Publications
Zhang C, Tunes L, Hsieh MH, Wang P, Kumar A, Khadgi BB, Yang Y, Doxtader KA, Herrell E, Koczy O, Setlem R, Zhang X, Evers B, Wang Y, Xing C, Zhu H, Nam Y. Cancer mutations rewire the RNA methylation specificity of METTL3-METTL14. bioRxiv. 2023 Mar 16;. doi: 10.1101/2023.03.16.532618. PubMed PMID: 36993753; PubMed Central PMCID: PMC10055151.
Zhang C, Tunes L, Hsieh MH, Wang P, Kumar A, Khadgi BB, Yang Y, Doxtader KA, Herrell E, Koczy O, Setlem R, Zhang X, Evers B, Wang Y, Xing C, Zhu H, Nam Y. Cancer mutations rewire the RNA methylation specificity of METTL3-METTL14. bioRxiv. 2023 Mar 16;. doi: 10.1101/2023.03.16.532618. PubMed PMID: 36993753; PubMed Central PMCID: PMC10055151.
Ruiz-Arroyo VM, Raj R, Babu K, Onolbaatar O, Roberts PH, Nam Y. Structures and mechanisms of tRNA methylation by METTL1-WDR4. Nature. 2023 Jan;613(7943):383-390. doi: 10.1038/s41586-022-05565-5. Epub 2023 Jan 4. PubMed PMID: 36599982; NIHMSID:NIHMS1866060.
Ruiz-Arroyo VM, Raj R, Babu K, Onolbaatar O, Roberts PH, Nam Y. Structures and mechanisms of tRNA methylation by METTL1-WDR4. Nature. 2023 Jan;613(7943):383-390. doi: 10.1038/s41586-022-05565-5. Epub 2023 Jan 4. PubMed PMID: 36599982; NIHMSID:NIHMS1866060.
Ruiz-Arroyo VM, Nam Y. Dynamic Protein-RNA recognition in primary MicroRNA processing. Curr Opin Struct Biol. 2022 Sep 2;76:102442. doi: 10.1016/j.sbi.2022.102442. PubMed PMID: 36067707; NIHMSID:NIHMS1835885.
Ruiz-Arroyo VM, Nam Y. Dynamic Protein-RNA recognition in primary MicroRNA processing. Curr Opin Struct Biol. 2022 Sep 2;76:102442. doi: 10.1016/j.sbi.2022.102442. PubMed PMID: 36067707; NIHMSID:NIHMS1835885.
Su R, Dong L, Li Y, Gao M, He PC, 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 CW, Huang W, Horne D, Rosen ST, He C, Chen J. METTL16 exerts an m6A-independent function to facilitate translation and tumorigenesis. Nat Cell Biol. 2022 Feb;24(2):205-216. doi: 10.1038/s41556-021-00835-2. Epub 2022 Feb 10. PubMed PMID: 35145225; PubMed Central PMCID: PMC9070413.
Su R, Dong L, Li Y, Gao M, He PC, 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 CW, Huang W, Horne D, Rosen ST, He C, Chen J. METTL16 exerts an m6A-independent function to facilitate translation and tumorigenesis. Nat Cell Biol. 2022 Feb;24(2):205-216. doi: 10.1038/s41556-021-00835-2. Epub 2022 Feb 10. PubMed PMID: 35145225; PubMed Central PMCID: PMC9070413.
Partin AC, Zhang K, Jeong BC, Herrell E, Li S, Chiu W, Nam Y. Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA. Mol Cell. 2020 May 7;78(3):411-422.e4. doi: 10.1016/j.molcel.2020.02.016. Epub 2020 Mar 27. PubMed PMID: 32220646; PubMed Central PMCID: PMC7214211.
Partin AC, Zhang K, Jeong BC, Herrell E, Li S, Chiu W, Nam Y. Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA. Mol Cell. 2020 May 7;78(3):411-422.e4. doi: 10.1016/j.molcel.2020.02.016. Epub 2020 Mar 27. PubMed PMID: 32220646; PubMed Central PMCID: PMC7214211.
Ngo TD, Partin AC, Nam Y. RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis. Cell Rep. 2019 Dec 17;29(12):4024-4035.e5. doi: 10.1016/j.celrep.2019.11.059. PubMed PMID: 31851931; PubMed Central PMCID: PMC6953907.
Ngo TD, Partin AC, Nam Y. RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis. Cell Rep. 2019 Dec 17;29(12):4024-4035.e5. doi: 10.1016/j.celrep.2019.11.059. PubMed PMID: 31851931; PubMed Central PMCID: PMC6953907.
Doxtader KA, Nam Y. Manipulation by Methylation: Garnishing mRNAs with m6Am. Mol Cell. 2019 Aug 8;75(3):417-418. doi: 10.1016/j.molcel.2019.07.019. PubMed PMID: 31398320; PubMed Central PMCID: PMC6860360.
Doxtader KA, Nam Y. Manipulation by Methylation: Garnishing mRNAs with m6Am. Mol Cell. 2019 Aug 8;75(3):417-418. doi: 10.1016/j.molcel.2019.07.019. PubMed PMID: 31398320; PubMed Central PMCID: PMC6860360.
Wang L, Rowe RG, Jaimes A, Yu C, Nam Y, Pearson DS, Zhang J, Xie X, Marion W, Heffron GJ, Daley GQ, Sliz P. Small-Molecule Inhibitors Disrupt let-7 Oligouridylation and Release the Selective Blockade of let-7 Processing by LIN28. Cell Rep. 2018 Jun 5;23(10):3091-3101. doi: 10.1016/j.celrep.2018.04.116. PubMed PMID: 29874593; PubMed Central PMCID: PMC6511231.
Wang L, Rowe RG, Jaimes A, Yu C, Nam Y, Pearson DS, Zhang J, Xie X, Marion W, Heffron GJ, Daley GQ, Sliz P. Small-Molecule Inhibitors Disrupt let-7 Oligouridylation and Release the Selective Blockade of let-7 Processing by LIN28. Cell Rep. 2018 Jun 5;23(10):3091-3101. doi: 10.1016/j.celrep.2018.04.116. PubMed PMID: 29874593; PubMed Central PMCID: PMC6511231.
Doxtader KA, Wang P, Scarborough AM, Seo D, Conrad NK, Nam Y. Structural Basis for Regulation of METTL16, an S-Adenosylmethionine Homeostasis Factor. Mol Cell. 2018 Sep 20;71(6):1001-1011.e4. doi: 10.1016/j.molcel.2018.07.025. Epub 2018 Sep 6. PubMed PMID: 30197297; PubMed Central PMCID: PMC6367934.
Doxtader KA, Wang P, Scarborough AM, Seo D, Conrad NK, Nam Y. Structural Basis for Regulation of METTL16, an S-Adenosylmethionine Homeostasis Factor. Mol Cell. 2018 Sep 20;71(6):1001-1011.e4. doi: 10.1016/j.molcel.2018.07.025. Epub 2018 Sep 6. PubMed PMID: 30197297; PubMed Central PMCID: PMC6367934.
Wang L, Nam Y, Lee AK, Yu C, Roth K, Chen C, Ransey EM, Sliz P. LIN28 Zinc Knuckle Domain Is Required and Sufficient to Induce let-7 Oligouridylation. Cell Rep. 2017 Mar 14;18(11):2664-2675. doi: 10.1016/j.celrep.2017.02.044. PubMed PMID: 28297670; NIHMSID:NIHMS857583.
Wang L, Nam Y, Lee AK, Yu C, Roth K, Chen C, Ransey EM, Sliz P. LIN28 Zinc Knuckle Domain Is Required and Sufficient to Induce let-7 Oligouridylation. Cell Rep. 2017 Mar 14;18(11):2664-2675. doi: 10.1016/j.celrep.2017.02.044. PubMed PMID: 28297670; NIHMSID:NIHMS857583.
Partin AC, Ngo TD, Herrell E, Jeong BC, Hon G, Nam Y. Heme enables proper positioning of Drosha and DGCR8 on primary microRNAs. Nat Commun. 2017 Nov 23;8(1):1737. doi: 10.1038/s41467-017-01713-y. PubMed PMID: 29170488; PubMed Central PMCID: PMC5700927.
Partin AC, Ngo TD, Herrell E, Jeong BC, Hon G, Nam Y. Heme enables proper positioning of Drosha and DGCR8 on primary microRNAs. Nat Commun. 2017 Nov 23;8(1):1737. doi: 10.1038/s41467-017-01713-y. PubMed PMID: 29170488; PubMed Central PMCID: PMC5700927.
Wang P, Doxtader KA, Nam Y. Structural Basis for Cooperative Function of Mettl3 and Mettl14 Methyltransferases. Mol Cell. 2016 Jul 21;63(2):306-317. doi: 10.1016/j.molcel.2016.05.041. Epub 2016 Jun 30. PubMed PMID: 27373337; PubMed Central PMCID: PMC4958592.
Wang P, Doxtader KA, Nam Y. Structural Basis for Cooperative Function of Mettl3 and Mettl14 Methyltransferases. Mol Cell. 2016 Jul 21;63(2):306-317. doi: 10.1016/j.molcel.2016.05.041. Epub 2016 Jun 30. PubMed PMID: 27373337; PubMed Central PMCID: PMC4958592.
Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Fromme JC, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P. Data publication with the structural biology data grid supports live analysis. Nat Commun. 2016 Mar 7;7:10882. doi: 10.1038/ncomms10882. PubMed PMID: 26947396; PubMed Central PMCID: PMC4786681.
Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Fromme JC, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P. Data publication with the structural biology data grid supports live analysis. Nat Commun. 2016 Mar 7;7:10882. doi: 10.1038/ncomms10882. PubMed PMID: 26947396; PubMed Central PMCID: PMC4786681.
Liu H, Liang C, Kollipara RK, Matsui M, Ke X, Jeong BC, Wang Z, Yoo KS, Yadav GP, Kinch LN, Grishin NV, Nam Y, Corey DR, Kittler R, Liu Q. HP1BP3, a Chromatin Retention Factor for Co-transcriptional MicroRNA Processing. Mol Cell. 2016 Aug 4;63(3):420-32. doi: 10.1016/j.molcel.2016.06.014. Epub 2016 Jul 14. PubMed PMID: 27425409; PubMed Central PMCID: PMC4975613.
Liu H, Liang C, Kollipara RK, Matsui M, Ke X, Jeong BC, Wang Z, Yoo KS, Yadav GP, Kinch LN, Grishin NV, Nam Y, Corey DR, Kittler R, Liu Q. HP1BP3, a Chromatin Retention Factor for Co-transcriptional MicroRNA Processing. Mol Cell. 2016 Aug 4;63(3):420-32. doi: 10.1016/j.molcel.2016.06.014. Epub 2016 Jul 14. PubMed PMID: 27425409; PubMed Central PMCID: PMC4975613.
O'Donovan DJ, Stokes-Rees I, Nam Y, Blacklow SC, Schröder GF, Brunger AT, Sliz P. A grid-enabled web service for low-resolution crystal structure refinement. Acta Crystallogr D Biol Crystallogr. 2012 Mar;68(Pt 3):261-7. doi: 10.1107/S0907444912001163. Epub 2012 Feb 14. PubMed PMID: 22349228; PubMed Central PMCID: PMC3282622.
O'Donovan DJ, Stokes-Rees I, Nam Y, Blacklow SC, Schröder GF, Brunger AT, Sliz P. A grid-enabled web service for low-resolution crystal structure refinement. Acta Crystallogr D Biol Crystallogr. 2012 Mar;68(Pt 3):261-7. doi: 10.1107/S0907444912001163. Epub 2012 Feb 14. PubMed PMID: 22349228; PubMed Central PMCID: PMC3282622.
Choi SH, Wales TE, Nam Y, O'Donovan DJ, Sliz P, Engen JR, Blacklow SC. Conformational locking upon cooperative assembly of notch transcription complexes. Structure. 2012 Feb 8;20(2):340-9. doi: 10.1016/j.str.2011.12.011. PubMed PMID: 22325781; PubMed Central PMCID: PMC3285698.
Choi SH, Wales TE, Nam Y, O'Donovan DJ, Sliz P, Engen JR, Blacklow SC. Conformational locking upon cooperative assembly of notch transcription complexes. Structure. 2012 Feb 8;20(2):340-9. doi: 10.1016/j.str.2011.12.011. PubMed PMID: 22325781; PubMed Central PMCID: PMC3285698.
Nam Y, Chen C, Gregory RI, Chou JJ, Sliz P. Molecular basis for interaction of let-7 microRNAs with Lin28. Cell. 2011 Nov 23;147(5):1080-91. doi: 10.1016/j.cell.2011.10.020. Epub 2011 Nov 10. PubMed PMID: 22078496; PubMed Central PMCID: PMC3277843.
Nam Y, Chen C, Gregory RI, Chou JJ, Sliz P. Molecular basis for interaction of let-7 microRNAs with Lin28. Cell. 2011 Nov 23;147(5):1080-91. doi: 10.1016/j.cell.2011.10.020. Epub 2011 Nov 10. PubMed PMID: 22078496; PubMed Central PMCID: PMC3277843.
Lazarus MB, Nam Y, Jiang J, Sliz P, Walker S. Structure of human O-GlcNAc transferase and its complex with a peptide substrate. Nature. 2011 Jan 27;469(7331):564-7. doi: 10.1038/nature09638. Epub 2011 Jan 16. PubMed PMID: 21240259; PubMed Central PMCID: PMC3064491.
Lazarus MB, Nam Y, Jiang J, Sliz P, Walker S. Structure of human O-GlcNAc transferase and its complex with a peptide substrate. Nature. 2011 Jan 27;469(7331):564-7. doi: 10.1038/nature09638. Epub 2011 Jan 16. PubMed PMID: 21240259; PubMed Central PMCID: PMC3064491.
Aster JC, Bodnar N, Xu L, Karnell F, Milholland JM, Maillard I, Histen G, Nam Y, Blacklow SC, Pear WS. Notch ankyrin repeat domain variation influences leukemogenesis and Myc transactivation. PLoS One. 2011;6(10):e25645. doi: 10.1371/journal.pone.0025645. Epub 2011 Oct 13. PubMed PMID: 22022427; PubMed Central PMCID: PMC3192765.
Aster JC, Bodnar N, Xu L, Karnell F, Milholland JM, Maillard I, Histen G, Nam Y, Blacklow SC, Pear WS. Notch ankyrin repeat domain variation influences leukemogenesis and Myc transactivation. PLoS One. 2011;6(10):e25645. doi: 10.1371/journal.pone.0025645. Epub 2011 Oct 13. PubMed PMID: 22022427; PubMed Central PMCID: PMC3192765.
Zimmer J, Nam Y, Rapoport TA. Structure of a complex of the ATPase SecA and the protein-translocation channel. Nature. 2008 Oct 16;455(7215):936-43. doi: 10.1038/nature07335. PubMed PMID: 18923516; PubMed Central PMCID: PMC7164768.
Zimmer J, Nam Y, Rapoport TA. Structure of a complex of the ATPase SecA and the protein-translocation channel. Nature. 2008 Oct 16;455(7215):936-43. doi: 10.1038/nature07335. PubMed PMID: 18923516; PubMed Central PMCID: PMC7164768.
Erlandson KJ, Miller SB, Nam Y, Osborne AR, Zimmer J, Rapoport TA. A role for the two-helix finger of the SecA ATPase in protein translocation. Nature. 2008 Oct 16;455(7215):984-7. doi: 10.1038/nature07439. PubMed PMID: 18923526; PubMed Central PMCID: PMC4354775.
Erlandson KJ, Miller SB, Nam Y, Osborne AR, Zimmer J, Rapoport TA. A role for the two-helix finger of the SecA ATPase in protein translocation. Nature. 2008 Oct 16;455(7215):984-7. doi: 10.1038/nature07439. PubMed PMID: 18923526; PubMed Central PMCID: PMC4354775.
Nam Y, Sliz P, Pear WS, Aster JC, Blacklow SC. Cooperative assembly of higher-order Notch complexes functions as a switch to induce transcription. Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2103-8. doi: 10.1073/pnas.0611092104. Epub 2007 Feb 6. PubMed PMID: 17284587; PubMed Central PMCID: PMC1892977.
Nam Y, Sliz P, Pear WS, Aster JC, Blacklow SC. Cooperative assembly of higher-order Notch complexes functions as a switch to induce transcription. Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2103-8. doi: 10.1073/pnas.0611092104. Epub 2007 Feb 6. PubMed PMID: 17284587; PubMed Central PMCID: PMC1892977.
Nam Y, Sliz P, Song L, Aster JC, Blacklow SC. Structural basis for cooperativity in recruitment of MAML coactivators to Notch transcription complexes. Cell. 2006 Mar 10;124(5):973-83. doi: 10.1016/j.cell.2005.12.037. PubMed PMID: 16530044; NIHMSID:NIHMS154980.
Nam Y, Sliz P, Song L, Aster JC, Blacklow SC. Structural basis for cooperativity in recruitment of MAML coactivators to Notch transcription complexes. Cell. 2006 Mar 10;124(5):973-83. doi: 10.1016/j.cell.2005.12.037. PubMed PMID: 16530044; NIHMSID:NIHMS154980.
Chiang MY, Xu ML, Histen G, Shestova O, Roy M, Nam Y, Blacklow SC, Sacks DB, Pear WS, Aster JC. Identification of a conserved negative regulatory sequence that influences the leukemogenic activity of NOTCH1. Mol Cell Biol. 2006 Aug;26(16):6261-71. doi: 10.1128/MCB.02478-05. PubMed PMID: 16880534; PubMed Central PMCID: PMC1592797.
Chiang MY, Xu ML, Histen G, Shestova O, Roy M, Nam Y, Blacklow SC, Sacks DB, Pear WS, Aster JC. Identification of a conserved negative regulatory sequence that influences the leukemogenic activity of NOTCH1. Mol Cell Biol. 2006 Aug;26(16):6261-71. doi: 10.1128/MCB.02478-05. PubMed PMID: 16880534; PubMed Central PMCID: PMC1592797.
Weng AP, Nam Y, Wolfe MS, Pear WS, Griffin JD, Blacklow SC, Aster JC. Growth suppression of pre-T acute lymphoblastic leukemia cells by inhibition of notch signaling. Mol Cell Biol. 2003 Jan;23(2):655-64. doi: 10.1128/MCB.23.2.655-664.2003. PubMed PMID: 12509463; PubMed Central PMCID: PMC151540.
Weng AP, Nam Y, Wolfe MS, Pear WS, Griffin JD, Blacklow SC, Aster JC. Growth suppression of pre-T acute lymphoblastic leukemia cells by inhibition of notch signaling. Mol Cell Biol. 2003 Jan;23(2):655-64. doi: 10.1128/MCB.23.2.655-664.2003. PubMed PMID: 12509463; PubMed Central PMCID: PMC151540.
Nam Y, Weng AP, Aster JC, Blacklow SC. Structural requirements for assembly of the CSL.intracellular Notch1.Mastermind-like 1 transcriptional activation complex. J Biol Chem. 2003 Jun 6;278(23):21232-9. doi: 10.1074/jbc.M301567200. Epub 2003 Mar 18. PubMed PMID: 12644465.
Nam Y, Weng AP, Aster JC, Blacklow SC. Structural requirements for assembly of the CSL.intracellular Notch1.Mastermind-like 1 transcriptional activation complex. J Biol Chem. 2003 Jun 6;278(23):21232-9. doi: 10.1074/jbc.M301567200. Epub 2003 Mar 18. PubMed PMID: 12644465.
Nam Y, Aster JC, Blacklow SC. Notch signaling as a therapeutic target. Curr Opin Chem Biol. 2002 Aug;6(4):501-9. doi: 10.1016/s1367-5931(02)00346-0. Review. PubMed PMID: 12133727.
Nam Y, Aster JC, Blacklow SC. Notch signaling as a therapeutic target. Curr Opin Chem Biol. 2002 Aug;6(4):501-9. doi: 10.1016/s1367-5931(02)00346-0. Review. PubMed PMID: 12133727.