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RNA

  • 1.
    King S, Singh M. Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. PLoS Comput Biol. 2023;19(3):e1010966. PMCID: PMC10035887
    Reference Link
  • 1.
    Wang D, Shalamberidze A, Arguello E, Purse B, Kleiner R. Live-Cell RNA Imaging with Metabolically Incorporated Fluorescent Nucleosides. J Am Chem Soc. 2022;144(32):14647–14656. PMCID: PMC9940818
    Reference Link
  • 1.
    Arguello E, Li A, Sun X, Eggert T, Mairhofer E, Kleiner R. Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases. Nat Commun. 2022;13(1):4176. PMCID: PMC9296451
    Reference Link
  • 1.
    Li A, Sun X, Arguello E, Kleiner R. Chemical Method to Sequence 5-Formylcytosine on RNA. ACS Chem Biol. 2022;17(3):503–508. PMCID: PMC9357364
    Reference Link
  • 1.
    Kleiner R. Interrogating the transcriptome with metabolically incorporated ribonucleosides. Mol Omics. 2021;17(6):833–841. PMCID: PMC8648987
    Reference Link
  • 1.
    Chen P, Hussmann J, Yan J, Knipping F, Ravisankar P, Chen P-F, Chen C, Nelson J, Newby G, Sahin M, Osborn M, Weissman J, Adamson B, Liu D. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell. 2021;184(22):5635–5652.e29. PMCID: PMC8584034
    Reference Link
  • 1.
    Dai W, Li A, Yu N, Nguyen T, Leach R, Wühr M, Kleiner R. Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated dihydrouridylation. Nat Chem Biol. 2021;17(11):1178–1187. PMCID: PMC8551019
    Reference Link
  • 1.
    Etzion-Fuchs A, Todd D, Singh M. dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. Nucleic Acids Res. 2021;49(13):e78. PMCID: PMC8287948
    Reference Link
  • 1.
    Moore R, Kaletsky R, Lesnik C, Cota V, Blackman E, Parsons L, Gitai Z, Murphy C. The role of the Cer1 transposon in horizontal transfer of transgenerational memory. Cell. 2021;184(18):4697–4712.e18. PMCID: PMC8812995
    Reference Link
  • 1.
    Moore R, Kaletsky R, Murphy C. Protocol for transgenerational learned pathogen avoidance behavior assays in . STAR Protoc. 2021;2(1):100384. PMCID: PMC7960678
    Reference Link
  • 1.
    Seo K, Kleiner R. Mechanisms of epitranscriptomic gene regulation. Biopolymers. 2021;112(1):e23403. PMCID: PMC7855325
    Reference Link
  • 1.
    Wang D, Zhang Y, Kleiner R. Cell- and Polymerase-Selective Metabolic Labeling of Cellular RNA with 2’-Azidocytidine. J Am Chem Soc. 2020;142(34):14417–14421. PMCID: PMC7720414
    Reference Link
  • 1.
    Chen H, Gregor T. Using RNA Tags for Multicolor Live Imaging of Chromatin Loci and Transcription in Drosophila Embryos. Methods Mol Biol. 2020;2166:373–384. PMCID: PMC8130451
    Reference Link
  • 1.
    Trcek T, Douglas T, Grosch M, Yin Y, Eagle W, Gavis E, Shroff H, Rothenberg E, Lehmann R. Sequence-Independent Self-Assembly of Germ Granule mRNAs into Homotypic Clusters. Mol Cell. 2020;78(5):941–950.e12. PMCID: PMC7325742
    Reference Link
  • 1.
    Garcia D, Leach R, Wadsworth G, Choudhary K, Li H, Aviran S, Kim H, Zakian V. Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP. Nat Commun. 2020;11(1):2173. PMCID: PMC7195438
    Reference Link
  • 1.
    Sanders D, Kedersha N, Lee D, Strom A, Drake V, Riback J, Bracha D, Eeftens J, Iwanicki A, Wang A, Wei M-T, Whitney G, Lyons S, Anderson P, Jacobs W, Ivanov P, Brangwynne C. Competing Protein-RNA Interaction Networks Control Multiphase Intracellular Organization. Cell. 2020;181(2):306–324.e28. PMCID: PMC7816278
    Reference Link
  • 1.
    Nechay M, Kleiner R. High-throughput approaches to profile RNA-protein interactions. Curr Opin Chem Biol. 2020;54:37–44. PMCID: PMC7131871
    Reference Link
  • 1.
    Kobren S, Singh M. Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions. Nucleic Acids Res. 2019;47(2):582–593. PMCID: PMC6344845
    Reference Link
  • 1.
    Nogalski M, Solovyov A, Kulkarni A, Desai N, Oberstein A, Levine A, Ting D, Shenk T, Greenbaum B. A tumor-specific endogenous repetitive element is induced by herpesviruses. Nat Commun. 2019;10(1):90. PMCID: PMC6327058
    Reference Link
  • 1.
    Arguello E, Srikumar T, Kleiner R. A Photocrosslinking-Based RNA Chemical Proteomics Approach to Profile m A-Regulated Protein-RNA Interactions. Curr Protoc Nucleic Acid Chem. 2018;75(1):e69. PMID: 30408339
    Reference Link
  • 1.
    Dine E, Gil A, Uribe G, Brangwynne C, Toettcher J. Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli. Cell Syst. 2018;6(6):655–663.e5. PMCID: PMC6023754
    Reference Link
  • 1.
    Kleiner R. Reading the RNA Code. Biochemistry. 2018;57(1):11–12. PMID: 28937209
    Reference Link
  • 1.
    Arguello E, DeLiberto A, Kleiner R. RNA Chemical Proteomics Reveals the N-Methyladenosine (mA)-Regulated Protein-RNA Interactome. J Am Chem Soc. 2017;139(48):17249–17252. PMID: 29140688
    Reference Link
  • 1.
    Dine E, Toettcher J. Optogenetic Reconstitution for Determining the Form and Function of Membraneless Organelles. Biochemistry. 2018;57(17):2432–2436. PMCID: PMC5972035
    Reference Link
  • 1.
    Yin P, Deng D, Yan C, Pan X, Xi J, Yan N, Shi Y. Specific DNA-RNA hybrid recognition by TAL effectors. Cell Rep. 2012;2(4):707–13. PMID: 23022487
    Reference Link
  • 1.
    Yin P, Li Q, Yan C, Liu Y, Liu J, Yu F, Wang Z, Long J, He J, Wang H-W, Wang J, Zhu J-K, Shi Y, Yan N. Structural basis for the modular recognition of single-stranded RNA by PPR proteins. Nature. 2013;504(7478):168–71. PMID: 24162847
    Reference Link
  • 1.
    Wang X, Paucek R, Gooding A, Brown Z, Ge E, Muir T, Cech T. Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA. Nat Struct Mol Biol. 2017;24(12):1028–1038. PMCID: PMC5771497
    Reference Link
  • 1.
    Webb C, Zakian V. Telomerase RNA is more than a DNA template. RNA Biol. 2016;13(8):683–9. PMCID: PMC4993324
    Reference Link
  • 1.
    Tamayo J, Teramoto T, Chatterjee S, Hall T, Gavis E. The Drosophila hnRNP F/H Homolog Glorund Uses Two Distinct RNA-Binding Modes to Diversify Target Recognition. Cell Rep. 2017;19(1):150–161. PMCID: PMC5392723
    Reference Link
  • 1.
    Sanders D, Brangwynne C. Neurodegenerative disease: RNA repeats put a freeze on cells. Nature. 2017;546(7657):215–216. PMID: 28562583
    Reference Link
  • 1.
    Son H, Seo M, Ham S, Hwang W, Lee D, An S, Artan M, Seo K, Kaletsky R, Arey R, Ryu Y, Ha C, Kim Y, Murphy C, Roh T-Y, Nam H, Lee S-J. RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans. Nat Commun. 2017;8:14749. PMCID: PMC5347137
    Reference Link
  • 1.
    Taylor N, Elbaum-Garfinkle S, Vaidya N, Zhang H, Stone H, Brangwynne C. Biophysical characterization of organelle-based RNA/protein liquid phases using microfluidics. Soft Matter. 2016;12(45):9142–9150. PMCID: PMC6724727
    Reference Link
  • 1.
    López-Panadès E, Gavis E, Casacuberta E. Specific Localization of the Drosophila Telomere Transposon Proteins and RNAs, Give Insight in Their Behavior, Control and Telomere Biology in This Organism. PLoS One. 2015;10(6):e0128573. PMCID: PMC4467039
    Reference Link
  • 1.
    Webb C, Zakian V. Telomerase RNA stem terminus element affects template boundary element function, telomere sequence, and shelterin binding. Proc Natl Acad Sci U S A. 2015;112(36):11312–7. PMCID: PMC4568702
    Reference Link
  • 1.
    Webb C, Zakian V. Telomere les(i/s)ons from a telomerase RNA mutant. Cell Cycle. 2015;14(24):3769–70. PMCID: PMC4825745
    Reference Link
  • 1.
    Svenningsen S, Tu K, Bassler B. Gene dosage compensation calibrates four regulatory RNAs to control Vibrio cholerae quorum sensing. EMBO J. 2009;28(4):429–39. PMCID: PMC2632942
    Reference Link

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