Jeffrey Kieft, PhD

Publications

• Lee S.J., Hyun S., Kieft J.S., Yu J. (2009) An approach to the construction of tailor-made amphiphilic peptides that strongly and selectively bind to hairpin RNA targets. J Am Chem Soc. 131, 2224-2230.
• Pfingsten, J.S., Castile, A.E., & Kieft, J.S. (2010) Mechanistic role of structurally dynamic regions in the Dicistroviridae IGR IRESs. J. Mol. Biol., 395, 205-217.
• Hammond, J.A., Rambo, R.P., Filbin, M.E., & Kieft, J.S. (2009) Comparison and functional implications of the 3-D architectures of viral tRNA-like structures. RNA,15, 294-307.
• Constantineau J, Greason E, West M, Filbin M, Kieft JS, Carletti MZ, Christenson LK, Rodriguez A. (2009) A synonymous variant in scavenger receptor, class B, type I gene is associated with lower SR-BI protein expression and function. Atherosclerosis. 2009 Nov 26. in press[Epub ahead of print]
• Plank TD, Whitehurst JT, Kieft JS. Cell type specificity and structural determinants of IRES activity from the 5' leaders of different HIV-1 transcripts. Nucleic Acids Res. 2013 Jul;41(13):6698-714. PubMed PMID: 23661682
• Wang H, Ru Y, Sanchez-Carbayo M, Wang X, Kieft JS, Theodorescu D. Translation initiation factor eIF3b expression in human cancer and its role in tumor growth and lung colonization. Clin Cancer Res. 2013 Jun 1;19(11):2850-60. PubMed PMID: 23575475
• Filbin ME, Vollmar BS, Shi D, Gonen T, Kieft JS. HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation. Nat Struct Mol Biol. 2013 Feb;20(2):150-8. PubMed PMID: 23262488
• Filbin ME, Kieft JS (2009) Toward a structural understanding of IRES RNA function. Curr Opin Struct Biol. 19: 267-76. Epub 2009 Apr 9. Review.
• Kieft, J.S. (2009) Comparing the three-dimensional structures of Dicistroviridae IGR IRES RNAs with other viral RNA structures. Virus Res. 139, 148-56. Virus Res. 139: 148-56.
• Jeffrey S. Kieft*, Elaine Chase, David A. Costantino, and Barbara L. Golden* (2010) Identification and characterization of anion binding sites in RNA RNA, in press
• Kieft JS. Experiences gathered and lessons learned from 20 years of RNA structure. RNA. 2015 Apr;21(4):661-3. PubMed PMID: 25780181
• Colussi TM, Costantino DA, Zhu J, Donohue JP, Korostelev AA, Jaafar ZA, Plank TD, Noller HF, Kieft JS. Initiation of translation in bacteria by a structured eukaryotic IRES RNA. Nature. 2015 Mar 5;519(7541):110-3. PubMed PMID: 25652826
• Hao Y, Kieft JS. Diverse self-association properties within a family of phage packaging RNAs. RNA. 2014 Nov;20(11):1759-74. PubMed PMID: 25246655
• Clayton GM, Wang Y, Crawford F, Novikov A, Wimberly BT, Kieft JS, Falta MT, Bowerman NA, Marrack P, Fontenot AP, Dai S, Kappler JW. Structural basis of chronic beryllium disease: linking allergic hypersensitivity and autoimmunity. Cell. 2014 Jul 3;158(1):132-42. PubMed PMID: 24995984
• Colussi TM, Costantino DA, Hammond JA, Ruehle GM, Nix JC, Kieft JS. The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA. Nature. 2014 Jul 17;511(7509):366-9. PubMed PMID: 24909993
• Chapman EG, Costantino DA, Rabe JL, Moon SL, Wilusz J, Nix JC, Kieft JS. The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production. Science. 2014 Apr 18;344(6181):307-10. PubMed PMID: 24744377
• Chapman EG, Moon SL, Wilusz J, Kieft JS. RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA. Elife. 2014 Apr 1;3:e01892. PubMed PMID: 24692447
• Plank, T-D.M., Whitehurst, J.T., Cencic, R., Pelletier, J. & Kieft, J.S. (2014) Internal translation initiation from HIV-1 transcripts is conferred by a common RNA structure. Translation, 2:e27694; DOI: 10.4161/trla.27694.
• Keel, A.Y. Easton, L.E., Lukavsky, P.J., & Kieft, J.S. (2009) Large-scale native preparation of in vitro transcribed RNA, Methods Enzymol, in press.
• Kieft, J.S., Chase, E., Costantino, D.A., Golden, B.L. (2010) Identification and characterization of anion binding sites in RNA. RNA, 16, 1118-1123.
• Feser J, Truong D, Das C, Carson JJ, Kieft J, Harkness T, Tyler JK. (2010) Elevated histone expression promotes life span extension. Mol. Cell, 39, 724-735.
• Zhu, J., Korostelev, A., Costantino, D.A., Donohue, J.P., Noller, H.F., & Kieft, J.S. (2011) Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome. Proc. Natl. Acad. Sci. U.S.A. 108, 1839-1844.
• Ruehle MD, Zhang H, Sheridan RM, Mitra S, Chen Y, Gonzalez RL, Cooperman BS, Kieft JS. A dynamic RNA loop in an IRES affects multiple steps of elongation factor-mediated translation initiation. Elife. 2015 Nov 2;4. PubMed PMID: 26523395
• Ruehle MD, Kieft JS. Molecular prejudice: RNA discrimination against purines allows response to a cellular alarm. Nat Struct Mol Biol. 2015 Oct;22(10):754-6. PubMed PMID: 26439636
• Kieft JS, Rabe JL, Chapman EG. New hypotheses derived from the structure of a flaviviral Xrn1-resistant RNA: Conservation, folding, and host adaptation. RNA Biol. 2015 Nov 2;12(11):1169-77. PubMed PMID: 26399159
• Kieft JS. Experiences gathered and lessons learned from 20 years of RNA structure. RNA. 2015 Apr;21(4):661-3. PubMed PMID: 25780181
• Colussi TM, Costantino DA, Zhu J, Donohue JP, Korostelev AA, Jaafar ZA, Plank TD, Noller HF, Kieft JS. Initiation of translation in bacteria by a structured eukaryotic IRES RNA. Nature. 2015 Mar 5;519(7541):110-3. PubMed PMID: 25652826
• Jaafar ZA, Oguro A, Nakamura Y, Kieft JS. Translation initiation by the hepatitis C virus IRES requires eIF1A and ribosomal complex remodeling. Elife. 2016 Dec 23;5. PubMed PMID: 28009256
• 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. PubMed PMID: 27934765
• Hussain T, Llácer JL, Wimberly BT, Kieft JS, Ramakrishnan V. Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation. Cell. 2016 Sep 22;167(1):133-144.e13. PubMed PMID: 27662086
• Filbin ME, Kieft JS. Linking ? to O: diverse and dynamic RNA-based mechanisms to regulate gene expression by 5'-to-3' communication. F1000Res. 2016 Aug 19;5. PubMed PMID: 27610229
• Hao Y, Kieft JS. Three-way junction conformation dictates self-association of phage packaging RNAs. RNA Biol. 2016 Jul 2;13(7):635-45. PubMed PMID: 27217219
• Akiyama BM, Eiler D, Kieft JS. Structured RNAs that evade or confound exonucleases: function follows form. Curr Opin Struct Biol. 2016 Feb;36:40-7. PubMed PMID: 26797676
• Batey RT, Kieft JS. Soaking Hexammine Cations into RNA Crystals to Obtain Derivatives for Phasing Diffraction Data. Methods Mol Biol. 2016;1320:219-32. PubMed PMID: 26227046
• Steckelberg AL, Vicens Q, Kieft JS. Exoribonuclease-Resistant RNAs Exist within both Coding and Noncoding Subgenomic RNAs. MBio. 2018 Dec 18;9(6). PubMed PMID: 30563900
• Vicens Q, Kieft JS, Rissland OS. Revisiting the Closed-Loop Model and the Nature of mRNA 5'-3' Communication. Mol Cell. 2018 Dec 6;72(5):805-812. PubMed PMID: 30526871
• Jaafar ZA, Kieft JS. Viral RNA structure-based strategies to manipulate translation. Nat Rev Microbiol. 2019 Jan;17(2):110-123. PubMed PMID: 30514982
• 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. 2018 Nov 29;9(1):5074. PubMed PMID: 30498211
• 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. 2018 Jun 19;115(25):6404-6409. PubMed PMID: 29866852
• MacFadden A, O'Donoghue Z, Silva PAGC, 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. 2018 Jan 9;9(1):119. PubMed PMID: 29317714
• Maricarmen Vallejos, Jules Deforges, Terra-Dawn M. Plank, Alejandro Letelier, Pablo Ramdohr1, Christopher G. Abraham, Fernando Valiente-Echeverría1, Jeffrey S. Kieft, Bruno Sargueil, and Marcelo López-Lastra (2011) Activity of the human immunodeficiency virus type 1 cell cycle dependent internal ribosomal entry site (IRES) is modulated by IRES trans-acting factors. Nucleic Acids Res, IN PRESS
• Redzic J.S., Armstrong G.S., Isern N.G., Jones D.N., Kieft J.S., Eisenmesser E.Z. 2011. The retinal specific CD147 Ig0 domain: from molecular structure to biological activity. J Mol Biol 411: 68-82.
• 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. PubMed PMID: 31427748
• 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. 2019 Mar 19;116(12):5514-5522. PubMed PMID: 30819901
• Jaafar ZA, Kieft JS. Viral RNA structure-based strategies to manipulate translation. Nat Rev Microbiol. 2019 Jan;17(2):110-123. PubMed PMID: 30514982
• Vallejos M., Deforges J., Plank T-D., Letelier A., Ramdohr P., Abraham C.G., Valiente-Echeverria F., Kieft J.S., Sargueil B., Lopez-Lastra M. 2011. Activity of the human immunodeficiency virus type 1 cell cycle-dependent internal ribosomal entry site is modulated by IRES trans-acting factors. Nucleic Acids Res 39: 6186-6200.
• Filbin, M.E. and Kieft, J.S. (2011) HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove. RNA 17: 1258-1273.
• Nichols PJ, Bevers S, Henen M, Kieft JS, Vicens Q, Vögeli B. Recognition of non-CpG repeats in Alu and ribosomal RNAs by the Z-RNA binding domain of ADAR1 induces A-Z junctions. Nat Commun. 2021 Feb 4;12(1):793. PubMed PMID: 33542240
• Sherlock ME, Hartwick EW, MacFadden A, Kieft JS. Structural diversity and phylogenetic distribution of valyl tRNA-like structures in viruses. RNA. 2021 Jan;27(1):27-39. PubMed PMID: 33008837
• Jones RA, Steckelberg AL, Vicens Q, Szucs MJ, Akiyama BM, Kieft JS. Different tertiary interactions create the same important 3D features in a distinct flavivirus xrRNA. RNA. 2021 Jan;27(1):54-65. PubMed PMID: 33004436
• Szucs MJ, Nichols PJ, Jones RA, Vicens Q, Kieft JS. A New Subclass of Exoribonuclease-Resistant RNA Found in Multiple Genera of Flaviviridae . mBio. 2020 Sep 29;11(5). PubMed PMID: 32994331
• Steckelberg AL, Vicens Q, Costantino DA, Nix JC, Kieft JS. The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold. RNA. 2020 Dec;26(12):1767-1776. PubMed PMID: 32848042
• Thulson E, Hartwick EW, Cooper-Sansone A, Williams MAC, Soliman ME, Robinson LK, Kieft JS, Mouzakis KD. An RNA pseudoknot stimulates HTLV-1 pro-pol programmed -1 ribosomal frameshifting. RNA. 2020 Apr;26(4):512-528. PubMed PMID: 31980578
• Akiyama, B.M., Graham, M.E., O’Donoghue, Z.G., Beckham, J.D. & Kieft, J.S. (2020) Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication. BioRxiv. [Preprint]. Available at: https://doi.org/10.1101/2020.09.17.300806. (Nucleic Acids Res., in revision).
• Bonilla, S., Sherlock, M.E., MacFadden, A., & Kieft, J.S. (2020) A structured viral RNA uses molecular mimicry and conformational dynamics to coordinate multiple functions. BioRxiv. [Preprint]. Available at: https://doi.org/10.1101/2020.09.18.302638 (Science, in revision).
• Langeberg, C.J., Sherlock, M.E., MacFadden, A., Kieft, J.S. An expanded class of histidine-accepting viral rRNA-like structures. bioRxiv 2020.12.02.408831; doi: https://doi.org/10.1101/2020.12.02.408831 (RNA, in revision)
• Eiler, D.R., Wimberly, B.T., Bilodeau, D.Y., Rissland, O.R., Kieft, J.S. The Giardia lamblia ribosome structure reveals divergences in translation and quality control pathways. BioRxiv. [Preprint]. Available at: 2020.09.30.321331; doi: https://doi.org/10.1101/2020.09.30.321331 (Cell Reports, in review)
• Franklin, A.N., MacFadden, A., Kieft, J.S., Hesselberth, J.R., & Chapman, E.G., Custom-designed, degraded-resistant messenger RNAs in yeast. BioRxiv. [Preprint]. Available at: https://doi.org/10.1101/2020.06.25.169177. (RNA Biology, in review)
• Balas, M.M., Hartwick, E.W., Barrington, C., Roberts, J.T., Wu, S.K., Bettcher, R., Griffin, A.M., Kieft, J.S., & Johnson, A.M. (2020) RNA matchmaking remodels lncRNA structure and promotes PRC2 activity. BioRxiv. [Preprint]. Available at: https://doi.org/10.1101/2020.04.13.040071. (Science Reports, in revision)
• Keel A.Y., Jha B.K., Kieft J.S.(2012)Structural architecture of an RNA that competitively inhibits RNase L. RNA 18:88-99
• Liu W, Jankowska-Anyszka M, Piecyk K, Dickson L, Wallace A, Niedzwiecka A, Stepinski J, Stolarski R, Darzynkiewicz E, Kieft J, Zhao R, Jones DN, Davis RE. (2011) Structural basis for nematode eIF4E binding an m(2,2,7)G-Cap and its implications for translation initiation. Nucleic Acids Res.39: 8820-8832.
• Plank TD, Kieft JS. (2012) The structures of nonprotein-coding RNAs that drive internal ribosome entry site function. Wiley Interdiscip Rev RNA. 3: 195-212
• Bonilla SL, Sherlock ME, MacFadden A, Kieft JS. A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure. Science. 2021 Nov 19;374(6570):955-960. PubMed PMID: 34793227
• Keel, A.Y., Jha, B.K., & Kieft, J.S. (2012) Structural architecture of an RNA that competitively inhibits RNase L. RNA 18, 88-99.
• Vicens Q, Kieft JS. Shared properties and singularities of exoribonuclease-resistant RNAs in viruses. Comput Struct Biotechnol J. 2021;19:4373-4380. PubMed PMID: 34471487
• Filbin, M.E. Vollmar, B. S., Shi, D., Gonen, T., & Kieft, J.S. (2013) HCV IRES manipulated the ribosome to promote the switch from translation to elongation. Nat Struct Mol Biol 20, 150-158.
• Plank, T-D. & Kieft, J.S. (2012) The structures of nonprotein-coding RNAs that drive internal ribosome entry site function. Wiley Interdiscip Rev RNA. 3, 195-212.
• Akiyama BM, Graham ME, O Donoghue Z, Beckham JD, Kieft JS. Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication. Nucleic Acids Res. 2021 Jul 9;49(12):7122-7138. PubMed PMID: 34133732
• Plank, T-D. M., Whitehurst, J.T. & Kieft, J.S. (2013) Cell type specificity and structural determinants of IRES activity from different HIV-1 transcripts Nucleic Acid Research, Accepted
• Balas MM, Hartwick EW, Barrington C, Roberts JT, Wu SK, Bettcher R, Griffin AM, Kieft JS, Johnson AM. Establishing RNA-RNA interactions remodels lncRNA structure and promotes PRC2 activity. Sci Adv. 2021 Apr;7(16). PubMed PMID: 33853770
• Wang, H., Ru, Y., Wang, X., Kieft, J.S. & Theodorescu, D. (2013) Translation initiation factor eIF3b expression in human cancer and its role in tumor growth and lung colonization. Clinical Cancer Research, Accepted
• Langeberg CJ, Sherlock ME, MacFadden A, Kieft JS. An expanded class of histidine-accepting viral tRNA-like structures. RNA. 2021 Jun;27(6):653-664. PubMed PMID: 33811147
• Nichols PJ, Bevers S, Henen M, Kieft JS, Vicens Q, Vögeli B. Recognition of non-CpG repeats in Alu and ribosomal RNAs by the Z-RNA binding domain of ADAR1 induces A-Z junctions. Nat Commun. 2021 Feb 4;12(1):793. PubMed PMID: 33542240
• Sherlock ME, Hartwick EW, MacFadden A, Kieft JS. Structural diversity and phylogenetic distribution of valyl tRNA-like structures in viruses. RNA. 2021 Jan;27(1):27-39. PubMed PMID: 33008837
• Jones RA, Steckelberg AL, Vicens Q, Szucs MJ, Akiyama BM, Kieft JS. Different tertiary interactions create the same important 3D features in a distinct flavivirus xrRNA. RNA. 2021 Jan;27(1):54-65. PubMed PMID: 33004436
• Llerena Cari E, Hagen-Lillevik S, Giornazi A, Post M, Komar AA, Appiah L, Bitler B, Polotsky AJ, Santoro N, Kieft J, Lai K, Johnson J. Integrated stress response control of granulosa cell translation and proliferation during normal ovarian follicle development. Mol Hum Reprod. 2021 Aug 7;27(8). PubMed PMID: 34314477
• Andrysik Z, Sullivan KD, Kieft JS, Espinosa JM. PPM1D suppresses p53-dependent transactivation and cell death by inhibiting the Integrated Stress Response. Nat Commun. 2022 Dec 1;13(1):7400. PubMed PMID: 36456590
• Rolband L, Beasock D, Wang Y, Shu YG, Dinman JD, Schlick T, Zhou Y, Kieft JS, Chen SJ, Bussi G, Oukhaled A, Gao X, Šulc P, Binzel D, Bhullar AS, Liang C, Guo P, Afonin KA. Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions. Comput Struct Biotechnol J. 2022;20:6120-6137. PubMed PMID: 36420155
• Park HJ, Gregory MA, Zaberezhnyy V, Goodspeed A, Jordan CT, Kieft JS, DeGregori J. Therapeutic resistance in acute myeloid leukemia cells is mediated by a novel ATM/mTOR pathway regulating oxidative phosphorylation. Elife. 2022 Oct 19;11. PubMed PMID: 36259537
• Bonilla SL, Kieft JS. The promise of cryo-EM to explore RNA structural dynamics. J Mol Biol. 2022 Sep 30;434(18):167802. PubMed PMID: 36049551
• Bonilla SL, Vicens Q, Kieft JS. Cryo-EM reveals an entangled kinetic trap in the folding of a catalytic RNA. Sci Adv. 2022 Aug 26;8(34):eabq4144. PubMed PMID: 36026457
• Khan YA, Loughran G, Steckelberg AL, Brown K, Kiniry SJ, Stewart H, Baranov PV, Kieft JS, Firth AE, Atkins JF. Evaluating ribosomal frameshifting in CCR5 mRNA decoding. Nature. 2022 Apr;604(7906):E16-E23. PubMed PMID: 35444316
• Vicens Q, Kieft JS. Thoughts on how to think (and talk) about RNA structure. Proc Natl Acad Sci U S A. 2022 Apr 26;119(17):e2112677119. PubMed PMID: 35439059