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Song Research Group

Department of Biochemistry

2023
  • TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons.
        Zhao S, Lu J, Pan B, Fan H, Byrum SD, Xu C, Kim A, Guo Y, Kanchi KL, Gong W, Sun T, Storey AJ, Burkholder NT, Machintosh SG, Kuhlers PC, Edmondson RD, Strahl BD, Diao Y, Tackett AJ, Raab JR, Cai L, Song J# and Wang GG#.
    ​​         Nature. (2023) 623 (7987)
  • DNA conformational dynamics in the context-dependent non-CG CHH methylation by plant methyltransferase DRM2.
       Chen J, Lu J, Liu J, Fang J, Zhong X, Song J#.
           J Biol Chem. (2023) 299(12):105433.
  • Structural basis for the allosteric regulation and dynamic assembly of DNMT3B.
        Lu J, Fang J, Zhu H, Liang KL, Khudaverdyan, Song J#.
             Nucleic Acids Res. (2023): gkad972.
  • RBM33 is a unique m6A RNA-binding protein that regulates ALKBH5 demethylase activity and substrate selectivity.
        Yu F, Zhu AC, Liu S, Gao B, Wang Y, Khudaverdyan N, Yu C, Wu Q, Jiang Y, Song J, Jin L, He C, Qian Z.
       ​​     Molecular Cell. (2023) 83.
  • The FAM86 domain of FAM86A confers substrate specificity to promote EEF2-Lys525 methylation.
        Francis JW, Shao Z, Narkhede P, Trinh AT, Lu J, Song J#, Gozani O#.
            J Biol Chem. (2023) 299(7).
2022
  • Structure of DNMT3B homo-oligomer reveals vulnerability to impairment by ICF mutations.
       Gao L, Guo Y, Biswal M, Lu J, Yin J, Fang J, Chen X, Shao Z, Huang M, Wang Y, Wang GG#, Song J#.
    ​​         Nature Communications. (2022) 13: 4249.
  • Mechanistic basis for maintenance of CHG DNA methylation in plants.
       Fang J, Jiang J, Leichter SM, Liu J, Biswal M, Khudaverdyan N, Zhong#, Song J#.
           Nature Communications. (2022) 13:3877.
  • SARS-CoV-2 nucleocapsid protein targets a conserved surface groove of the NTF2-like domain of G3BP1.
        Biswal M, Lu J, Song J#
             J. Mol. Biol. (2022): 434(9).
2021
  • Two conserved oligomer interfaces of NSP7 and NSP8 underpin the dynamic assembly of SARS-CoV-2 RdRP.
       Biswal M, Diggs S, Xu D, Khudaverdyan N, Lu J, Fang J, Blaha G, Hai R#, Song J#.
    ​​        Nucleic Acids Res. (2021) 48.
  • Substrate deformation regulates DRM2-mediated DNA methylation in plants.
       Fang J, Leichter SM, Jiang J, Biswal M, Lu J, Zhang ZM, Ren W, Zhai J, Cui Q, Zhong X#, Song J#.
    ​​        Science Adv. (2021) 7:eabd9224.
  • DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation.
        Ren W, Fan H, Grimm SA, Guo Y, Kim, JJ, Li L, Petell CJ, Tan XF, Zhang ZM, Coan JP, Yin J, Gao L, Cai L, Khudaverdyan N, Çetin B, Patel DJ, Wang Y, Cui Q, Strahl BD, Gozani O, Miller KM, O’Leary SE, Wade PA, Wang GG#, Song J#.
    ​​        Nature Communications. (2021) 12:2490.
  • YY1 Interacts with Guanine Quadruplex to Regulate DNA Looping and Gene Expression.
       Lin L., Williams P, Ren W, Wang MY, Gao Z, Miao W, Huang M, Song J, Wang Y.
    ​​        Nat Chem, Biol. (2021) 17(2).
  • UVR8 interacts with de novo DNA methyltransferase and suppresses DNA methylation in Arabidopsis.
        Jiang J, Liu J, Sanders D, Qian S, Ren W, Song J, Liu F, Zhong X.
    ​​        Nature Plants. (2021) doi: 10.1038/s41477-020-00843-4.
2020
  • Structural basis for impairment of DNA methylation by the DNMT3A R882H mutation.
        Anteneh H, Fang J, Song J#.
    ​​         Nature Communications. (2020) 11: 2294.
  • Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms.
       Gao L, Emperele M, Guo Y, Grimm SA, Ren W, Adam S, Uryu H, Zhang ZM, Chen D, Yin J, Dukatz M, Anteneh H, Jurkowska RZ, Lu J, Wang Y, Bashtrykov P, Wade PA, Wang G.G.#, Jeltsch A#, Song J#.
           Nature Communications. (2020) 11:3723.
  • Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation.
        Ren W, Fan H, Grimm SA, Guo Y, Kim, JJ, Li L, Petell CJ, Tan XF, Zhang ZM, Coan JP, Yin J, Gao L, Cai L, Detrick B, Çetin B, Wang Y, Cui Q, Strahl BD, Gozani O, Miller KM, O’Leary SE, Wade PA, Patel DJ#, Wang GG#, Song J#.
             Proceedings of the National Academy of Sciences of the United States of America. (2020): 117(31).
  • Structural basis for STAT2 suppression by flavivirus NS5.
        Wang B, Thurmond S, Zhou K, Sánchez-Aparicio MT, Fang J, Lu J, Gao L, Ren W, Cui Y, Hong H, O’Leary SE, Garcia-Sastre A,     Zhou ZH#, Hao R#, Song J#.
       ​​     Nature Structural & Molecular Biology. (2020) 20.
  • Inhibiting matrix metalloproteinase-2 activation by perturbing protien-protein interactions using a cyclic peptide.
         Sarkar P, Li Z, Ren W, Wang S, Shao S, Sun J, Ren X, Perkins, N, Guo Z, Chang CE, Song J, Xue M.
            J Med Chem. (2020) 63:6979-6990.
  • Protein interactions at oxidized 5-methylcytosine bases.
        Pfeifer GP, Szabó PE and Song J.
           J. Mol. Biol.2020; 432(6):1718-1730.
2019
  • Chemical Proteomic Profiling of Lysophosphatidic Acid-Binding Proteins.
        Dong X, Gao L, Song J, Wang Y.       
            Anal. Chem. 2019; 91 (24): 15365-15369.
  • Dissect the DNMT3A- and DNMT3B-mediated DNA co-methylation through a covalent complex approach.
        Gao L, Anteneh H, Song J#.       
            J. Mol. Biol. 2019; 432(2):569-575.
  • A DNA Aptamer for Binding and Inhibition of DNA methyltransferase 1.
       Wang L, Lee J, Gao L, Yin J, Duan Y, Jimenez LA, Adkins GB, Ren W, Li L, Fang J, Wang Y, Song J# and Zhong W#.
           Nucleic Acids Res. 2019; 47(22):11527-11537.
  • Structure and regulation of ZCCHC4 in m6A-methylation of 28S rRNA.
        Ren W, Lu J, Huang M, Gao L, Li D, Wang GG, Song J#.       
            Nature Communications. 2019: (10): 5042.
  • Structural basis for the ORC1-Cyclin A association.
        Boxiao Wang, Song J#. ​​
            Protein Sci. 2019; 28(9):1727-1733.
  • METTL13 Methylation of eEF1A IncreasesTranslational Output to Promote Tumorigenesis.
       Liu S, Hausmann S, Carison SM, Fuentes ME, Francis JW, Pillai R, Lofgren SM, Hulea L, Tandoc K, Lu J, Li A, Nguyen ND, Caporicci M, Kim MP, Maitra A, Wang H, Wistuba II, Porco JA Jr, Bassik MC, Elias JE, Song J, Topisirovic I, Rechem CV, Mazur PK, Gozani O.
            Cell 2019; (176): 491-504.
2018
  • CARM1 suppresses de novo serine synthesis by promoting PKM2 activity.
        Abeywardana T, Oh M, Jiang L, Yang Y, Kong M, Song J, Yang Y.
            J Biol Chem. 2018; 293(39):15290-15303.
  • Structure-Based Design of Novel EphA2 Agonistic Agents with Nanomolar Affinity in Vitro and in Cell.
       Gambini L, Salem AF, Udompholkul P, Tan XF, Baggio C, Shah N, Aronson A, Song J, Pellecchia M.
            ACS Chem Biol. 2018; 13(9):2633-2644.
  • Structural basis for DNMT3A-mediated de novo DNA methylation.
        Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L, Liu S, Ji D, Rothbart SB, Wang Y, Wang GG#, Song J#.
            Nature. 2018; 554: 387-391.
  • An Intramolecular Interaction of UHRF1 Reveals Dual Control for Its Histone Association.
        Gao L, Tan XF, Zhang S, Wu T, Zhang ZM, Ai HW, Song J#.
            Structure. 2018; 26: 304-311.
  • Structural Basis of DNMT1- and DNMT3A-Mediated DNA Methylation.
        Ren W, Gao L, Song J#.  
            Genes. 2018 9(12), 620.
  • Suppression of Type I Interferon Signaling by Flavivirus NS5.
        Thurmond S, Wang B, Song J#, Hai R#.
            Viruses. 2018 10(12):712.
  • Protein interactions at oxidized 5-methylcytosine bases.
        Pfeifer GP, Szabó PE and Song J.
            J. Mol. Biol.2020; 432(6):1718-1730.
2017
  • Mechanism of host substrate acetylation by a YopJ family effector.
        Zhang, Z., Ma, K., Gao, L., Hu, Z., Schwizer, S., Ma, W. #,Song, J#.
            Nature Plants. 2017; 3:17115.
  • The structure of Zika virus NS5 reveals a conserved domain conformation.
        Wang B, Tan XF, Thurmond S, Zhang ZM, Lin A, Hai R#, Song J#.
            Nature Communications. 2017; 8:14763.
2016
  • BS69/ZMYND11 C-Terminal Domains Bind and Inhibit EBNA2.
        Harter MR, Liu CD, Shen CL, Gonzalez-Hurtado E, Zhang ZM, Xu M, Martinez E, Peng CW#, Song J#.
            PLoS pathogens. 2016; 12(2):e1005414.
  • Tet3 Reads 5-Carboxylcytosine through Its CXXC Domain and Is a Potential Guardian against Neurodegeneration.
        Jin SG, Zhang ZM, Dunwell TL, Harter MR, Wu X, Johnson J, Li Z, Liu J, Szabó PE, Lu Q, Xu GL, Song J#, Pfeifer GP#.
            Cell reports. 2016; 14(3):493-505.
  • Structure of a pathogen effector reveals enzymatic mechanism of a novel acetyltransferase family.
        Zhang ZM, Ma KW, Yuan S, Luo Y, Jiang S, Hawara E, Pan S, Ma W#, Song J#.
            Nature Structural & Molecular Biology. 2016; 23(9):847-852.
  • Are there specific readers of oxidized 5-methylcytosine bases? 
        Song J#, Pfeifer GP#.
            BioEssays. 2016; 38(10):1038-1047.
2015
  • Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis.
        Zhang C, Brown MQ, van de Ven W, Zhang ZM, Wu B, Young MC, Synek L, Borchardt D,  Harrison R, Pan S, Luo N, Huang YM, Ghang YJ, Ung N, Li R, Isley J, Morikis D, Song J, Guo W, Hooley RJ, Chang CE, Yang Z, Zarsky V, Muday GK, Hicks GR, Raikhel NV.
            Proceedings of the National Academy of Sciences of the United States of America. 2015; 113(1):E41-50.
  • An Allosteric Interaction Links USP7 to Deubiquitination and Chromatin Targeting of UHRF1.
        Zhang ZM, Rothbart SB, Allison DF, Cai Q, Harrison JS, Li L, Wang Y, Strahl BD, Wang GG, Song J#.
            Cell reports. 2015; 12(9):1400-6.
  • Two serine residues in Pseudomonas syringae effector HopZ1a are required for acetyltransferase activity and association with the host co-factor.
        Ma KW, Jiang S, Hawara E, Lee D, Pan S, Coaker G, Song J, Ma W.
             The New phytologist. 2015; 208(4):1157-68.
  • Crystal Structure of Human DNA Methyltransferase 1.
        Zhang ZM, Liu S, Lin K, Luo Y, Perry JJ, Wang Y, Song J#.
             Journal of molecular biology. 2015; 427(15):2520-31.
  • A Meier-Gorlin syndrome mutation impairs the ORC1-nucleosome association.
        Zhang W, Sankaran S, Gozani O, Song J#.
            ACS chemical biology. 2015; 10(5):1176-80.
2014
  • Effects of Tet-induced oxidation products of 5-methylcytosine on Dnmt1- and DNMT3a-mediated cytosine methylation.
        Ji D, Lin K, Song J, Wang Y.
         Molecular bioSystems. 2014; 10(7):1749-52. PMID: 24789765, PMCID: PMC4052722
  • Arsenite binds to the RING finger domains of RNF20-RNF40 histone E3 ubiquitin ligase and inhibits DNA double-strand break repair.
        Zhang F, Paramasivam M, Cai Q, Dai X, Wang P, Lin K, Song J, Seidman MM, Wang Y.
            Journal of the American Chemical Society. 2014; 136(37):12884-7.

2013

  • Bacterial effector activates jasmonate signaling by directly targeting JAZ transcriptional repressors.
        Jiang S, Yao J, Ma KW, Zhou H, Song J, He SY, Ma W.  
            PLoS pathogens. 2013; 9(10):e1003715.
  • An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting.
        Cai L, Rothbart SB, Lu R, Xu B, Chen WY, Tripathy A, Rockowitz S, Zheng D, Patel DJ, Allis CD, Strahl BD, Song J#, Wang GG#.
            Molecular cell. 2013; 49(3):571-82.
Memorial Sloan-Kettering Cancer Center: 2007-2011
  • Structure-based Mechanistic Insights into DNMT1-mediated Maintenance DNA methylation.
        Song J, Teplova M, Ishibe-Murakami S, Patel, DJ.
            Science. 2012, 335(6069):709-712.
  • ORC1 BAH domain links dimethylation of H4K20 to DNA replication licensing and Meier-Gorlin syndrome.
        Kuo AJ*, Song J*, Cheung P*, Ishibe-Murakami S, Yamazoe S, Chen JK, Patel DJ, Gozani, O.
        Nature. 2012, 484:115-110.
  • Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1.
        Teplova M, Malinina L, Darnell JC, Song J, Lu M, Abagyan R, Musunuru K, Teplova A, Burley SK, Darnell RB, Patel DJ.
            Structure. 2011, 19(7):930-44.
  • Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation.
        Song J, Rechkoblit O, Bestor TH, Patel DJ.
            Science. 2011, 331(6020):1036-40.
  • Structural insights into RNA recognition by the Alternate-splicing Regulator CUG Binding Protein 1.
        Teplova M, Song J, Gaw HY, Teplov A, Patel DJ.
            Structure. 2010, 18(10):1364-77.
  • Molecular Events Underlying MLL1 Regulation by H3K4me3 Readout and Cyclophilin-mediated Proline Isomerization.
        Wang Z*, Song J*, Milne TA, Wang GG, Li H, Allis CD, Patel DJ.
            Cell. 2010, 141(7):1183-94.
  • Haematopoietic Malignancies Caused by Dysregulation of a Chromatin-binding PHD Finger.
        Wang GG, Song J, Wang Z, Dormann HL, Casadio F, Li H, Luo JL, Patel DJ, Allis CD.
            Nature. 2009, 459(7248): 847-51.
University of Wisconsin-Madison: 1997-2007
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