Publications

Cryo-EM reveals how ASX-173 inhibits human asparagine synthetase to activate the integrated stress response. Staschke, K.A., Walda, N.T., Pearce, L.A., Wek, R.C., Zhu, W., and Takagi, Y. (2025). bioRxiv, 2025.2010.2016.682859. 10.1101/2025.10.16.682859.

3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase. Coricello A, Nardone AJ, Lupia A, Gratteri C, Vos M, Chaptal V, Alcaro S, Zhu W, Takagi Y, Richards NGJ.Nat Commun. 2024 Dec 3;15(1):10538. doi: 10.1038/s41467-024-54912-9.PMID: 39627226

An atlas of substrate specificities for the human serine/threonine kinome.  Johnson JL, Yaron TM, Huntsman EM, Kerelsky A, Song J, Regev A, Lin TY, Liberatore K, Cizin DM, Cohen BM, Vasan N, Ma Y, Krismer K, Robles JT, van de Kooij B, van Vlimmeren AE, Andrée-Busch N, Käufer NF, Dorovkov MV, Ryazanov AG, Takagi Y, Kastenhuber ER, Goncalves MD, Hopkins BD, Elemento O, Taatjes DJ, Maucuer A, Yamashita A, Degterev A, Uduman M, Lu J, Landry SD, Zhang B, Cossentino I, Linding R, Blenis J, Hornbeck PV, Turk BE, Yaffe MB, Cantley LC.Nature. 2023 Jan;613(7945):759-766. doi: 10.1038/s41586-022-05575-3. Epub 2023 Jan 11.PMID: 36631611

Isha is a su(Hw) mRNA-binding protein required for gypsy insulator function.  Bag I, Chen Y, D’Orazio K, Lopez P, Wenzel S, Takagi Y, Lei EP.G3 (Bethesda). 2022 Aug 25;12(9):jkac152. doi: 10.1093/g3journal/jkac152.PMID: 35708663

Structure and RNA template requirements of Arabidopsis RNA-DEPENDENT RNA POLYMERASE 2.  Fukudome A, Singh J, Mishra V, Reddem E, Martinez-Marquez F, Wenzel S, Yan R, Shiozaki M, Yu Z, Wang JC, Takagi Y, Pikaard CS.Proc Natl Acad Sci U S A. 2021 Dec 21;118(51):e2115899118. doi: 10.1073/pnas.2115899118.PMID: 34903670

Assembly of a dsRNA synthesizing complex: RNA-DEPENDENT RNA POLYMERASE 2 contacts the largest subunit of NUCLEAR RNA POLYMERASE IV.  Mishra V, Singh J, Wang F, Zhang Y, Fukudome A, Trinidad JC, Takagi Y, Pikaard CS.Proc Natl Acad Sci U S A. 2021 Mar 30;118(13):e2019276118. doi: 10.1073/pnas.2019276118.PMID: 33753485

The yeast Hrq1 helicase stimulates Pso2 translesion nuclease activity and thereby promotes DNA interstrand crosslink repair.  Rogers CM, Lee CY, Parkins S, Buehler NJ, Wenzel S, Martínez-Márquez F, Takagi Y, Myong S, Bochman ML.J Biol Chem. 2020 Jul 3;295(27):8945-8957. doi: 10.1074/jbc.RA120.013626. Epub 2020 May 5.PMID: 32371399

High-resolution crystal structure of human asparagine synthetase enables analysis of inhibitor binding and selectivity.  Zhu W, Radadiya A, Bisson C, Wenzel S, Nordin BE, Martínez-Márquez F, Imasaki T, Sedelnikova SE, Coricello A, Baumann P, Berry AH, Nomanbhoy TK, Kozarich JW, Jin Y, Rice DW, Takagi Y, Richards NGJ.Commun Biol. 2019 Sep 17;2:345. doi: 10.1038/s42003-019-0587-z. eCollection 2019.PMID: 31552298

Parkinson’s disease-associated mutations in the GTPase domain of LRRK2 impair its nucleotide-dependent conformational dynamics.  Wu CX, Liao J, Park Y, Reed X, Engel VA, Hoang NC, Takagi Y, Johnson SM, Wang M, Federici M, Nichols RJ, Sanishvili R, Cookson MR, Hoang QQ.J Biol Chem. 2019 Apr 12;294(15):5907-5913. doi: 10.1074/jbc.RA119.007631. Epub 2019 Feb 22.PMID: 30796162

A practical method for efficient and optimal production of Seleno-methionine-labeled recombinant protein complexes in the insect cells.  Wenzel S, Imasaki T, Takagi Y.Protein Sci. 2019 Apr;28(4):808-822. doi: 10.1002/pro.3575. Epub 2019 Feb 4.PMID: 30663186

A protein-protein interaction underlies the molecular basis for substrate recognition by an adenosine-to-inosine RNA-editing enzyme.  Rajendren S, Manning AC, Al-Awadi H, Yamada K, Takagi Y, Hundley HA.Nucleic Acids Res. 2018 Oct 12;46(18):9647-9659. doi: 10.1093/nar/gky800.PMID: 30202880

Titer estimation for quality control (TEQC) method: A practical approach for optimal production of protein complexes using the baculovirus expression vector system.  Imasaki T, Wenzel S, Yamada K, Bryant ML, Takagi Y.PLoS One. 2018 Apr 3;13(4):e0195356. doi: 10.1371/journal.pone.0195356. eCollection 2018.PMID: 29614134

Yeast Hrq1 shares structural and functional homology with the disease-linked human RecQ4 helicase.  Rogers CM, Wang JC, Noguchi H, Imasaki T, Takagi Y, Bochman ML.Nucleic Acids Res. 2017 May 19;45(9):5217-5230. doi: 10.1093/nar/gkx151.PMID: 28334827

Structures and Functions of the Multiple KOW Domains of Transcription Elongation Factor Spt5.  Meyer PA, Li S, Zhang M, Yamada K, Takagi Y, Hartzog GA, Fu J.Mol Cell Biol. 2015 Oct;35(19):3354-69. doi: 10.1128/MCB.00520-15. Epub 2015 Jul 27.PMID: 26217010

Expression and purification of functional human glycogen synthase-1 (hGYS1) in insect cells.  Khanna M, Imasaki T, Chikwana VM, Perez-Miller S, Hunter GO, Mosley A, Takagi Y, Hurley TD.Protein Expr Purif. 2013 Aug;90(2):78-83. doi: 10.1016/j.pep.2013.05.007. Epub 2013 May 24.PMID: 23711380

Substrate specificity of lymphoid-specific tyrosine phosphatase (Lyp) and identification of Src kinase-associated protein of 55 kDa homolog (SKAP-HOM) as a Lyp substrate.  Yu X, Chen M, Zhang S, Yu ZH, Sun JP, Wang L, Liu S, Imasaki T, Takagi Y, Zhang ZY.J Biol Chem. 2011 Sep 2;286(35):30526-30534. doi: 10.1074/jbc.M111.254722. Epub 2011 Jun 30.PMID: 21719704

Architecture of the Mediator head module.  Imasaki T, Calero G, Cai G, Tsai KL, Yamada K, Cardelli F, Erdjument-Bromage H, Tempst P, Berger I, Kornberg GL, Asturias FJ, Kornberg RD, Takagi Y.Nature. 2011 Jul 3;475(7355):240-3. doi: 10.1038/nature10162.PMID: 21725323

Interaction of the mediator head module with RNA polymerase II.  Cai G, Chaban YL, Imasaki T, Kovacs JA, Calero G, Penczek PA, Takagi Y, Asturias FJ.Structure. 2012 May 9;20(5):899-910. doi: 10.1016/j.str.2012.02.023.PMID: 22579255

Mediator head module structure and functional interactions.  Cai G, Imasaki T, Yamada K, Cardelli F, Takagi Y, Asturias FJ.Nat Struct Mol Biol. 2010 Mar;17(3):273-9. doi: 10.1038/nsmb.1757. Epub 2010 Feb 14.PMID: 20154708

Mediator structural conservation and implications for the regulation mechanism.  Cai G, Imasaki T, Takagi Y, Asturias FJ.Structure. 2009 Apr 15;17(4):559-67. doi: 10.1016/j.str.2009.01.016.PMID: 19368889

Head module control of mediator interactions.  Takagi Y, Calero G, Komori H, Brown JA, Ehrensberger AH, Hudmon A, Asturias F, Kornberg RD.Mol Cell. 2006 Aug 4;23(3):355-64. doi: 10.1016/j.molcel.2006.06.007.PMID: 16885025

Mediator as a general transcription factor.  Takagi Y, Kornberg RD.J Biol Chem. 2006 Jan 6;281(1):80-9. doi: 10.1074/jbc.M508253200. Epub 2005 Nov 1.PMID: 16263706

Ubiquitin ligase activity of TFIIH and the transcriptional response to DNA damage.  Takagi Y, Masuda CA, Chang WH, Komori H, Wang D, Hunter T, Joazeiro CA, Kornberg RD.Mol Cell. 2005 Apr 15;18(2):237-43. doi: 10.1016/j.molcel.2005.03.007.PMID: 15837426

Preponderance of free mediator in the yeast Saccharomyces cerevisiae.  Takagi Y, Chadick JZ, Davis JA, Asturias FJ.J Biol Chem. 2005 Sep 2;280(35):31200-7. doi: 10.1074/jbc.C500150200. Epub 2005 Jul 6.PMID: 16002404

Revised subunit structure of yeast transcription factor IIH (TFIIH) and reconciliation with human TFIIH.  Takagi Y, Komori H, Chang WH, Hudmon A, Erdjument-Bromage H, Tempst P, Kornberg RD.J Biol Chem. 2003 Nov 7;278(45):43897-900. doi: 10.1074/jbc.C300417200. Epub 2003 Sep 18.PMID: 14500720

Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction.  Davis JA, Takagi Y, Kornberg RD, Asturias FA.Mol Cell. 2002 Aug;10(2):409-15. doi: 10.1016/s1097-2765(02)00598-1.PMID: 12191485

A multiprotein complex that interacts with RNA polymerase II elongator.  Li Y, Takagi Y, Jiang Y, Tokunaga M, Erdjument-Bromage H, Tempst P, Kornberg RD.J Biol Chem. 2001 Aug 10;276(32):29628-31. doi: 10.1074/jbc.C100274200. Epub 2001 Jun 4.PMID: 11390369

The elongin B ubiquitin homology domain. Identification of Elongin B sequences important for interaction with Elongin C.  Brower CS, Shilatifard A, Mather T, Kamura T, Takagi Y, Haque D, Treharne A, Foundling SI, Conaway JW, Conaway RC.J Biol Chem. 1999 May 7;274(19):13629-36. doi: 10.1074/jbc.274.19.13629.PMID: 10224134

Identification of elongin C sequences required for interaction with the von Hippel-Lindau tumor suppressor protein.  Takagi Y, Pause A, Conaway RC, Conaway JW.J Biol Chem. 1997 Oct 24;272(43):27444-9. doi: 10.1074/jbc.272.43.27444.PMID: 9341197

Characterization of elongin C functional domains required for interaction with elongin B and activation of elongin A.  Takagi Y, Conaway RC, Conaway JW.J Biol Chem. 1996 Oct 11;271(41):25562-8. doi: 10.1074/jbc.271.41.25562.PMID: 8810329

A novel activity associated with RNA polymerase II elongation factor SIII. SIII directs promoter-independent transcription initiation by RNA polymerase II in the absence of initiation factors.  Takagi Y, Conaway JW, Conaway RC.J Biol Chem. 1995 Oct 13;270(41):24300-5. doi: 10.1074/jbc.270.41.24300.PMID: 7592640

Phosrestin I undergoes the earliest light-induced phosphorylation by a calcium/calmodulin-dependent protein kinase in Drosophila photoreceptors.  Matsumoto H, Kurien BT, Takagi Y, Kahn ES, Kinumi T, Komori N, Yamada T, Hayashi F, Isono K, Pak WL, et al.Neuron. 1994 May;12(5):997-1010. doi: 10.1016/0896-6273(94)90309-3.PMID: 8185954