16. FTO mediates LINE1 m6A demethylation and chromatin regulation in mESCs and mouse development. Science. 2022 05 27; 376(6596):968-973. View in: PubMed

  17. m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome. Nat Biotechnol. 2022 08; 40(8):1210-1219. View in: PubMed

  18. 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 02; 6:e2100337. View in: PubMed

  19. ACS Chemical Biology-2022 Editorial Statement. ACS Chem Biol. 2022 01 21; 17(1):1. View in: PubMed

  20. The METTL5-TRMT112 N6-methyladenosine methyltransferase complex regulates mRNA translation via 18S rRNA methylation. J Biol Chem. 2022 03; 298(3):101590. View in: PubMed

  21. KAS-seq: genome-wide sequencing of single-stranded DNA by N3-kethoxal-assisted labeling. Nat Protoc. 2022 02; 17(2):402-420. View in: PubMed

  22. HRD1-mediated METTL14 degradation regulates m6A mRNA modification to suppress ER proteotoxic liver disease. Mol Cell. 2021 12 16; 81(24):5052-5065.e6. View in: PubMed

  23. METTL14 facilitates global genome repair and suppresses skin tumorigenesis. Proc Natl Acad Sci U S A. 2021 08 31; 118(35). View in: PubMed

  24. N6-methyladenosine promotes induction of ADAR1-mediated A-to-I RNA editing to suppress aberrant antiviral innate immune responses. PLoS Biol. 2021 07; 19(7):e3001292. View in: PubMed

  25. ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing. Nat Cell Biol. 2021 07; 23(7):684-691. View in: PubMed

  26. Transcriptome-Wide Detection of Internal N7-Methylguanosine. Methods Mol Biol. 2021; 2298:97-104. View in: PubMed

  27. Autophagy of the m6A mRNA demethylase FTO is impaired by low-level arsenic exposure to promote tumorigenesis. Nat Commun. 2021 04 12; 12(1):2183. View in: PubMed

  28. N6 -methyladenosine modification of lncRNA Pvt1 governs epidermal stemness. EMBO J. 2021 04 15; 40(8):e106276. View in: PubMed

  29. Chromatin and transcriptional regulation by reversible RNA methylation. Curr Opin Cell Biol. 2021 06; 70:109-115. View in: PubMed

  30. Alterations of 5-hydroxymethylation in circulating cell-free DNA reflect molecular distinctions of subtypes of non-Hodgkin lymphoma. NPJ Genom Med. 2021 Feb 11; 6(1):11. View in: PubMed

  31. m6 A RNA methylation: from mechanisms to therapeutic potential. EMBO J. 2021 02 01; 40(3):e105977. View in: PubMed

  32. Global Detection of RNA Methylation by Click Degradation. ACS Cent Sci. 2020 Dec 23; 6(12):2126-2129. View in: PubMed

  33. A human tissue map of 5-hydroxymethylcytosines exhibits tissue specificity through gene and enhancer modulation. Nat Commun. 2020 12 02; 11(1):6161. View in: PubMed

  34. N6-Adenosine Methylation of Socs1 mRNA Is Required to Sustain the Negative Feedback Control of Macrophage Activation. Dev Cell. 2020 12 21; 55(6):737-753.e7. View in: PubMed

  35. Stabilization of ERK-Phosphorylated METTL3 by USP5 Increases m6A Methylation. Mol Cell. 2020 11 19; 80(4):633-647.e7. View in: PubMed

  36. LEAD-m6 A-seq for Locus-Specific Detection of N6 -Methyladenosine and Quantification of Differential Methylation. Angew Chem Int Ed Engl. 2021 01 11; 60(2):873-880. View in: PubMed

  37. Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution. Nat Biotechnol. 2021 02; 39(2):225-235. View in: PubMed

  38. A New Model of Spontaneous Colitis in Mice Induced by Deletion of an RNA m6A Methyltransferase Component METTL14 in T Cells. Cell Mol Gastroenterol Hepatol. 2020; 10(4):747-761. View in: PubMed

  39. Control of Early B Cell Development by the RNA N6-Methyladenosine Methylation. Cell Rep. 2020 06 30; 31(13):107819. View in: PubMed

  40. Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability. Nat Genet. 2020 09; 52(9):939-949. View in: PubMed

  41. Author Correction: Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ. Nat Methods. 2020 Jul; 17(7):749. View in: PubMed

  42. REPIC: a database for exploring the N6-methyladenosine methylome. Genome Biol. 2020 04 28; 21(1):100. View in: PubMed

  43. YTHDF2 promotes mitotic entry and is regulated by cell cycle mediators. PLoS Biol. 2020 04; 18(4):e3000664. View in: PubMed

  44. Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ. Nat Methods. 2020 05; 17(5):515-523. View in: PubMed

  45. N6-Deoxyadenosine Methylation in Mammalian Mitochondrial DNA. Mol Cell. 2020 05 07; 78(3):382-395.e8. View in: PubMed

  46. DNA 5-Methylcytosine-Specific Amplification and Sequencing. J Am Chem Soc. 2020 03 11; 142(10):4539-4543. View in: PubMed

  47. Keth-seq for transcriptome-wide RNA structure mapping. Nat Chem Biol. 2020 05; 16(5):489-492. View in: PubMed

  48. N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription. Science. 2020 01 31; 367(6477):580-586. View in: PubMed

  49. m6A mRNA Methylation Is Essential for Oligodendrocyte Maturation and CNS Myelination. Neuron. 2020 01 22; 105(2):293-309.e5. View in: PubMed

  50. RADAR: differential analysis of MeRIP-seq data with a random effect model. Genome Biol. 2019 12 23; 20(1):294. View in: PubMed

  51. 5-Hydroxymethylcytosine Profiles in Circulating Cell-Free DNA Associate with Disease Burden in Children with Neuroblastoma. Clin Cancer Res. 2020 03 15; 26(6):1309-1317. View in: PubMed

  52. The RNA-binding protein FMRP facilitates the nuclear export of N6-methyladenosine-containing mRNAs. J Biol Chem. 2019 12 27; 294(52):19889-19895. View in: PubMed

  53. Prognostic implications of 5-hydroxymethylcytosines from circulating cell-free DNA in diffuse large B-cell lymphoma. Blood Adv. 2019 10 08; 3(19):2790-2799. View in: PubMed

  54. Evolution of a reverse transcriptase to map N1-methyladenosine in human messenger RNA. Nat Methods. 2019 12; 16(12):1281-1288. View in: PubMed

  55. Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG. Mol Cell. 2019 10 03; 76(1):70-81.e9. View in: PubMed

  56. Site-specific m6A editing. Nat Chem Biol. 2019 09; 15(9):848-849. View in: PubMed

  57. Detailed modeling of positive selection improves detection of cancer driver genes. Nat Commun. 2019 07 30; 10(1):3399. View in: PubMed

  58. FMRP Modulates Neural Differentiation through m6A-Dependent mRNA Nuclear Export. Cell Rep. 2019 07 23; 28(4):845-854.e5. View in: PubMed

  59. m6A mRNA demethylase FTO regulates melanoma tumorigenicity and response to anti-PD-1 blockade. Nat Commun. 2019 06 25; 10(1):2782. View in: PubMed

  60. 5-Hydroxymethylcytosine Profiles Are Prognostic of Outcome in Neuroblastoma and Reveal Transcriptional Networks That Correlate With Tumor Phenotype. JCO Precis Oncol. 2019; 3. View in: PubMed

  61. Jump-seq: Genome-Wide Capture and Amplification of 5-Hydroxymethylcytosine Sites. J Am Chem Soc. 2019 06 05; 141(22):8694-8697. View in: PubMed

  62. Where, When, and How: Context-Dependent Functions of RNA Methylation Writers, Readers, and Erasers. Mol Cell. 2019 05 16; 74(4):640-650. View in: PubMed

  63. Transcriptome-wide Mapping of Internal N7-Methylguanosine Methylome in Mammalian mRNA. Mol Cell. 2019 06 20; 74(6):1304-1316.e8. View in: PubMed

  64. METTL14 is essential for ?-cell survival and insulin secretion. Biochim Biophys Acta Mol Basis Dis. 2019 09 01; 1865(9):2138-2148. View in: PubMed

  65. Cytokine-Regulated Phosphorylation and Activation of TET2 by JAK2 in Hematopoiesis. Cancer Discov. 2019 06; 9(6):778-795. View in: PubMed

  66. Regulation of Gene Expression by N6-methyladenosine in Cancer. Trends Cell Biol. 2019 06; 29(6):487-499. View in: PubMed

  67. Inhibition of Copper Transport Induces Apoptosis in Triple-Negative Breast Cancer Cells and Suppresses Tumor Angiogenesis. Mol Cancer Ther. 2019 05; 18(5):873-885. View in: PubMed

  68. Special Issue on Regulating the Central Dogma. Biochemistry. 2019 02 05; 58(5):295-296. View in: PubMed

  69. mRNA acetylation: a new addition to the epitranscriptome. Cell Res. 2019 02; 29(2):91-92. View in: PubMed

  70. Transcriptome-wide reprogramming of N6-methyladenosine modification by the mouse microbiome. Cell Res. 2019 02; 29(2):167-170. View in: PubMed

  71. High-Resolution Mapping of N 6-Methyladenosine Using m6A Crosslinking Immunoprecipitation Sequencing (m6A-CLIP-Seq). Methods Mol Biol. 2019; 1870:69-79. View in: PubMed

  72. Single base resolution mapping of 2'-O-methylation sites in human mRNA and in 3' terminal ends of small RNAs. Methods. 2019 03 01; 156:85-90. View in: PubMed

  73. Circadian Clock Regulation of Hepatic Lipid Metabolism by Modulation of m6A mRNA Methylation. Cell Rep. 2018 11 13; 25(7):1816-1828.e4. View in: PubMed

  74. m6A facilitates hippocampus-dependent learning and memory through YTHDF1. Nature. 2018 11; 563(7730):249-253. View in: PubMed

  75. Publisher Correction: Post-transcriptional gene regulation by mRNA modifications. Nat Rev Mol Cell Biol. 2018 Dec; 19(12):808. View in: PubMed

  76. RNA modifications modulate gene expression during development. Science. 2018 09 28; 361(6409):1346-1349. View in: PubMed

  77. Chemical Modifications in the Life of an mRNA Transcript. Annu Rev Genet. 2018 11 23; 52:349-372. View in: PubMed

  78. Differential m6A, m6Am, and m1A Demethylation Mediated by FTO in the Cell Nucleus and Cytoplasm. Mol Cell. 2018 09 20; 71(6):973-985.e5. View in: PubMed

  79. m6A mRNA methylation regulates AKT activity to promote the proliferation and tumorigenicity of endometrial cancer. Nat Cell Biol. 2018 09; 20(9):1074-1083. View in: PubMed

  80. Mettl14 Is Essential for Epitranscriptomic Regulation of Striatal Function and Learning. Neuron. 2018 07 25; 99(2):283-292.e5. View in: PubMed

  81. Author Correction: RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia. Nat Commun. 2018 06 06; 9(1):2286. View in: PubMed

  82. RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia. Nat Commun. 2018 03 21; 9(1):1163. View in: PubMed

  83. Wnt signaling pathway involvement in genotypic and phenotypic variations in Waardenburg syndrome type 2 with MITF mutations. J Hum Genet. 2018 May; 63(5):639-646. View in: PubMed

  84. Phasing Gene Expression: mRNA N6-Methyladenosine Regulates Temporal Progression of Mammalian Cortical Neurogenesis. Biochemistry. 2018 02 20; 57(7):1055-1056. View in: PubMed

  85. Our views of dynamic N6-methyladenosine RNA methylation. RNA. 2018 03; 24(3):268-272. View in: PubMed

  86. Identifying the m6A Methylome by Affinity Purification and Sequencing. Methods Mol Biol. 2018; 1649:49-57. View in: PubMed

  87. Making Changes: N6-Methyladenosine-Mediated Decay Drives the Endothelial-to-Hematopoietic Transition. Biochemistry. 2017 11 21; 56(46):6077-6078. View in: PubMed

  88. Epigenetics: Making your mark on DNA. Nat Chem. 2017 Oct 24; 9(11):1040-1042. View in: PubMed

  89. Epitranscriptomic influences on development and disease. Genome Biol. 2017 10 23; 18(1):197. View in: PubMed

  90. YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs. Elife. 2017 10 06; 6. View in: PubMed

  91. "Gamete On" for m6A: YTHDF2 Exerts Essential Functions in Female Fertility. Mol Cell. 2017 Sep 21; 67(6):903-905. View in: PubMed

  92. Functional analysis of a SOX10 gene mutation associated with Waardenburg syndrome II. Biochem Biophys Res Commun. 2017 11 04; 493(1):258-262. View in: PubMed

  93. Ythdc2 is an N6-methyladenosine binding protein that regulates mammalian spermatogenesis. Cell Res. 2017 Sep; 27(9):1115-1127. View in: PubMed

  94. Dynamic RNA Modifications in Gene Expression Regulation. Cell. 2017 Jun 15; 169(7):1187-1200. View in: PubMed

  95. DNA N6-methyladenine in metazoans: functional epigenetic mark or bystander? Nat Struct Mol Biol. 2017 Jun 06; 24(6):503-506. View in: PubMed

  96. Nm-seq maps 2'-O-methylation sites in human mRNA with base precision. Nat Methods. 2017 Jul; 14(7):695-698. View in: PubMed

  97. m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition. Nature. 2017 02 23; 542(7642):475-478. View in: PubMed

  98. Chromate Binding and Removal by the Molybdate-Binding Protein ModA. Chembiochem. 2017 04 04; 18(7):633-637. View in: PubMed

  99. YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA. Cell Res. 2017 Mar; 27(3):315-328. View in: PubMed

  100. Evolution of transcript modification by N6-methyladenosine in primates. Genome Res. 2017 03; 27(3):385-392. View in: PubMed

  101. Developing drugs targeting transition metal homeostasis. Curr Opin Chem Biol. 2017 Apr; 37:26-32. View in: PubMed

  102. FTO Plays an Oncogenic Role in Acute Myeloid Leukemia as a N6-Methyladenosine RNA Demethylase. Cancer Cell. 2017 01 09; 31(1):127-141. View in: PubMed

  103. The emerging biology of RNA post-transcriptional modifications. RNA Biol. 2017 02; 14(2):156-163. View in: PubMed

  104. Post-transcriptional gene regulation by mRNA modifications. Nat Rev Mol Cell Biol. 2017 01; 18(1):31-42. View in: PubMed

  105. ALKBH1-Mediated tRNA Demethylation Regulates Translation. Cell. 2016 Oct 20; 167(3):816-828.e16. View in: PubMed

  106. Abundant DNA 6mA methylation during early embryogenesis of zebrafish and pig. Nat Commun. 2016 10 07; 7:13052. View in: PubMed

  107. A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations. Mol Cell. 2016 08 18; 63(4):711-719. View in: PubMed

  108. A glance at N(6)-methyladenosine in transcript isoforms. Nat Methods. 2016 07 28; 13(8):624-5. View in: PubMed

  109. FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function. Nucleic Acids Res. 2016 09 30; 44(17):8153-64. View in: PubMed

  110. Characterization of eukaryotic DNA N(6)-methyladenine by a highly sensitive restriction enzyme-assisted sequencing. Nat Commun. 2016 Apr 15; 7:11301. View in: PubMed

  111. Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing. Trends Genet. 2016 06; 32(6):320-321. View in: PubMed

  112. Structure and mechanism of the essential two-component signal-transduction system WalKR in Staphylococcus aureus. Nat Commun. 2016 Mar 18; 7:11000. View in: PubMed

  113. Nucleic Acid Modifications in Regulation of Gene Expression. Cell Chem Biol. 2016 Jan 21; 23(1):74-85. View in: PubMed

  114. The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature. 2016 Feb 25; 530(7591):441-6. View in: PubMed

  115. Identification of MLL-fusion/MYC?miR-26?TET1 signaling circuit in MLL-rearranged leukemia. Cancer Lett. 2016 Mar 28; 372(2):157-65. View in: PubMed

  116. Weakened N3 Hydrogen Bonding by 5-Formylcytosine and 5-Carboxylcytosine Reduces Their Base-Pairing Stability. ACS Chem Biol. 2016 Feb 19; 11(2):470-7. View in: PubMed

  117. RNA epigenetics--chemical messages for posttranscriptional gene regulation. Curr Opin Chem Biol. 2016 Feb; 30:46-51. View in: PubMed

  118. Detecting hepatocellular carcinoma in blood. Cell Res. 2015 Dec; 25(12):1279-80. View in: PubMed

  119. Inhibition of human copper trafficking by a small molecule significantly attenuates cancer cell proliferation. Nat Chem. 2015 Dec; 7(12):968-79. View in: PubMed

  120. DNA N(6)-methyladenine: a new epigenetic mark in eukaryotes? Nat Rev Mol Cell Biol. 2015 Dec; 16(12):705-10. View in: PubMed

  121. Chemical decaging in living systems. Natl Sci Rev. 2015 Sep; 2(3):250-251. View in: PubMed

  122. High-Resolution Mapping of N6-Methyladenosine in Transcriptome and Genome Using a Photo-Crosslinking-Assisted Strategy. Methods Enzymol. 2015; 560:161-85. View in: PubMed

  123. Preparation of Human Nuclear RNA m6A Methyltransferases and Demethylases and Biochemical Characterization of Their Catalytic Activity. Methods Enzymol. 2015; 560:117-30. View in: PubMed

  124. Efficient and quantitative high-throughput tRNA sequencing. Nat Methods. 2015 Sep; 12(9):835-837. View in: PubMed

  125. Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing. Nucleic Acids Res. 2015 Dec 02; 43(21):e148. View in: PubMed

  126. RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation. Genes Dev. 2015 Jul 01; 29(13):1343-55. View in: PubMed

  127. Visualizing a protein's sugars. Natl Sci Rev. 2014 Dec; 1(4):480-481. View in: PubMed

  128. Decoding the transcriptome and DNA methylome of human primordial germ cells. Sci China Life Sci. 2015 Jul; 58(7):729-30. View in: PubMed

  129. N(6)-methyladenosine Modulates Messenger RNA Translation Efficiency. Cell. 2015 Jun 04; 161(6):1388-99. View in: PubMed

  130. N6-methyldeoxyadenosine marks active transcription start sites in Chlamydomonas. Cell. 2015 May 07; 161(4):879-892. View in: PubMed

  131. Live Cell MicroRNA Imaging Using Cascade Hybridization Reaction. J Am Chem Soc. 2015 May 20; 137(19):6116-9. View in: PubMed

  132. Introduction: epigenetics. Chem Rev. 2015 Mar 25; 115(6):2223-4. View in: PubMed

  133. N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature. 2015 Feb 26; 518(7540):560-4. View in: PubMed

  134. TET family proteins: oxidation activity, interacting molecules, and functions in diseases. Chem Rev. 2015 Mar 25; 115(6):2225-39. View in: PubMed

  135. Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics. Cell Res. 2015 Mar; 25(3):386-9. View in: PubMed

  136. Kinetic gating mechanism of DNA damage recognition by Rad4/XPC. Nat Commun. 2015 Jan 06; 6:5849. View in: PubMed

  137. High-resolution N(6) -methyladenosine (m(6) A) map using photo-crosslinking-assisted m(6) A sequencing. Angew Chem Int Ed Engl. 2015 Jan 26; 54(5):1587-90. View in: PubMed

  138. Detection of mismatched 5-hydroxymethyluracil in DNA by selective chemical labeling. Methods. 2015 Jan 15; 72:16-20. View in: PubMed

  139. Unique features of the m6A methylome in Arabidopsis thaliana. Nat Commun. 2014 Nov 28; 5:5630. View in: PubMed

  140. Pseudouridine in a new era of RNA modifications. Cell Res. 2015 Feb; 25(2):153-4. View in: PubMed

  141. Dynamic RNA modifications in posttranscriptional regulation. Mol Cell. 2014 Oct 02; 56(1):5-12. View in: PubMed

  142. Molecular mechanisms of two-component system RhpRS regulating type III secretion system in Pseudomonas syringae. Nucleic Acids Res. 2014 Oct; 42(18):11472-86. View in: PubMed

  143. Blood-brain barrier permeable gold nanoparticles: an efficient delivery platform for enhanced malignant glioma therapy and imaging. Small. 2014 Dec 29; 10(24):5137-50. View in: PubMed

  144. Synthesis of a FTO inhibitor with anticonvulsant activity. ACS Chem Neurosci. 2014 Aug 20; 5(8):658-65. View in: PubMed

  145. Reading RNA methylation codes through methyl-specific binding proteins. RNA Biol. 2014; 11(6):669-72. View in: PubMed

  146. Steady-state hydrogen peroxide induces glycolysis in Staphylococcus aureus and Pseudomonas aeruginosa. J Bacteriol. 2014 Jul; 196(14):2499-513. View in: PubMed

  147. Cancer: Damage prevention targeted. Nature. 2014 Apr 10; 508(7495):191-2. View in: PubMed

  148. Gene expression regulation mediated through reversible m6A RNA methylation. Nat Rev Genet. 2014 May; 15(5):293-306. View in: PubMed

  149. 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 Apr 02; 136(13):4801-4. View in: PubMed

  150. Molecular mechanism and structure of the Saccharomyces cerevisiae iron regulator Aft2. Proc Natl Acad Sci U S A. 2014 Mar 18; 111(11):4043-8. View in: PubMed

  151. Nucleic acid oxidation in DNA damage repair and epigenetics. Chem Rev. 2014 Apr 23; 114(8):4602-20. View in: PubMed

  152. Crystal structure of the RNA demethylase ALKBH5 from zebrafish. FEBS Lett. 2014 Mar 18; 588(6):892-8. View in: PubMed

  153. A protein engineered to bind uranyl selectively and with femtomolar affinity. Nat Chem. 2014 Mar; 6(3):236-41. View in: PubMed

  154. Identification and functional analysis of a novel mutation in the SOX10 gene associated with Waardenburg syndrome type IV. Gene. 2014 Mar 15; 538(1):36-41. View in: PubMed

  155. Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis. Cell Rep. 2014 Jan 16; 6(1):231-244. View in: PubMed

  156. A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat Chem Biol. 2014 Feb; 10(2):93-5. View in: PubMed

  157. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 2014 Jan 02; 505(7481):117-20. View in: PubMed

  158. Potential functional roles of DNA demethylation intermediates. Trends Biochem Sci. 2013 Oct; 38(10):480-4. View in: PubMed

  159. A highly sensitive and genetically encoded fluorescent reporter for ratiometric monitoring of quinones in living cells. Chem Commun (Camb). 2013 Sep 21; 49(73):8027-9. View in: PubMed

  160. TET1 plays an essential oncogenic role in MLL-rearranged leukemia. Proc Natl Acad Sci U S A. 2013 Jul 16; 110(29):11994-9. View in: PubMed

  161. Nonenzymatic labeling of 5-hydroxymethylcytosine in nanopore sequencing. Chembiochem. 2013 Jul 22; 14(11):1289-90. View in: PubMed

  162. Chemical modification-assisted bisulfite sequencing (CAB-Seq) for 5-carboxylcytosine detection in DNA. J Am Chem Soc. 2013 Jun 26; 135(25):9315-7. View in: PubMed

  163. HMGA2/TET1/HOXA9 signaling pathway regulates breast cancer growth and metastasis. Proc Natl Acad Sci U S A. 2013 Jun 11; 110(24):9920-5. View in: PubMed

  164. FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA. Nat Commun. 2013; 4:1798. View in: PubMed

  165. Sprouts of RNA epigenetics: the discovery of mammalian RNA demethylases. RNA Biol. 2013 Jun; 10(6):915-8. View in: PubMed

  166. Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell. 2013 Apr 25; 153(3):678-91. View in: PubMed

  167. Proteome-wide quantification and characterization of oxidation-sensitive cysteines in pathogenic bacteria. Cell Host Microbe. 2013 Mar 13; 13(3):358-70. View in: PubMed

  168. Molecular mechanism of quinone signaling mediated through S-quinonization of a YodB family repressor QsrR. Proc Natl Acad Sci U S A. 2013 Mar 26; 110(13):5010-5. View in: PubMed

  169. Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing. Nat Commun. 2013; 4:1517. View in: PubMed

  170. Engineering bacterial two-component system PmrA/PmrB to sense lanthanide ions. J Am Chem Soc. 2013 Feb 13; 135(6):2037-9. View in: PubMed

  171. Reversible RNA adenosine methylation in biological regulation. Trends Genet. 2013 Feb; 29(2):108-15. View in: PubMed

  172. Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nat Protoc. 2012 Dec; 7(12):2159-70. View in: PubMed

  173. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell. 2013 Jan 10; 49(1):18-29. View in: PubMed

  174. Mapping recently identified nucleotide variants in the genome and transcriptome. Nat Biotechnol. 2012 Nov; 30(11):1107-16. View in: PubMed

  175. Nucleic acid modifications with epigenetic significance. Curr Opin Chem Biol. 2012 Dec; 16(5-6):516-24. View in: PubMed

  176. Blockade of miR-150 maturation by MLL-fusion/MYC/LIN-28 is required for MLL-associated leukemia. Cancer Cell. 2012 Oct 16; 22(4):524-35. View in: PubMed

  177. The oxidation-sensing regulator (MosR) is a new redox-dependent transcription factor in Mycobacterium tuberculosis. J Biol Chem. 2012 Nov 02; 287(45):37703-12. View in: PubMed

  178. A selective fluorescent probe for carbon monoxide imaging in living cells. Angew Chem Int Ed Engl. 2012 Sep 17; 51(38):9652-6. View in: PubMed

  179. Protein cysteine phosphorylation of SarA/MgrA family transcriptional regulators mediates bacterial virulence and antibiotic resistance. Proc Natl Acad Sci U S A. 2012 Sep 18; 109(38):15461-6. View in: PubMed

  180. Synthesis of DNA oligos containing 2'-deoxy-2'-fluoro-D-arabinofuranosyl-5-carboxylcytosine as hTDG inhibitor. Tetrahedron. 2012 Jul 01; 68(26):5145-5151. View in: PubMed

  181. Isopeptide bonds of the major pilin protein BcpA influence pilus structure and bundle formation on the surface of Bacillus cereus. Mol Microbiol. 2012 Jul; 85(1):152-63. View in: PubMed

  182. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell. 2012 Jun 08; 149(6):1368-80. View in: PubMed

  183. Quorum-sensing agr mediates bacterial oxidation response via an intramolecular disulfide redox switch in the response regulator AgrA. Proc Natl Acad Sci U S A. 2012 Jun 05; 109(23):9095-100. View in: PubMed

  184. Staphylococcus aureus CymR is a new thiol-based oxidation-sensing regulator of stress resistance and oxidative response. J Biol Chem. 2012 Jun 15; 287(25):21102-9. View in: PubMed

  185. The Pseudomonas aeruginosa global regulator VqsR directly inhibits QscR to control quorum-sensing and virulence gene expression. J Bacteriol. 2012 Jun; 194(12):3098-108. View in: PubMed

  186. Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA. Nat Chem Biol. 2012 Feb 12; 8(4):328-30. View in: PubMed

  187. Expression of multidrug resistance efflux pump gene norA is iron responsive in Staphylococcus aureus. J Bacteriol. 2012 Apr; 194(7):1753-62. View in: PubMed

  188. Preparation of DNA containing 5-hydroxymethyl-2'-deoxycytidine modification through phosphoramidites with TBDMS as 5-hydroxymethyl protecting group. Curr Protoc Nucleic Acid Chem. 2011 Dec; Chapter 4:Unit 4.47.1-18. View in: PubMed

  189. AirSR, a [2Fe-2S] cluster-containing two-component system, mediates global oxygen sensing and redox signaling in Staphylococcus aureus. J Am Chem Soc. 2012 Jan 11; 134(1):305-14. View in: PubMed

  190. Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine. Nat Methods. 2011 Nov 20; 9(1):75-7. View in: PubMed

  191. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol. 2011 Oct 16; 7(12):885-7. View in: PubMed

  192. Selective fluorescent probes for live-cell monitoring of sulphide. Nat Commun. 2011 Oct 11; 2:495. View in: PubMed

  193. Gold(I)-catalyzed formation of 3-pyrazolines through cycloaddition of diaziridine to alkynes. Org Lett. 2011 Nov 04; 13(21):5842-5. View in: PubMed

  194. Targeting MgrA-mediated virulence regulation in Staphylococcus aureus. Chem Biol. 2011 Aug 26; 18(8):1032-41. View in: PubMed

  195. Binding of ReO4(-) with an engineered MoO4(2-)-binding protein: towards a new approach in radiopharmaceutical applications. J Biol Inorg Chem. 2012 Jan; 17(1):97-106. View in: PubMed

  196. Selective recognition of americium by peptide-based reagents. Inorg Chem. 2011 Sep 05; 50(17):7937-9. View in: PubMed

  197. Structural and biochemical characterization of N5-carboxyaminoimidazole ribonucleotide synthetase and N5-carboxyaminoimidazole ribonucleotide mutase from Staphylococcus aureus. Acta Crystallogr D Biol Crystallogr. 2011 Aug; 67(Pt 8):707-15. View in: PubMed

  198. Detection of 5-hydroxymethylcytosine in DNA by transferring a keto-glucose by using T4 phage ?-glucosyltransferase. Chembiochem. 2011 Jul 25; 12(11):1682-5. View in: PubMed

  199. Syntheses of 5-formyl- and 5-carboxyl-dC containing DNA oligos as potential oxidation products of 5-hydroxymethylcytosine in DNA. Org Lett. 2011 Jul 01; 13(13):3446-9. View in: PubMed

  200. Crystal structures of SlyA protein, a master virulence regulator of Salmonella, in free and DNA-bound states. J Biol Chem. 2011 Jun 24; 286(25):22178-85. View in: PubMed

  201. Bioorthogonal labeling of 5-hydroxymethylcytosine in genomic DNA and diazirine-based DNA photo-cross-linking probes. Acc Chem Res. 2011 Sep 20; 44(9):709-17. View in: PubMed

  202. Detection of 5-hydroxymethylcytosine in a combined glycosylation restriction analysis (CGRA) using restriction enzyme Taq(a)I. Bioorg Med Chem Lett. 2011 Sep 01; 21(17):5075-7. View in: PubMed

  203. Syntheses of two 5-hydroxymethyl-2'-deoxycytidine phosphoramidites with TBDMS as the 5-hydroxymethyl protecting group and their incorporation into DNA. J Org Chem. 2011 May 20; 76(10):4182-8. View in: PubMed

  204. Aureusimines in Staphylococcus aureus are not involved in virulence. PLoS One. 2010 Dec 29; 5(12):e15703. View in: PubMed

  205. The tightly regulated copper window in yeast. Chem Commun (Camb). 2011 Mar 07; 47(9):2571-3. View in: PubMed

  206. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol. 2011 Jan; 29(1):68-72. View in: PubMed

  207. Grand challenge commentary: RNA epigenetics? Nat Chem Biol. 2010 Dec; 6(12):863-5. View in: PubMed

  208. Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase. Nature. 2010 Nov 11; 468(7321):330-3. View in: PubMed

  209. The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the wobble position of tRNA. Angew Chem Int Ed Engl. 2010 Nov 15; 49(47):8885-8. View in: PubMed

  210. Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs. RNA. 2010 Jul; 16(7):1317-27. View in: PubMed

  211. Golden pigment production and virulence gene expression are affected by metabolisms in Staphylococcus aureus. J Bacteriol. 2010 Jun; 192(12):3068-77. View in: PubMed

  212. Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system. Nucleic Acids Res. 2010 Jul; 38(13):4415-25. View in: PubMed

  213. In the Staphylococcus aureus two-component system sae, the response regulator SaeR binds to a direct repeat sequence and DNA binding requires phosphorylation by the sensor kinase SaeS. J Bacteriol. 2010 Apr; 192(8):2111-27. View in: PubMed

  214. Dynamic copper(I) imaging in mammalian cells with a genetically encoded fluorescent copper(I) sensor. J Am Chem Soc. 2010 Mar 03; 132(8):2567-9. View in: PubMed

  215. Pseudomonas aeruginosa OspR is an oxidative stress sensing regulator that affects pigment production, antibiotic resistance and dissemination during infection. Mol Microbiol. 2010 Jan; 75(1):76-91. View in: PubMed

  216. Intramolecular amide bonds stabilize pili on the surface of bacilli. Proc Natl Acad Sci U S A. 2009 Nov 24; 106(47):19992-7. View in: PubMed

  217. A non-heme iron-mediated chemical demethylation in DNA and RNA. Acc Chem Res. 2009 Apr 21; 42(4):519-29. View in: PubMed

  218. Chemical methods to study protein-nucleic acid interactions. Nucleic Acids Symp Ser (Oxf). 2009; (53):43. View in: PubMed

  219. Highly sensitive and selective gold(I) recognition by a metalloregulator in Ralstonia metallidurans. J Am Chem Soc. 2009 Aug 12; 131(31):10869-71. View in: PubMed

  220. Crystal structures of the reduced, sulfenic acid, and mixed disulfide forms of SarZ, a redox active global regulator in Staphylococcus aureus. J Biol Chem. 2009 Aug 28; 284(35):23517-24. View in: PubMed

  221. Platinum(II)-catalyzed intramolecular cyclization of o-substituted aryl alkynes through sp3 C-H activation. Angew Chem Int Ed Engl. 2009; 48(22):3999-4001. View in: PubMed

  222. Using the bias from flow to elucidate single DNA repair protein sliding and interactions with DNA. Biophys J. 2009 Mar 04; 96(5):1911-7. View in: PubMed

  223. Engineering a uranyl-specific binding protein from NikR. Angew Chem Int Ed Engl. 2009; 48(13):2339-41. View in: PubMed

  224. A new 1'-methylenedisulfide deoxyribose that forms an efficient cross-link to DNA cytosine-5 methyltransferase (DNMT). J Am Chem Soc. 2008 Dec 31; 130(52):17634-5. View in: PubMed

  225. Capsule anchoring in Bacillus anthracis occurs by a transpeptidation reaction that is inhibited by capsidin. Mol Microbiol. 2009 Jan; 71(2):404-20. View in: PubMed

  226. A new oxidative sensing and regulation pathway mediated by the MgrA homologue SarZ in Staphylococcus aureus. Mol Microbiol. 2009 Jan; 71(1):198-211. View in: PubMed

  227. A diazirine-based nucleoside analogue for efficient DNA interstrand photocross-linking. J Am Chem Soc. 2008 Nov 05; 130(44):14398-9. View in: PubMed

  228. Oxidative demethylation of 3-methylthymine and 3-methyluracil in single-stranded DNA and RNA by mouse and human FTO. FEBS Lett. 2008 Oct 15; 582(23-24):3313-9. View in: PubMed

  229. The Pseudomonas aeruginosa multidrug efflux regulator MexR uses an oxidation-sensing mechanism. Proc Natl Acad Sci U S A. 2008 Sep 09; 105(36):13586-91. View in: PubMed

  230. Gold-catalyzed organic transformations. Chem Rev. 2008 Aug; 108(8):3239-65. View in: PubMed

  231. Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature. 2008 Apr 24; 452(7190):961-5. View in: PubMed

  232. Selective recognition of metal ions by metalloregulatory proteins. Curr Opin Chem Biol. 2008 Apr; 12(2):214-21. View in: PubMed

  233. Synthesis of photoactive analogues of a cystine knot trypsin inhibitor protein. Org Lett. 2007 Dec 20; 9(26):5497-500. View in: PubMed

  234. Diazirine-based DNA photo-cross-linking probes for the study of protein-DNA interactions. Angew Chem Int Ed Engl. 2008; 47(1):90-3. View in: PubMed

  235. Spectroscopic insights into lead(II) coordination by the selective lead(II)-binding protein PbrR691. J Am Chem Soc. 2007 Oct 17; 129(41):12350-1. View in: PubMed

  236. Gold(III)-catalyzed nitrene insertion into aromatic and benzylic C-H groups. J Am Chem Soc. 2007 Oct 10; 129(40):12058-9. View in: PubMed

  237. Silver-catalyzed intermolecular amination of C--H groups. Angew Chem Int Ed Engl. 2007; 46(27):5184-6. View in: PubMed

  238. Design of an emission ratiometric biosensor from MerR family proteins: a sensitive and selective sensor for Hg2+. J Am Chem Soc. 2007 Mar 28; 129(12):3474-5. View in: PubMed

  239. An oxidation-sensing mechanism is used by the global regulator MgrA in Staphylococcus aureus. Nat Chem Biol. 2006 Nov; 2(11):591-5. View in: PubMed

  240. Br?nsted acid catalyzed addition of phenols, carboxylic acids, and tosylamides to simple olefins. Org Lett. 2006 Sep 14; 8(19):4175-8. View in: PubMed

  241. Nitrene transfer reactions catalyzed by gold complexes. J Org Chem. 2006 Aug 04; 71(16):5876-80. View in: PubMed

  242. Oxidative dealkylation DNA repair mediated by the mononuclear non-heme iron AlkB proteins. J Inorg Biochem. 2006 Apr; 100(4):670-8. View in: PubMed

  243. Gold(I)-catalyzed intra- and intermolecular hydroamination of unactivated olefins. J Am Chem Soc. 2006 Feb 15; 128(6):1798-9. View in: PubMed

  244. Direct reversal of DNA alkylation damage. Chem Rev. 2006 Feb; 106(2):215-32. View in: PubMed

  245. Efficient gold-catalyzed hydroamination of 1,3-dienes. Angew Chem Int Ed Engl. 2006 Mar 03; 45(11):1744-7. View in: PubMed

  246. Direct repair of the exocyclic DNA adduct 1,N6-ethenoadenine by the DNA repair AlkB proteins. J Am Chem Soc. 2005 Oct 26; 127(42):14594-5. View in: PubMed

  247. Intramolecular additions of alcohols and carboxylic acids to inert olefins catalyzed by silver(I) triflate. Org Lett. 2005 Oct 13; 7(21):4553-6. View in: PubMed

  248. The structure of the human AGT protein bound to DNA and its implications for damage detection. J Mol Biol. 2005 Jul 22; 350(4):657-66. View in: PubMed

  249. Gold(I)-catalyzed intermolecular addition of phenols and carboxylic acids to olefins. J Am Chem Soc. 2005 May 18; 127(19):6966-7. View in: PubMed

  250. An exceptionally selective lead(II)-regulatory protein from Ralstonia metallidurans: development of a fluorescent lead(II) probe. Angew Chem Int Ed Engl. 2005 Apr 29; 44(18):2715-2719. View in: PubMed

  251. Preparation and characterization of the native iron(II)-containing DNA repair AlkB protein directly from Escherichia coli. J Am Chem Soc. 2004 Dec 29; 126(51):16930-6. View in: PubMed

  252. Direct functionalization of arenes by primary alcohol sulfonate esters catalyzed by gold(III). J Am Chem Soc. 2004 Oct 27; 126(42):13596-7. View in: PubMed

  253. A silver-catalyzed intramolecular amidation of saturated C--h bonds. Angew Chem Int Ed Engl. 2004 Aug 13; 43(32):4210-2. View in: PubMed

  254. Efficient functionalization of aromatic C-H bonds catalyzed by gold(III) under mild and solvent-free conditions. J Org Chem. 2004 May 28; 69(11):3669-71. View in: PubMed

  255. An Au-catalyzed cyclialkylation of electron-rich arenes with epoxides to prepare 3-chromanols. J Am Chem Soc. 2004 May 19; 126(19):5964-5. View in: PubMed

  256. Modeling non-heme iron proteins. Curr Opin Chem Biol. 2004 Apr; 8(2):201-8. View in: PubMed

  257. Interaction of human and bacterial AlkB proteins with DNA as probed through chemical cross-linking studies. Nucleic Acids Res. 2004; 32(4):1548-54. View in: PubMed

  258. A general strategy to convert the MerR family proteins into highly sensitive and selective fluorescent biosensors for metal ions. J Am Chem Soc. 2004 Jan 28; 126(3):728-9. View in: PubMed

  259. Efficient aziridination of olefins catalyzed by a unique disilver(I) compound. J Am Chem Soc. 2003 Dec 31; 125(52):16202-3. View in: PubMed

  260. How do DNA repair proteins locate potential base lesions? a chemical crosslinking method to investigate O6-alkylguanine-DNA alkyltransferases. Chem Biol. 2003 Sep; 10(9):827-35. View in: PubMed

  261. Probing the structure and function of the Escherichia coli DNA alkylation repair AlkB protein through chemical cross-linking. J Am Chem Soc. 2003 Jul 23; 125(29):8730-1. View in: PubMed
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