Princeton publications:
51. Activity-based profiling of bacterial RNA-modifying enzymes reveals species-specific 5-methyluridine modification in Bacillus subtilis 23S rRNA. Jaber, Q.Z.; Yu, N.J.; Masuda, I. Hou, Y.M.; Kleiner, R.E. Proc. Natl. Acad. Sci. USA (2026) https://doi.org/10.1073/pnas.2613881123 web
50. Quantitative profiling of RNA modifications enriched in non-membrane-bound cellular structures using APEX-RNA-MS. Seo, K.W.; Dhingani, D.Y.; Kleiner, R. E. Cell Chem. Biol. (2026) in press web
49. Structure of ergosteryl-aspartate synthase reveals how an entrapped tRNA is used like a prosthetic swinging arm in the synthesis of aminoacylated sterols. Murayama, H.; Yakobov, N.; Mahmoudi, N.; Legrosdidier, S.; Fournier, N.; Zuttion, S.; Matsumoto, K.; Nishimura, M.; Ji, J.; Senger, B.; Huck, L.; Gamper, H.B.; Kise, Y.; Kleiner, R.E.; Frechin, M.; Hou, Y.M.; Becker, H.D.; Itoh, Y.; Fischer, F.; Nureki, O. Nat. Commun. (2026) 17, 4455 web
48. Metabolism of epigenetic ribonucleosides leads to nucleolar stress and cytotoxicity. Sun, X.; Donlic, A.; Boyer, J.A.; Press, T.E.; Kim, M.; Reddy, N.K.; Brangwynne, C.P.; Rabinowitz, J.D.; Kleiner, R.E. ACS Chem. Biol. (2026) 21, 446 web
47. Targeted RNA editing by direct delivery of an adenosine deaminase-antisense oligo conjugate. Eggert, T.W.; Dhingani, D.Y.; Kleiner, R. E. bioRxiv (2025) https://doi.org/10.1101/2025.07.11.664364 web
46. Amino acid changes in two viral proteins drive attenuation of the yellow fever 17D vaccine. Zhang, J.; Chavez, E.C.; Winkler, M.; Liu, J.; Carver, S.; Lin, A.E.; Biswas, A.; Tamura, T.; Tseng, A.; Wang, D.; Benhamou, A.; O’Connell, A.K.; Matsuo, M.; Norton, J.E.; Kenney, D.; Adamson, B.; Kleiner, R.E.; Burwitz, B.; Crossland, N.A.; Douam, F.; Ploss, A. Nat. Microbiol. (2025) 10, 1902 web
45. Dynamic regulation of 5-formylcytidine on tRNA. Sun, X.; Kleiner, R.E. ACS Chem. Biol. (2025) 20:907-916 web
44. Genome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes. Nakano, Y.; Gamper, H.; McGuigan, H.; Maharjan, S.; Li, J.; Sun, Z.; Yigit, E.; Grunberg, S.; Krishnan, K.; Li, N.S.; Piccirilli, J.A.; Kleiner, R.E.; Nichols, N.; Gregory, B.D.; Hou, Y.M. Nat. Commun. (2025) 16, 1047 web
43. Drugging the Epitranscriptome in RNA as a Drug Target: The Next Frontier for Medicinal Chemistry. Eggert, T.W.; Kleiner, R.E. Chpt. 12, pg 321-354. Wiley (2024) web
42. Global characterization of RNA modifying enzymes with RNA-mediated activity-based protein profiling (RNABPP). Yu, N.J.; Jaber, Q.Z.; Kleiner, R.E. Methods Enzymol. (2024) 705: 111-125 web
41. Introduction to The Epitranscriptome. Kleiner, R.E.; Hobartner, C.; Jia, G. RSC Chem. Biol. (2024) 5:271-271 web
40. The impact of epitranscriptomic modifications on liver disease. Berggren, K.A.; Schwartz, R.E.; Kleiner, R.E.; Ploss, A. Trends Endocrinol. Metab. (2024) web
39. Sequence- and structure-specific tRNA dihydrouridylation by hDUS2. Ji, J.; Yu, N.J.; Kleiner, R.E. ACS Cent. Sci. (2024) 10: 803-812 web
38. Cell type-specific translational regulation by human DUS enzymes. Yu, N.J.; Dai, W.; Li, A.; He, M.; Kleiner, R.E. bioRxiv (2023) web
37. Transcriptome-wide RNA structure probing with temporal resolution. Wang, D.; Tang, Y.; Li, A.; Sun, L.; Kleiner, R.E. bioRxiv (2023) web
36. Chemoproteomic profiling of 8-oxoguanosine-sensitive RNA-protein interactions.
Villers, J.; McCann Smith, E.; DeLiberto, A.N.; Arguello, A.E.; Nyaanga, J.; Kleiner, R.E. Biochemistry (2023), 62:3411-3419. web
35. Chemoproteomic approaches to studying RNA modification-associated proteins.
Dai, W.; Yu, N.J.; Kleiner R.E. Acc. Chem. Res. (2023), 56:2726-2739. web
34. Viscoelasticity and advective flow of RNA underlies nucleolar form and function.
Riback, J.A.; Eeftens, J.M.; Lee, D.S.W.; Quinodoz, S.A.; Donlic, A.; Orlovsky, N.; Wiesner, L,; Beckers, L.; Becker, L.A.; Strom, A.R.; Rana, U.; Tolbert, M.; Purse, B.W.; Kleiner, R.E.; Kriwacki, R.; Brangwynne, C.P. Mol. Cell (2023), 83:3095-3107.e9. web
33. Chemical approaches to investigate post-transcriptional RNA regulation.
Kleiner, R. E. ACS Chem. Biol. (2023), 18:1684-1697. web
32. Inhibition of nucleolar transcription by oxaliplatin involves ATM/ATR kinase signaling.
Nechay, M.; Wang, D.; Kleiner, R.E. Cell Chem. Biol. (2023), 30:906-919.e4. web
31. Profiling dynamic RNA-protein interactions using small molecule-induced RNA editing.
Seo, K.W.; Kleiner, R.E. Nat. Chem. Biol. (2023), 19:1361-1371. web
30. Global Discovery of Covalent Modulators of Ribonucleoprotein Granules.
Ciancone, A.M.*; Seo, K.W.*; Chen, M.*; Borne, A.L.; Libby, A.H.; Bai, D.L.; Kleiner, R.E.*; Hsu*, K.L. J. Am. Chem. Soc. (2023), 145:11056-11066. web
29. Tracking chromatin state changes using nanoscale photo-proximity labeling.
Seath, C.P.*; Burton, A.J.*; Sun, X.; Lee, G.; Kleiner, R.E.; MacMillan, D.W.C.*; Muir, T.W.* Nature (2023), 616:574-580. web
28. Live-cell RNA imaging with metabolically incorporated fluorescent nucleosides.
Wang, D.; Shalamberidze, A.; Arguello, A.E.; Purse, B. Kleiner, R.E. J. Am. Chem. Soc. (2022), 144:14647-14656. web
27. Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases.
Arguello, A.E.; Li, A.; Sun, X.; Eggert, T.W.; Mairhofer, E.; Kleiner, R.E. Nat. Commun. (2022), 13:4176. web
26. Chemical Method to Sequence 5-Formylcytosine on RNA.
Li, A.; Sun, X.; Arguello, A.E.; Kleiner, R.E. ACS Chem. Biol. (2022), 17:503-508. web
25. Interrogating the Transcriptome with Metabolically Incorporated Ribonucleosides.
Kleiner, R.E. Mol. Omics. (2021), 17:833-41. web
24. Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated dihydrouridylation.
Dai, W.; Li, A.; Yu, N.J.; Nguyen, T.; Leach, R.W.; Wuhr, M.; Kleiner, R.E. Nat. Chem. Biol. (2021), 17:1178-87. web
Highlighted in:
“Activity-based profiling in RNA” Nat. Chem. Biol. (2021), 17:1121-22. web
23. A neural m6A/Ythdf pathway is required for learning and memory in Drosophila.
Kan, L.; Ott, S.; Joseph, B.; Park, E.S.; Dai, W.; Kleiner, R.E.; Claridge-Chang, A.; Lai, E.C. Nat. Commun. (2021), 12:1458. web
22. Mechanisms of Epitranscriptomic Gene Regulation.
Seo, K.W.; Kleiner, R.E. Biopolymers (2020) doi: 10.1002/bip.23403 web
21. Cell- and Polymerase-Selective Metabolic Labeling of Cellular RNA with 2′-Azidocytidine.
Wang, D.; Zhang, Y.; Kleiner, R.E. J. Am. Chem. Soc. (2020), 142:14417-14421. web
20. YTHDF2 recognition of N1-methyladenosine (m1A)-modified RNA is associated with transcript destabilization.
Seo, K. W.; Kleiner, R. E. ACS Chem. Biol. (2020), 15(1): 132-139. web
19. High-throughput approaches to profile RNA-protein interactions.
Nechay, M.; Kleiner, R. E. Curr. Opin. Chem. Biol. (2019), 54:37-44. web
18. In Vitro Selection with a Site-Specifically Modified RNA Library Reveals the Binding Preferences of N6-Methyladenosine Reader Proteins.
Arguello, A. E.; Leach, R. W.; Kleiner, R. E. Biochemistry (2019), 58:3386-3395. web
17. A Metabolic Engineering Approach to Incorporate Modified Pyrimidine Nucleosides into Cellular RNA.
Zhang, Y.; Kleiner, R.E. J. Am. Chem. Soc. (2019), 141:3347-3351. web
16. A Photocrosslinking-Based RNA Chemical Proteomics Approach to Profile m6 A-Regulated Protein-RNA Interactions.
Arguello, A.E.; Srikumar, T; Kleiner, R.E. Curr. Protoc. Nucleic Acid Chem. (2018), 75(1). web
15. RNA Chemical Proteomics Reveals the N6-Methyladenosine (m6A)-Regulated Protein-RNA Interactome.
Arguello, A. E.; DeLiberto, A. N.; Kleiner, R. E. J. Am. Chem. Soc. (2017), 139:17249–17252. web
JACS Spotlight: Photo-cross-linking Finds Partners of a Widespread RNA Modification
14. Reading the RNA Code
Kleiner, R. E. Biochemistry (2017), 57:11–12. web
PhD and Postdoc publications:
13. A Chemical Proteomics Approach to Reveal Direct Protein-Protein Interactions in Living Cells
Kleiner, R. E.; Hang, L. E.; Molloy, K. R.; Chait, B. T.; Kapoor, T. M. Cell Chem. Biol. (2017) 25 (1), 110-120.e3. web
12. Structural and Biochemical Basis for Intracellular Kinase Inhibition by Src-specific Peptidic Macrocycles
Aleem, S. U.*; Georghiou, G.*; Kleiner, R. E.*; Guja, K. E.; Craddock, B. P.; Lyczek, A.; Chan, A. I.; Garcia-Diaz, M.; Miller, W. T.; Liu, D. R.; Seeliger, M. A. Cell Chem. Biol. 23, 1103-1112 (2016).
11. Mutations in Human Tubulin Proximal to the Kinesin-Binding Site Alter Dynamic Instability at Microtubule Plus- and Minus-Ends
Ti, S. C.; Pamula, M. C.; Howes, S. C.; Duellberg, C.; Cade, N. I.; Kleiner, R. E.; Forth, S.; Surrey, T.; Nogales, E.; Kapoor, T. M. Cell 4, 72-84 (2016).
10. Chemical Proteomics Reveals a γH2AX-53BP1 Interaction in the DNA Damage Response
Kleiner, R. E.; Verma, P.; Molloy, K. R.; Chait, B. T.; Kapoor, T. M. Nat. Chem. Biol. 10, 807-814 (2015).
9. Anti-Diabetic Activity of Insulin-Degrading Enzyme Inhibitors Mediated by Multiple Hormones
Maianti, J. P.; McFedries, A.; Foda, Z. H.; Kleiner, R. E.; Du, X.; Lessring, M.; Tang, W.; Charron, M. J.; Seeliger, M. A.; Saghatelian, A.; Liu, D. R. Nature 511, 94-98 (2014).
8. Bumping Up Kinase Activity with an ATP-Derived Neo-Substrate
Kleiner, R. E.; Kapoor, T. M. Cell 154, 716-718 (2013).
7. Site-Specific Chemistry on the Microtubule Polymer
Kleiner, R. E.; Ti, S. C.; Kapoor, T. M. J. Am. Chem. Soc. 135, 12520-12523 (2013).
6. Highly specific, bisubstrate-competitive Src inhibitors from DNA-templated macrocycles
Georghiou, G.*; Kleiner, R. E.*; Pulkoski-Gross, M.; Liu, D. R.; Seeliger, M. A. Nat. Chem. Biol. 8, 366-374 (2012).
5. Small-Molecule Discovery from DNA-Encoded Chemical Libraries
Kleiner, R. E.*; Dumelin, C. E.*; Liu, D. R. Chem. Soc. Rev. 40, 5707-5717 (2011).
4. In Vitro Selection of a DNA-Templated Small-Molecule Library Reveals a Class of Macrocyclic Kinase Inhibitors
Kleiner, R. E.; Dumelin, C. E.; Tiu, G. C.; Sakurai, K.; Liu, D. R. J. Am. Chem. Soc. 132, 11779-11791 (2010).
3. An In Vitro Translation, Selection and Amplification System for Peptide Nucleic Acid
Brudno, Y.; Birnbaum, M. E.; Kleiner, R. E.; Liu, D. R. Nat. Chem. Biol. 6, 148-155 (2010).
2. DNA-Templated Polymerization of Side-Chain-Functionalized Peptide Nucleic Acid Aldehydes
Kleiner, R. E.; Brudno, Y.; Birnbaum, M. E.; Liu, D. R. J. Am. Chem. Soc. 130, 4646-4659 (2008).
1. An Intein-Based Genetic Selection Enables Construction of a High-Quality Library of Binary Patterned De Novo Sequences
Bradley, L. H.; Kleiner, R. E.; Wang, A. F.; Hecht, M. H.; Wood, D.W. Protein Eng. Des. Sel. 18, 201-207 (2005).