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*The following publications were made possible through the support of CRNA’s NIH NIAID grant #U54 AI170660-01:
2025
Banna HA, Berg K, Sadat T, Das NK, Paudel R, D'Souza V, Koirala D. Synthetic anti-RNA antibody derivatives for RNA visualization in mammalian cells. Nucleic Acids Res. 2025 Feb 8;53(4):gkae1275. doi: 10.1093/nar/gkae1275. PubMed Link
Chen YL, Reddy S, Suzuki A. Reversible and effective cell cycle synchronization method for studying stage-specific processes.
Life Sci Alliance. 2025 Mar 4;8(5):e202403000. doi: 10.26508/lsa.202403000. Print 2025 May. PubMed Link
Gonçalves-Carneiro D, Mastrocola E, Lei X, Bieniasz PD. Modulation of host gene expression by the zinc finger antiviral protein. Proc Natl Acad Sci U S A. 2025 Apr;122(13):e2420819122. doi: 10.1073/pnas.2420819122. Epub 2025 Mar 27. PubMed Link
Gc K, Lesko S, Emery A, Burnett C, Gopal K, Clark S, Swanstrom R, Sherer NM, Telesnitsky A, Kharytonchyk S. HIV-1 single-transcription start-site mutants display complementary replication functions that are restored by reversion. J Virol. 2025 Apr 15;99(4):e0213924. doi: 10.1128/jvi.02139-24. Epub 2025 Mar 4. PubMed Link
Grossman BD, Beyene BG, Tekle B, Sakowicz W, Ji X, Camacho JM, Vaishnav N, Ahmed A, Bhandari N, Desai K, Hardy J, Hollman NM, Marchant J, Summers MF. Optimized Preparation of Segmentally Labeled RNAs for NMR Structure Determination.
J Mol Biol. 2025 May 15;437(10):169073. doi: 10.1016/j.jmb.2025.169073. Epub 2025 Mar 5. PubMed Link
Hilber S, Attionu SK, Dayie TK, Kreutz C. Advances in Isotope Labeling for Solution Nucleic Acid Nuclear Magnetic Resonance Spectroscopy. Chempluschem. 2025 Apr 9:e2400752. doi: 10.1002/cplu.202400752. Online ahead of print. PubMed Link
Jin L, Zhou Y, Zhang S, Chen SJ. mRNA vaccine sequence and structure design and optimization: Advances and challenges.
J Biol Chem. 2025 Jan;301(1):108015. doi: 10.1016/j.jbc.2024.108015. Epub 2024 Nov 26. PubMed Link
Norman RX, Chen YC, Recchia EE, Loi J, Rosemarie Q, Lesko SL, Patel S, Sherer N, Takaku M, Burkard ME, Suzuki A. One step 4× and 12× 3D-ExM enables robust super-resolution microscopy of nanoscale cellular structures.
J Cell Biol. 2025 Feb 3;224(2):e202407116. doi: 10.1083/jcb.202407116. Epub 2024 Dec 3. PubMed Link
Ojha M, Hudson L, Photenhauer A, Zang T, Lerew L, Ekesan Ş, Daniels J, Nguyen M, Paudyal H, York DM, Ohi MD, Marchant J, Bieniasz PD, Koirala D. Structural Plasticity of RRE Stem-Loop II Modulates Nuclear Export of HIV-1 RNA.
bioRxiv [Preprint]. 2025 Feb 26:2025.02.20.639096. doi: 10.1101/2025.02.20.639096. PubMed Link
van der Toorn W, Bohn P, Liu-Wei W, Olguin-Nava M, Gribling-Burrer AS, Smyth RP, von Kleist M. Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing. Nat Commun. 2025 Apr 21;16(1):3742. doi: 10.1038/s41467-025-59102-9. PubMed Link
2024
Bohn JA, Meagher JL, Takata MA, Gonçalves-Carneiro D, Yeoh ZC, Ohi MD, Smith JL, Bieniasz PD. Functional anatomy of zinc finger antiviral protein complexes. Nat Commun. 2024 Dec 30;15(1):10834. doi: 10.1038/s41467-024-55192-z. PubMed Link
Chen YC, Kilic E, Wang E, Rossman W, Suzuki A. CENcyclopedia: Dynamic Landscape of Kinetochore Architecture Throughout the Cell Cycle. bioRxiv [Preprint]. 2024 Dec 5:2024.12.05.627000. doi: 10.1101/2024.12.05.627000. PubMed Link
Chen YL, Chen YC, Suzuki A. ImmunoCellCycle-ID - a high-precision immunofluorescence-based method for cell cycle identification. J Cell Sci. 2024 Nov 15;137(22):jcs263414. doi: 10.1242/jcs.263414. Epub 2024 Nov 20. PubMed Link
Eschbach JE, Puray-Chavez M, Mohammed S, Wang Q, Xia M, Huang L-C, Shan L, Kutluay SB. HIV-1 capsid stability and reverse transcription are finely balanced to minimize sensing of reverse transcription products via the cGAS-STING pathway. mBio. 2024 May 8;15(5):e0034824. doi: 10.1128/mbio.00348-24. Epub 2024 Mar 26. PubMed Link
Ghone D, Evans EL 3rd, Bandini M, Stephenson KG, Sherer NM, Suzuki A. HIV-1 Vif disrupts phosphatase feedback regulation at the kinetochore, leading to a pronounced pseudo-metaphase arrest. bioRxiv [Preprint]. 2024 Nov 25:2024.07.30.605839. doi: 10.1101/2024.07.30.605839.
Update in: Elife. 2025 Mar 13;13:RP101136. doi: 10.7554/eLife.101136. PubMed Link
Guerrero JF, Lesko SL, Evans EL, Sherer NM. Studying Retroviral Life Cycles Using Visible Viruses and Live Cell Imaging. Annu Rev Virol. 2024 Sep;11(1):125-146. doi: 10.1146/annurev-virology-100422-012608. Epub 2024 Aug 30. PubMed Link
Jin L, Zhang S, Song Z, Heng X, Chen SJ. Kinetic pathway of HIV-1 TAR cotranscriptional folding. Nucleic Acids Res. 2024 Jun 10;52(10):6066-6078. doi: 10.1093/nar/gkae362. PubMed Link
Levengood JD, Potoyan D, Penumutchu S, Kumar A, Zhou Q, Wang Y, Hansen AL, Kutluay S, Roche J, Tolbert BS. Thermodynamic coupling of the tandem RRM domains of hnRNP A1 underlie its pleiotropic RNA binding functions. Sci Adv. 2024 Jul 12;10(28):eadk6580. doi: 10.1126/sciadv.adk6580. Epub 2024 Jul 10. PubMed Link
Nichols Doyle R, Yang V, Kayode YI, Damoiseaux R, Taylor HE, Fregoso OI. NSC95397 Is a Novel HIV-1 Latency-Reversing Agent. Viruses. 2024 Nov 16;16(11):1783. doi: 10.3390/v16111783. PubMed Link
Su PA, Chang CH, Yen SB, Wu HY, Tung WJ, Hu YP, Chen YI, Lin MH, Shih C, Chen PJ, Tsai K. Epitranscriptomic cytidine methylation of the hepatitis B viral RNA is essential for viral reverse transcription and particle production.
Proc Natl Acad Sci U S A. 2024 Jun 11;121(24):e2400378121. doi: 10.1073/pnas.2400378121. Epub 2024 Jun 3.
Whitworth IT, Knoener RA, Puray-Chavez M, Halfmann P, Romero S, Baddouh M, Scalf M, Kawaoka Y, Kutluay SB, Smith LM, Sherer NM. Defining Distinct RNA-Protein Interactomes of SARS-CoV-2 Genomic and Subgenomic RNAs. J Proteome Res. 2024 Jan 5;23(1):149-160. doi: 10.1021/acs.jproteome.3c00506. Epub 2023 Dec 3. PubMed Link
Yasin S, Lesko SL, Kharytonchyk S, Brown JD, Chaudry I, Geleta SA, Tadzong NF, Zheng MY, Patel HB, Kengni G, Neubert E, Quiambao JMC, Becker G, Ghinger FG, Thapa S, Williams A, Radov MH, Boehlert KX, Hollmann NM, Singh K, Bruce JW, Marchant J, Telesnitsky A, Sherer NM, Summers MF. Role of RNA structural plasticity in modulating HIV-1 genome packaging and translation. Proc Natl Acad Sci U S A. 2024 Aug 13;121(33):e2407400121. doi: 10.1073/pnas.2407400121. Epub 2024 Aug 7. PubMed Link
Yeoh ZC, Meagher JL, Kang CY, Bieniasz PD, Smith JL, Ohi MD. A minimal complex of KHNYN and zinc-finger antiviral protein binds and degrades single-stranded RNA. Proc Natl Acad Sci U S A. 2024 Dec 24;121(52):e2415048121. doi: 10.1073/pnas.2415048121. Epub 2024 Dec 18. PubMed Link
Zhou Y, Chen SJ. Harnessing Computational Approaches for RNA-Targeted Drug Discovery. RNA Nanomed. 2024 Dec;1(1):1-15. doi: 10.59566/isrnn.2024.0101001.
2023
Behrens RT, Rajashekar JK, Bruce JW, Evans EL 3rd, Hansen AM, Salazar-Quiroz N, Simons LM, Ahlquist P, Hultquist JF, Kumar P, Sherer NM. Exploiting a rodent cell block for intrinsic resistance to HIV-1 gene expression in human T cells.
mBio. 2023 Oct 31;14(5):e0042023. doi: 10.1128/mbio.00420-23. Epub 2023 Sep 7. PubMed Link
Behrens RT, Sherer NM. Retroviral hijacking of host transport pathways for genome nuclear export. mBio. 2023 Dec 19;14(6):e0007023. doi: 10.1128/mbio.00070-23. Epub 2023 Nov 1. PubMed Link
Emery A, Joseph SB, Swanstrom R. Nonsuppressible viremia during HIV-1 therapy meets molecular virology.
J Clin Invest. 2023 Mar 15;133(6):e167925. doi: 10.1172/JCI167925. PubMed Link
Geng A, Ganser L, Roy R, Shi H, Pratihar S, Case DA, Al-Hashimi HM. An RNA excited conformational state at atomic resolution.
Nat Commun. 2023 Dec 19;14(1):8432. doi: 10.1038/s41467-023-43673-6. PubMed Link
Haslecker R, Pham VV, Glänzer D, Kreutz C, Dayie TK, D'Souza VM. Extending the toolbox for RNA biology with SegModTeX: a polymerase-driven method for site-specific and segmental labeling of RNA. Nat Commun. 2023 Dec 18;14(1):8422. doi: 10.1038/s41467-023-44254-3.
Hymon D, Martins J, Richter C, Sreeramulu S, Wacker A, Ferner J, Patwardhan NN, Hargrove AE, Schwalbe H. NMR 1H,19F-based screening of the four stem-looped structure 5_SL1-SL4 located in the 5'-untranslated region of SARS-CoV 2 RNA. RSC Med Chem. 2023 Nov 28;15(1):165-177. doi: 10.1039/d3md00322a. eCollection 2024 Jan 25. PubMed Link
Jin D, Zhu Y, Schubert HL, Goff SP, Musier-Forsyth K. HIV-1 Gag Binds the Multi-Aminoacyl-tRNA Synthetase Complex via the EPRS Subunit.
Viruses. 2023 Feb 8;15(2):474. doi: 10.3390/v15020474. PubMed Link
Ken ML, Roy R, Geng A, Ganser LR, Manghrani A, Cullen BR, Schulze-Gahmen U, Herschlag D, Al-Hashimi HM. RNA conformational propensities determine cellular activity. Nature. 2023 May;617(7962):835-841. doi: 10.1038/s41586-023-06080-x. Epub 2023 May 17. PubMed Link
Kharytonchyk S, Burnett C, Gc K, Telesnitsky A. Transcription start site heterogeneity and its role in RNA fate determination distinguish HIV-1 from other retroviruses and are mediated by core promoter elements. bioRxiv. 2023 May 22:2023.05.22.541776. doi: 10.1101/2023.05.22.541776. Preprint.
Lei X, Gonçalves-Carneiro D, Zang TM, Bieniasz PD. Initiation of HIV-1 Gag lattice assembly is required for recognition of the viral genome packaging signal. Elife. 2023 Jan 23;12:e83548. doi: 10.7554/eLife.83548. PubMed Link
Tang Y, Behrens RT, St Gelais C, Wu S, Vivekanandan S, Razin E, Fang P, Wu L, Sherer N, Musier-Forsyth K. Human lysyl-tRNA synthetase phosphorylation promotes HIV-1 proviral DNA transcription. Nucleic Acids Res. 2023 Dec 11;51(22):12111-12123. doi: 10.1093/nar/gkad941. PubMed Link
2022
Bevilacqua PC, Tolbert BS. Regulatory Mechanisms through RNA Conformational Switching and Dynamics. J Mol Biol. 2022 Sep 30;434(18):167794. doi: 10.1016/j.jmb.2022.167794. Epub 2022 Aug 18. PubMed PMID: 35988750; PubMed Link
Cai Z, Zafferani M, Akande OM, Hargrove AE. Quantitative Structure-Activity Relationship (QSAR) Study Predicts Small-Molecule Binding to RNA Structure. J Med Chem. 2022 May 26;65(10):7262-7277. doi: 10.1021/acs.jmedchem.2c00254. Epub 2022 May 6. PubMed Link
Chiu LY, Emery A, Jain N, Sugarman A, Kendrick N, Luo L, Ford W, Swanstrom R, Tolbert BS. Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for Differential Binding of hnRNP Splicing Auxiliary Factors.
J Mol Biol. 2022 Sep 30;434(18):167728. doi: 10.1016/j.jmb.2022.167728. Epub 2022 Jul 21.
Donlic A, Swanson EG, Chiu LY, Wicks SL, Juru AU, Cai Z, Kassam K, Laudeman C, Sanaba BG, Sugarman A, Han E, Tolbert BS, Hargrove AE. R-BIND 2.0: An Updated Database of Bioactive RNATargeting Small Molecules and Associated RNA Secondary Structures. ACS Chem Biol. 2022 Jun 17;17(6):1556-1566. doi: 10.1021/acschembio.2c00224. Epub 2022 May 20. PubMed Link
Gonçalves-Carneiro D, Mastrocola E, Lei X, DaSilva J, Chan YF, Bieniasz PD. Rational attenuation of RNA viruses with zinc finger antiviral protein. Nat Microbiol. 2022 Oct;7(10):1558-1567. doi: 10.1038/s41564-022-01223-8. Epub 2022 Sep 8. PubMed Link
Shema Mugisha C, Dinh T, Kumar A, Tenneti K, Eschbach JE, Davis K, Gifford R, Kvaratskhelia M, Kutluay SB. Emergence of Compensatory Mutations Reveals the Importance of Electrostatic Interactions between HIV-1 Integrase and Genomic RNA. mBio. 2022 Oct 26;13(5):e0043122. doi: 10.1128/mbio.00431-22. Epub 2022 Aug 17. PubMed Link
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