Selected High-Impact Publications

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Wang J, Murphy EJ, Nix JC, Jones DNM. Aedes aegypti Odorant Binding Protein 22 selectively binds fatty acids through a conformational change in its C-terminal tail. Sci Rep. 2020 Feb 24;10(1):3300. doi: 10.1038/s41598-020-60242-9. PubMed PMID: 32094450.

Anantharajan J, Zhou H, Zhang L, Hotz T, Vincent MY, Blevins MA, Jansson AE, Kuan JWL, Ng EY, Yeo YK, Baburajendran N, Lin G, Hung AW, Joy J, Patnaik S, Marugan J, Rudra P, Ghosh D, Hill J, Keller TH, Zhao R, Ford HL, Kang C. Structural and Functional Analyses of an Allosteric EYA2 Phosphatase Inhibitor That Has On-Target Effects in Human Lung Cancer Cells. Mol Cancer Ther. 2019 Sep;18(9):1484-1496. doi: 10.1158/1535-7163.MCT-18-1239. Epub 2019 Jul 8. PubMed PMID: 31285279; PubMed Central PMCID: PMC6726557.

Dostal V, Churchill MEA. Cytosine methylation of mitochondrial DNA at CpG sequences impacts transcription factor A DNA binding and transcription. Biochim Biophys Acta Gene Regul Mech 1862(5):598-607, 2019. PMID:30807854 /

Eisenmesser EZ, Gottschlich A, Redzic JS, Paukovich N, Nix JC, Azam T, Zhang L, Zhao R, Kieft JS, The E, Meng X, Dinarello CA. Interleukin-37 monomer is the active form for reducing innate immunity. Proc Natl Acad Sci U S A 116(12):5514-5522, 2019. PMID:30819901 / PMC6431183

Klein BJ, Cox KL, Jang SM, Côté J, Poirier MG, Kutateladze TG. Molecular Basis for the PZP Domain of BRPF1 Association with Chromatin. Structure. 2020 Jan 7;28(1):105-110.e3. doi: 10.1016/j.str.2019.10.014. Epub 2019 Nov 8. PubMed PMID: 31711755; PubMed Central PMCID: PMC6949404.

Klein BJ, Jang SM, Lachance C, Mi W, Lyu J, Sakuraba S, Krajewski K, Wang WW, Sidoli S, Liu J, Zhang Y, Wang X, Warfield BM, Kueh AJ, Voss AK, Thomas T, Garcia BA, Liu WR, Strahl BD, Kono H, Li W, Shi X, Côté J, Kutateladze TG. Histone H3K23- specific acetylation by MORF is coupled to H3K14 acylation. Nat Commun. 2019 Oct 17;10(1):4724. doi: 10.1038/s41467-019-12551-5. PubMed PMID: 31624313; PubMed Central PMCID: PMC6797804.

Koneru PC, Francis AC, Deng N, Rebensburg SV, Hoyte AC, Lindenberger J, Adu- Ampratwum D, Larue RC, Wempe MF, Engelman AN, Lyumkis D, Fuchs JR, Levy RM, Melikyan GB, Kvaratskhelia M. HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors. Elife. 2019 May 23;8. pii: e46344. doi:

10.7554/eLife.46344. PubMed PMID: 31120420; PubMed Central PMCID: PMC6581505.

Wilson TA, Koneru PC, Rebensburg SV, Lindenberger JJ, Kobe MJ, Cockroft NT, Adu- Ampratwum D, Larue RC, Kvaratskhelia M, Fuchs JR. An Isoquinoline Scaffold as a Novel Class of Allosteric HIV-1 Integrase Inhibitors. ACS Med Chem Lett. 2019 Jan 30;10(2):215-220. doi: 10.1021/acsmedchemlett.8b00633. eCollection 2019 Feb 14. PubMed PMID: 30783506; PubMed Central PMCID: PMC6378678.

Yesselman JD, Eiler D, Carlson ED, Gotrik MR, d'Aquino AE, Ooms AN, Kladwang W, Carlson PD, Shi X, Costantino DA, Herschlag D, Lucks JB, Jewett MC, Kieft JS, Das R. Computational design of three-dimensional RNA structure and function. Nat Nanotechnol. 2019 Sep;14(9):866-873. doi: 10.1038/s41565-019-0517-8. Epub 2019 Aug 19. PubMed PMID: 31427748.

Zhang Y, Ahn J, Green KJ, Vann KR, Black J, Brooke CB, Kutateladze TG. MORC3 Is a Target of the Influenza A Viral Protein NS1. Structure. 2019 Jun 4;27(6):1029- 1033.e3. doi: 10.1016/j.str.2019.03.015. Epub 2019 Apr 18. PubMed PMID: 31006586.

Zhang Y, Klein BJ, Cox KL, Bertulat B, Tencer AH, Holden MR, Wright GM, Black J, Cardoso MC, Poirier MG, Kutateladze TG. Mechanism for autoinhibition and activation of the MORC3 ATPase. Proc Natl Acad Sci U S A 116(13):6111-6119, 2019. PMID:30850548 / PMC6442546

Zhang Y, Mun SR, Linares JF, Towers CG, Thorburn A, Diaz-Meco MT, Kwon YT, Kutateladze TG. Mechanistic insight into the regulation of SQSTM1/p62. Autophagy 15(4):735-737, 2019. PMID:30653391 / PMC6526835

Zhang Y, Jang Y, Lee JE, Ahn J, Xu L, Holden MR, Cornett EM, Krajewski K, Klein BJ, Wang SP, Dou Y, Roeder RG, Strahl BD, Rothbart SB, Shi X, Ge K, Kutateladze TG. Selective binding of the PHD6 finger of MLL4 to histone H4K16ac links MLL4 and MOF. Nat Commun 10(1):2314, 2019. PMID:31127101 / PMC6534582

Klein BJ, Vann KR, Andrews FH, Wang WW, Zhang J, Zhang Y, Beloglazkina AA, Mi W, Li Y, Li H, Shi X, Kutateladze AG, Strahl BD, Liu WR, Kutateladze TG. Structural insights into the pi-pi-pi stacking mechanism and DNA-binding activity of the YEATS domain. Nat Commun 9(1):4574, 2018. PMID:30385749 / PMC6212594

Klein BJ, Krajewski K, Restrepo S, Lewis PW, Strahl BD, Kutateladze TG. Recognition of cancer mutations in histone H3K36 by epigenetic writers and readers. Epigenetics

13(7):683-692, 2018. PMID:30045670 / PMC6224213

Klein BJ, Ahmad S, Vann KR, Andrews FH, Mayo ZA, Bourriquen G, Bridgers JB, Zhang J, Strahl BD, Cote J, Kutateladze TG. Yaf9 subunit of the NuA4 and SWR1 complexes targets histone H3K27ac through its YEATS domain. Nucleic Acids Res 46: 421-430, 2018. PMID: 29145630 / PMC5758897

Liu H, Wang C, Lee S, Ning F, Wang Y, Zhang Q, Chen Z, Zang J, Nix J, Dai S, Marrack P, Hagman J, Kappler J, Zhang G. Specific recognition of arginine methylated histone tails by JMJD5 and JMJD7. Sci Rep 8: 3275, 2018. PMID: 29459673 / PMC5818494

MacFadden A, O'Donoghue Z, Silva P, Chapman EG, Olsthoorn RC, Sterken MG, Pijlman GP, Bredenbeek PJ, Kieft JS. Mechanism and structural diversity of exoribonuclease-resistant RNA structures in flaviviral RNAs. Nat Commun 9: 119, 2018. PMID: 29317714 / PMC5760640

Mi W, Zhang Y, Lyu J, Wang X, Tong Q, Peng D, Xue Y, Tencer AH, Wen H, Li W, Kutateladze TG, Shi X. The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex- mediated histone acetylation and gene activation. Nat Commun 9(1):3759, 2018. PMID:30217978 / PMC6138639

Nichols PJ, Henen MA, Born A, Strotz D, Guntert P, Vogeli B. High-resolution small RNA structures from exact nuclear Overhauser enhancement measurements without additional restraints. Commun Biol 1: 61, 2018. PMID: 30271943 / PMC6123705

Salmon L, Stull F, Sayle S, Cato C, Akgul S, Foit L, Ahlstrom LS, Eisenmesser EZ, Al- Hashimi HM, Bardwell JCA, Horowitz S. The mechanism of HdeA unfolding and chaperone activation. J Mol Biol 430: 33-40, 2018. PMID: 29138002 / PMC5738273

Steckelberg AL, Akiyama BM, Costantino DA, Sit TL, Nix JC, Kieft JS. A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure. Proc Natl Acad Sci U S A 115: 6404-6409, 2018. PMID: 29866852 / PMC6016793

Zhang Y, Mun SR, Linares JF, Ahn J, Towers CG, Ji CH, Fitzwalter BE, Holden MR, Mi W, Shi X, Moscat J, Thorburn A, Diaz-Meco MT, Kwon YT, Kutateladze TG. ZZ- dependent regulation of p62/SQSTM1 in autophagy. Nat Commun. 2018 Oct 22;9(1):4373. doi: 10.1038/s41467-018-06878-8. PubMed PMID: 30349045; PubMed Central PMCID: PMC6197226.

Zhang Y, Xue Y, Shi J, Ahn J, Mi W, Ali M, Wang X, Klein BJ, Wen H, Li W, Shi X, Kutateladze TG. The ZZ domain of p300 mediates specificity of the adjacent HAT domain for histone H3. Nat Struct Mol Biol 25(9):841-849, 2018. PMID:30150647 / PMC6482957

Andrews FH, Singh AR, Joshi S, Smith CA, Morales GA, Garlich JR, Durden DL, Kutateladze TG. Dual-activity PI3K-BRD4 inhibitor for the orthogonal inhibition of MYC to block tumor growth and metastasis. Proc Natl Acad Sci U S A 114: E1072-E1080, 2017. PMID: 28137841 / PMC5320964

Blevins MA, Huang M, Zhao R. The role of CtBP1 in oncogenic processes and its potential as a therapeutic target. Mol Cancer Ther 16: 981-990, 2017. PMID: 28576945 / PMC5458631

Brown DA, Di Cerbo V, Feldmann A, Ahn J, Ito S, Blackledge NP, Nakayama M, McClellan M, Dimitrova E, Turberfield AH, Long HK, King HW, Kriaucionis S, Schermelleh L, Kutateladze TG, Koseki H, Klose RJ. The SET1 complex selects actively transcribed target genes via multivalent interaction with CpG island chromatin. Cell Rep 20: 2313-2327, 2017. PMID: 28877467 / PMC5603731

Espinosa S, Zhang L, Li X, Zhao R. Understanding pre-mRNA splicing through crystallography. Methods Epub ahead of print, 2017. PMID: 28506657

Gatchalian J, Ali M, Andrews FH, Zhang Y, Barrett AS, Kutateladze TG. Structural insight into recognition of methylated histone H3K4 by Set3. J Mol Biol 429: 2066-2074, 2017. PMID: 27697561 / PMC5374059

Gibson MD, Gatchalian J, Slater A, Kutateladze TG, Poirier MG. PHF1 Tudor and N- terminal domains synergistically target partially unwrapped nucleosomes to increase DNA accessibility. Nucleic Acids Res 45: 3767-3776, 2017. PMID: 28082396 / PMC5397176

Holliday MJ, Camilloni C, Armstrong GS, Vendruscolo M, Eisenmesser EZ. Networks of dynamic allostery regulate enzyme function. Structure 25: 276-286, 2017. PMID: 28089447 / PMC5336394

Hoyte AC, Jamin AV, Koneru PC, Kobe MJ, Larue RC, Fuchs JR, Engelman AN, Kvaratskhelia M. Resistance to pyridine-based inhibitor KF116 reveals an unexpected role of integrase in HIV-1 Gag-Pol polyprotein proteolytic processing. J Biol Chem 292: 19814-19825, 2017. PMID: 28972144 / PMC5712621

Kendrick AA, Schafer J, Dzieciatkowska M, Nemkov T, D'Alessandro A, Neelakantan D, Ford HL, Pearson CG, Weekes CD, Hansen KC, Eisenmesser EZ. CD147: A small molecule transporter ancillary protein at the crossroad of multiple hallmarks of cancer and metabolic reprogramming. Oncotarget 8: 6742-6762, 2017. PMID: 28039486 / PMC5341751

Klein BJ, Simithy J, Wang X, Ahn J, Andrews FH, Zhang Y, Cote J, Shi X, Garcia BA, Kutateladze TG. Recognition of histone H3K14 acylation by MORF. Structure 25: 650-

654 e2, 2017. PMID: 28286003 / PMC5415407

Liu H, Wang C, Lee S, Deng Y, Wither M, Oh S, Ning F, Dege C, Zhang Q, Liu X, Johnson AM, Zang J, Chen Z, Janknecht R, Hansen K, Marrack P, Li CY, Kappler JW, Hagman J, Zhang G. Clipping of arginine-methylated histone tails by JMJD5 and JMJD7. Proc Natl Acad Sci U S A 114: Epub ahead of print, 2017. PMID: 28847961 / PMC5604019

Liu S, Li X, Zhang L, Jiang J, Hill RC, Cui Y, Hansen KC, Zhou ZH, Zhao R. Structure of the yeast spliceosomal postcatalytic P complex. Science 358: 1278-1283, 2017. PMID: 29146870 / Required

Mi W, Guan H, Lyu J, Zhao D, Xi Y, Jiang S, Andrews FH, Wang X, Gagea M, Wen H, Tora L, Dent SYR, Kutateladze TG, Li W, Li H, Shi X. YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer. Nat Commun. 2017 Oct 20;8(1):1088. doi: 10.1038/s41467-017-01173-4. PubMed PMID: 29057918; PubMed Central PMCID: PMC5651844.

Tencer AH, Gatchalian J, Klein BJ, Khan A, Zhang Y, Strahl BD, van Wely KHM, Kutateladze TG. A Unique pH-Dependent Recognition of Methylated Histone H3K4 by PPS and DIDO. Structure. 2017 Oct 3;25(10):1530-1539.e3. doi: 10.1016/j.str.2017.08.009. Epub 2017 Sep 14. PubMed PMID: 28919441; PubMed Central PMCID: PMC5679713.

Zhou H, Zhang L, Vartuli RL, Ford HL, Zhao R. The Eya phosphatase: Its unique role in cancer. Int J Biochem Cell Biol, Epub ahead of print, 2017. PMID: 28887153

Akiyama BM, Laurence HM, Massey AR, Costantino DA, Xie X, Yang Y, Shi PY, Nix JC, Beckham JD, Kieft JS. Zika virus produces noncoding RNAs using a multi- pseudoknot structure that confounds a cellular exonuclease. Science. 2016 Dec 2;354(6316):1148-1152. Epub 2016 Nov 10. PubMed PMID: 27934765; PubMed Central PMCID: PMC5476369.

Andrews FH, Shinsky SA, Shanle EK, Bridgers JB, Gest A, Tsun IK, Krajewski K, Shi X, Strahl BD, Kutateladze TG. The Taf14 YEATS domain is a reader of histone crotonylation. Nat Chem Biol 12: 396-8, 2016. PMID: 27089029 / PMC4871749

Andrews FH, Tong Q, Sullivan KD, Cornett EM, Zhang Y, Ali M, Ahn J, Pandey A, Guo AH, Strahl BD, Costello JC, Espinosa JM, Rothbart SB, Kutateladze TG. Multivalent chromatin engagement and inter-domain crosstalk regulate MORC3 ATPase. Cell Rep 16: 3195-3207, 2016. PMID: 27653685 / PMC5074691

Gatchalian J, Ali M, Andrews FH, Zhang Y, Barrett AS, Kutateladze TG. Structural Insight into Recognition of Methylated Histone H3K4 by Set3. J Mol Biol. 2017 Jun

30;429(13):2066-2074. doi: 10.1016/j.jmb.2016.09.020. Epub 2016 Sep 30. PubMed PMID: 27697561; PubMed Central PMCID: PMC5374059.

Gatchalian J, Gallardo CM, Shinsky SA, Ospina RR, Liendo AM, Krajewski K, Klein BJ, Andrews FH, Strahl BD, KH MvW, Kutateladze TG. Chromatin condensation and recruitment of PHD finger proteins to histone H3K4me3 are mutually exclusive. Nucleic Acids Res 44: 6102-12, 2016. PMID: 27016734 / PMC5291243

Jaafar ZA, Oguro A, Nakamura Y, Kieft JS. Translation initiation by the hepatitis C virus IRES requires eIF1A and ribosomal complex remodeling. Elife 5: e21198, 2016. PMID: 28009256 / PMC5238962

Klein BJ, Muthurajan UM, Lalonde ME, Gibson MD, Andrews FH, Hepler M, Machida S, Yan K, Kurumizaka H, Poirier MG, Cote J, Luger K, Kutateladze TG. Bivalent interaction of the PZP domain of BRPF1 with the nucleosome impacts chromatin dynamics and acetylation. Nucleic Acids Res 44: 472-84, 2016. PMID: 26626149 / PMC4705663

Klein BJ, Wang X, Cui G, Yuan C, Botuyan MV, Lin K, Lu Y, Wang X, Zhao Y, Bruns CJ, Mer G, Shi X, Kutateladze TG. PHF20 Readers link methylation of histone H3K4 and p53 with H4K16 acetylation. Cell Rep 17: 1158-1170, 2016. PMID: 27760318 / PMC5125728

Liu WH, Roemer SC, Zhou Y, Shen ZJ, Dennehey BK, Balsbaugh JL, Liddle JC, Nemkov T, Ahn NG, Hansen KC, Tyler JK, Churchill ME. The Cac1 subunit of histone chaperone CAF-1 organizes CAF-1-H3/H4 architecture and tetramerizes histones. Elife 5: e18023, 2016. PMID: 27690308 / PMC5045291

Malarkey CS, Gustafson CE, Saifee JF, Torres RM, Churchill ME, Janoff EN. Mechanism of mitochondrial transcription factor a attenuation of CpG-induced antibody production. PLoS One 11: e0157157, 2016. PMID: 27280778 / PMC4900672

Zhang X, Peng D, Xi Y, Yuan C, Sagum CA, Klein BJ, Tanaka K, Wen H, Kutateladze TG , Li W, Bedford MT, Shi X. G9a-mediated methylation of ERalpha links the PHF20/MOF histone acetyltransferase complex to hormonal gene expression. Nat Commun 7: 10810, 2016. PMID: 26960573 / PMC4792926

Zhu L, Li Q, Wong SH, Huang M, Klein BJ, Shen J, Ikenouye L, Onishi M, Schneidawind D, Buechele C, Hansen L, Duque-Afonso J, Zhu F, Martin GM, Gozani O, Majeti R, Kutateladze TG, Cleary ML. ASH1L Links histone H3 Lysine 36 dimethylation to MLL leukemia. Cancer Discov 6: 770-83, 2016. PMID: 27154821 / PMC4930721

Hartwick EW, Costantino DA, MacFadden A, Nix JC, Tian S, Das R, Kieft JS. Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels. Nat Commun 9(1):5074, 2018. PMID:30498211 / PMC6265322