Selected Publications:
Berríos KN, Barka A, Gill J, Serrano JC, Bailer PF, Parker JB, Evitt NH, Gajula KS, Shi J, Kohli RM. Cooperativity between Cas9 and hyperactive AID establishes broad and diversifying mutational footprints in base editors. Nucleic Acids Res. 2024 Feb 28. doi: 10.1093/nar/gkae024. (PMID: 38261989)
Lee SM, Loo CE, Prasasya RD, Bartolomei MS, Kohli RM, Zhou W. Low-input and single-cell methods for Infinium DNA methylation BeadChips. Nucleic Acids Res. 2024 Feb 26. doi: 10.1093/nar/gkae127. Epub ahead of print. (PMID: 38407446)
Medina-Munoz HC, Kofman E, Jagannatha P, Boyle EA, Yu T, Jones KL, Mueller JR, Lykins GD, Doudna AT, Park SS, Blue SM, Ranzau BL, Kohli RM, Komor AC, Yeo GW. Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies. Nat Commun. 2024 Jan 29. doi: 10.1038/s41467-024-45009-4. (PMID: 38287010)
Sroka MW, Skopelitis D, Vermunt MW, Preall JB, El Demerdash O, de Almeida LMN, Chang K, Utama R, Gryder B, Caligiuri G, Ren D, Nalbant B, Milazzo JP, Tuveson DA, Dobin A, Hiebert SW, Stengel KR, Mantovani R, Khan J, Kohli RM, Shi J, Blobel GA, Vakoc CR. Myo-differentiation reporter screen reveals NF-Y as an activator of PAX3-FOXO1 in rhabdomyosarcoma. Proc Natl Acad Sci USA. 2023 Sep 5. doi: 10.1073/pnas.2303859120. Epub 2023 Aug 28. (PMID: 37639593)
Fabyanic EB, Hu P, Qiu Q, Berríos KN, Connolly DR, Wang T, Flournoy J, Zhou Z, Kohli RM, Wu H. Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects. Nat Biotechnol. 2023 Aug 28. doi: 10.1038/s41587-023-01909-2 (PMID: 37640946)
Loo CE, Hix MA, Wang T, Cisneros GA, Kohli RM. Revealing Drivers for Carboxy-S-adenosyl-l-methionine Use by Neomorphic Variants of a DNA Methyltransferase. ACS Chem Biol. 2023 Jun 28. doi: 10.1021/acschembio.3c00184. Epub 2023 Jun 15. (PMID: 37379458)
Barka A, Kohli RM, Shi J. CRISPR tiling screen reveals cancer epigenetic ‘Goldilocks’ state. Trends Pharmacol Sci. 2023 Sept;44(9):555-557. doi: 10.1016/j.tips.2023.05.007. Epub 2023 Jun 14. (PMID: 37328396)
Wang T, Fowler JM, Liu L, Loo CE, Luo M, Schutsky EK, Berríos KN, DeNizio JE, Dvorak A, Downey N, Montermoso S, Pingul BY, Nasrallah M, Gosal WS, Wu H, Kohli RM. Direct enzymatic sequencing of 5-methylcytosine at single-base resolution. Nat Chem Biol. 2023 Aug;19(8):1004-1012. doi: 10.1038/s41589-023-01318-1. Epub 2023 Jun 15. (PMID: 37322153)
Zhang Z, Baxter AE, Ren D, Qin K, Chen Z, Collins SM, Huang H, Komar CA, Bailer PF, Parker JB, Blobel GA, Kohli RM, Wherry EJ, Berger SL, Shi J. Efficient engineering of human and mouse primary cells using peptide-assisted genome editing. Nat Biotechnol. 2023 APr 24. doi: 10.1038/s41587-023-01756-1. Online ahead of print. (PMID: 37095348)
Cory MB, Jones CM, Shaffer KD, Venkatesh Y, Giannakoulias S, Perez RM, Lougee MG, Hummingbird E, Pagar VV, Hurley CM, Li A, Mach RH, Kohli RM, Petersson EJ. FRETing About the Details: Case studies in the use of a genetically encoded fluorescent amino acid for distance-dependent energy transfer. Protein Sci. 2023 Mar 28:e4633 doi: 10.1002/pro.4633. Online ahead of print. (PMID: 36974585)
Kohli RM, Isaacs SN. Mpox Evolution: Has the Current Outbreak Revealed a Pox on “U”? J Infect Dis. 2023 Mar 28; 227(6):828-830. doi: 10.1093/infdis/jiac471. (PMID: 36481811)
Serrano JC, von Trentini D, Berríos KN, Barka A, Dmochowski IJ, Kohli RM. Structure-Guided Design of a Potent and Specific Inhibitor against the Genomic Mutator APOBEC3A. ACS Chem Biol. 2022 Dec 8. doi:10.1021/acschembio.2c00796. Online ahead of print. (PMID: 36475588)
Cory MB, Li A, Hurley CM, Hostetler ZM, Venkatesh Y, Jones CM, Petersson EJ, Kohli RM. Engineered RecA Constructs Reveal the Minimal SOS Activation Complex. Biochemistry. 2022 Dec 6. doi: 10.1021/acs.biochem.2c00505. Online ahead of print. (PMID: 36473084)
Lee IK, Jacome DA, Cho JK, Tu V, Young AJ, Dominguez T, Northrup JD, Etersque JM, Lee HS, Ruff A, Aklilu O, Bittinger K, Glaser LJ, Dorgan D, Hadjiliadis D, Kohli RM, Mach RH, Mankoff DA, Doot RK, Sellmyer MA. Imaging sensitive and drug-resistant bacterial infection with [11C]-trimethoprim. J Clin Invest. 2022 Sep 15; 132(18):e156679. doi:10.1172/JCI156679. (PMID: 36106638)
Yeaton A, Cayanan G, Loghavi S, Dolgalev I, Leddin EM, Loo CE, Torabifard H, Nicolet D, Wang J, Corrigan K, Paraskevopoulou V, Starczynowski DT, Wang E, Abdel-Wahab O, Viny AD, Stone RM, Byrd JC, Buryanova OA, Kohli RM, Cisneros GA, Tsirigos A, Eisfeld AK, Aifantis I, Guillamot M. The impact of inflammation-induced tumor plasticity during myeloid transformation. Cancer Discov. 2022 Aug 4; CD-21-1146. doi: 10.1158/2159-8290.CD-21-1146. (PMID: 35924979)
Jaramillo AVC, Cory MB, Li A, Kohli RM, Wuest WM. Exploration of Inhibitors of the Bacterial LexA Repressor-Protease. Bioorg Med Chem Lett. 2022 Jun 1; 65:128702. doi:10.1016/j.bmcl.2022.128702. (Epub ahead of print). (PMID: 35351585)
Cory MB, Hostetler ZM, Kohli RM. Kinetic dissection of macromolecular complex formation with minimally perturbing fluorescent probes. Methods Enzymol. 2022; 664:151-171. doi: 10.1016/bs.mie.2022.01.009. (Epub 2022 Jan 29). (PMID: 35331372)
Barka A, Berríos KN, Bailer P, Schutsky EK, Wang T, Kohli RM. The Base-Editing Enzyme APOBEC3A Catalyzes Cytosine Deamination in RNA with Low Proficiency and High Selectivity. ACS Chem Biol. 2022 Mar 18; 17(3): 629-636. doi: 10.1021/acschembio.1c009919. (PMID: 35262324)
Wu MJ, Shi L, Dubrot J, Merritt J, Vijay V, Wei TY, Kessler E, Olander KE, Adil R, Pankaj A, Tummala KS, Weeresekara V, Zhen Y, Wu Q, Luo M, Shen W, Garcia-Beccaria M, Fernandez-Vaquero M, Hudson C, Ronseaux S, Sun Y, Saad-Berreta R, Jenkins RW, Wang T, Heikenwalder M, Ferrone CR, Goyal L, Nicolay B, Deshpande V, Kohli RM, Zheng H, Manguso RT, Bardeesy N. Mutant-IDH inhibits interferon-TET2 signaling to promote immunoevasion and tumor maintenance in cholangiocarcinoma. Cancer Discov. 2022 Mar 1; 12(3): 812-835. doi: 10.1158/2159-8290.CD-21-1077. (PMID: 34848557)
Berríos KN, Evitt NH, Deweerd RA, Ren D, Luo M, Barka A, Wang T, Bartman CR, Lan Y, Green AM, Shi J, Kohli RM. Controllable genome editing with split-engineered base editors. Nat. Chem Biol. 2021 Oct 18. doi: 10.1038/s41589-021-00880-w (Epub ahead of print) (PMID: 34663942)
Wang T, Loo CE, Kohli RM. Enzymatic approaches for profiling cytosine methylation and hydroxymethylation. Mol Metab. 2022 Mar; 57:101314. doi: 10.1016/j.molmet.2021.101314 (Epub ahead of print) (PMID: 34375743)
DeNizio JE, Dow BJ, Serrano JC, Ghanty U, Drohat AC, Kohli RM. TET-TDG active DNA demethylation at CpG and non-CpG sites. J Mol Biol. 2021 Feb 6; 166877. doi: 10.1016/j.jmb.2021.166877. (Epub ahead of print). (PMID: 33561435)
Caldwell BA, Liu MY, Prasasya RD, Wang T, DeNizio JE, Leu NA, Amoh NYA, Krapp NYA, Krapp C, Lan Y, Shields EF, Bonasio R, Lengner CJ, Kohli RM, Bartolomei MS. Functionally distinct roles for TET-oxidized 5-methylcytosine bases in somatic reprogramming to pluripotency. Mol Cell. 2020 Dec 11; S1097-2765(20)30887-X. doi: 10.1016/j.molcel.2020.11.045. (Epub ahead of print). (PMID: 33352108)
Wang F, Zahid OK, Ghanty U, Kohli RM, Hall AR. Modular affinity-labeling of the cytosine demethylation base elements in DNA. Sci Rep. 2020 Nov 20; 10(1):20253. doi: 10.1038/s41598-020-76544-x. (PMID: 33219273)
Shen H, Ontiveros RJ, Owens MC, Liu MY, Ghanty U, Kohli RM, Liu KF. TET-mediated 5-methylcytosine oxidation in tRNA promotes translation. J Biol Chem. 2020 Nov 16; jbc.RA120.014226. doi: 10.1074/jbc.RA120.014226. (Epub ahead of print). (PMID: 33199375)
Wang T, Kohli RM. Discovery of an Unnatural DNA Modification Derived from a Natural Secondary Metabolite. Cell Chem Biol. 2020 Oct9; S2451-9456(20)30378-0. doi: 10.1016/j.chembiol.2020.09.006. (Epub ahead of print). (PMID: 33053370)
Wang T, Luo M, Berrios KN, Schutsky EK, Wu H, Kohli RM. Bisulfite-Free Sequencing of 5-Hydroxymethylcytosine with APOBEC-Coupled Epigenetic Sequencing (ACE-Seq). Methods Mol Biol. 2021; 2198:349-367. doi: 10.1007/978-1-0716-0876-0_27. (PMID: 32822044)
Huang Z, Meng Y, Szabó PE, Kohli RM, Pfeifer GP. High-Resolution Analysis of 5-Hydroxymethylcytosine by TET-Assisted Bisulfite Sequencing. Methods Mol Biol. 2021; 2198:321-331. doi: 10.1007/978-1-0716-0876-0_25. (PMID: 32822042)
Gier RA, Bundinich KA, Evitt NH, Cao Z, Freilich ES, Chen Q, Qi J, Lan Y, Kohli RM, Shi J. High-performance CRISPR-Cas12a genome editing for combinatorial genetic screening. Nature Communications. 2020 Jul 13; 11(1):3455. doi: 10.1038/s41467-020-17209-1. (PMID: 32661245)
Merrikh H, Kohli RM. Targeting Evolution to Inhibit Antibiotic Resistance. FEBS J. 2020 May 20. doi: 10.1111/febs.15370. [Epub ahead of print] (PMID: 32434280)
Samuels, AN, Roggiani M, Smith KA, Zhu J, Goulian M, Kohli RM. Deciphering the Role of Colicins during Colonization of the Mammalian Gut by Commensal E. coli . Microorganisms. 2020. doi: 10.3390/microorganisms8050664. [Epub ahead of print]
Ghanty U, Wang T, Kohli RM. Nucleobase Modifiers Identify TET Enzymes as Bifunctional DNA Dioxygenases Capable of Direct N-Demethylation. Angew Chem Int. Ed. Engl. 2020 Apr 9. doi: 10.1002/anie.202002751. [Epub ahead of print] (PMID: 32271979)
Hostetler ZM, Cory MB, Jones CM, Petersson EJ, Kohli RM. The Kinetic and Molecular Basis for the Interaction of LexA and Activated RecA Revealed by a Fluorescent Amino Acid Probe. ACS Chem Biol. 2020 Jan 30. doi: 10.1021/acschembio.9b00886. [Epub ahead of print] (PMID: 31999086)
Xue JH, Chen GD, Hao F, Chen H, Fang Z, Chen FF, Pang B, Yang QL, Wei X, Fan QQ, Xin C, Zhao J, Deng X, Wang BA, Zhang XJ, Chu Y, Tang H, Yin H, Ma W, Chen L, Ding J, Weinhold E, Kohli RM, Liu W, Zhu ZJ, Huang K, Tang H, Xu GL. A vitamin-C-derived DNA modification catalysed by an algal TET homologue. Nature. 2019 May; 569(7757):581-585. doi: 10.1038/s41586-019-1160-0. (PMID: 31043749)
Sungwienwong I, Ferrie JJ, Jun JV, Liu C, Barrett TM, Hostetler ZM, Ieda N, Hendricks A, Muthusamy AK, Kohli RM, Chenoweth DM, Petersson GA, Petersson EJ. Improving the Fluorescent Probe Acridonlyalanine Through a Combination of Theory and Experiment. J Phys Org Chem. 2018 Aug; 31(8). doi: 10.1002/poc.3813. (PMID: 30983696)
Selwood T, Larsen BJ, Mo CY, Culyba MJ, Hostetler ZM, Kohli RM, Reitz AB, Baugh SDP. Advancement of the 5-Amino-1-(Carbamoylmethyl)-1H-1,2,3-Triazole-4-Carboxamide Scaffold to Disarm the Bacterial SOS Response. Front. Microbiol. 2018 Dec 18; 9:2961. doi: 10.3389/fmicb.2018.02961. (PMID: 30619111)
Ghanty U, DeNizio JE, Liu MY, Kohli RM. Exploiting Substrate Promiscuity to Develop Activity-Based Probes for TET Family Enzymes. J Am Chem Soc. 2018 Dec 6. doi: 10.1021/jacs.8b04722 [Epub ahead of print] (PMID: 30518204)
DeNizio JE, Liu MY, Leddin EM, Cisneros GA, Kohli RM. Selectivity and Promiscuity in TET-Mediated Oxidation of 5-Methylcytosine in DNA and RNA. Biochemsitry. 2018 Nov 14. doi: 10.1021/acs.biochem.8b00912. (PMID: 30387995)
Hostetler ZM, Ferrie JJ, Bornstein MR, Sungwienwong I, Petersson EJ, Kohli RM. Systematic Evaluation of Soluble Protein Expression Using a Fluorescent Unnatural Amino Acid Reveals No Reliable Predictors of Tolerability. ACS Chem Biol. 2018 Oct 19. doi: 10.1021/acschembio.8b00696 (PMID: 30216041)
Schutsky EK, DeNizio JE, Hu P, Liu MY, Nabel CS, Fabyanic EB, Hwang Y, Bushman FD, Wu H, Kohli RM. Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase. Nat Biotechnol. 2018 Oct 8. doi: 10.1038/nbt.4204 (PMID: 30295673)
Culyba MJ, Kubiak JM, Mo CY, Goulian M, Kohli RM. Non-equilibrium repressor binding kinetics link DNA damage dose to transcriptional timing within the SOS gene network. PLoS Genet. 2018 Jun 1. doi: 10.1371/journal.pgen.1007405 (PMID: 29856734)
DeNizio JE, Schutsky EK, Berrios KN, Liu MY, Kohli RM. Harnessing natural DNA modifying activities for editing of the genome and epigenome. Curr Opin Chem Biol. 2018 Aug. doi: 10.1016/j.cbpa.2018.01.016 (PMID: 29452938)
Mo CY, Culyba MJ, Selwood T, Kubiak JM, Hostetler ZM, Jurewicz AJ, Keller PM, Pope AJ, Quinn A, Schneck J, Widdowson KL, Kohli RM. Inhibitors of LexA Autoproteolysis and the Bacterial SOS Response Discovered by an Academic-Industry Partnership. ACS Infect Dis. 2018 Mar 9. doi: 10.1021/acsinfecdis.7b00122 (PMID: 29275629)
Kubiak JM, Culyba MJ, Liu MY, Mo CY, Goulian M, Kohli RM. A Small-Molecule Inducible Synthetic Circuit for Control of the SOS Gene Network without DNA Damage. ACS Synth Biol. 2017 Nov 17. doi: 10.1021/acssynbio.7b00108 (PMID: 28826208)
Schutsky EK, Nabel CS, Davis AKF, DeNizio JE, Kohli RM. APOBEC3A efficiently deaminates methylated, but not TET-oxidized, cytosine bases in DNA. Nucleic Acids Res. 2017 Jul 27. doi: 10.1093/nar/gkx345 (PMID: 28472485)
Nabel CS, DeNizio JE, Carroll M, Kohli RM. DNA Methyltransferases Demonstrate Reduced Activity against Arabinosylcytosine: Implications for Epigenetic Instability in Acute Myeloid Leukemia. Biochemistry. 2017 Apr 25. doi: 10.1021/acs.biochem.7b00208 (PMID: 28394581)
Schutsky EK, Hostetler ZM, Kohli RM. Mechanisms for targeted, purposeful mutation revealed in an APOBEC-DNA complex. Nat Struct Mol Biol. 2017 Feb 6. doi: 10.1038/nsmb.3373 (PMID: 28169999)
Liu MY, Torabifard H, Crawford DJ, DeNizio JE, Cao XJ, Garcia BA, Cisneros GA, Kohli RM. Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine. Nat Chem Biol. 2017 Feb. doi: 10.1038/nchembio.2250 (PMID: 27918559)
Kohli RM, Van Duyne GD. Introduction: Genome Modifying Mechanisms. Chem Rev. 2016 Oct 26. (PMID: 27780353)
Mo CY, Manning SA, Roggiani M, Culyba MJ, Samuels AN, Sniegowski PD, Goulian M, Kohli RM. Systematically Altering Bacterial SOS Activity under Stress Reveals Therapeutic Strategies for Potentiating Antibiotics. mSphere. 2016 Aug 10. doi: 10.1128/mSphere.00163-16 (PMID: 27536734)
Liu MY, DeNizio JE, Kohli RM. Quantification of Oxidized 5-Methylcytosine Bases and TET Enzyme Activity. Methods Enzymol. 2016. doi: 10.1016/bs.mie.2015.12.006 (PMID: 27372762)
Liu MY, DeNizio JE, Schutsky EK, Kohli RM. The expanding scope and impact of epigenetic cytosine modifications. Curr Opin Chem Biol. 2016 Aug. doi: 10.1016/j.cbpa.2016.05.029 (PMID: 27315338)
Crawford DJ, Liu MY, Nabel CS, Cao XJ, Garcia BA, Kohli RM. Tet2 Catalyzes Stepwise 5-Methylcytosine Oxidation by an Iterative and de novo Mechanism. J Am Chem Soc. 2016 Jan 27. doi: 10.1021/jacs.5b10554 (PMID: 26734843)
Culyba MJ, Mo CY, Kohli RM. Targets for Combating the Evolution of Acquired Antibiotic Resistance. Biochemistry. 2015 Jun 16. doi: 10.1021/acs.biochem.5b00109 (PMID: 26016604)
Gajula KS, Huwe PJ, Mo CY, Crawford DJ, Stivers JT, Radhakrishnan R, Kohli RM. High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase. Nucleic Acids Res. 2014 Sep. doi: 10.1093/nar/gku689 (PMID: 25064858)
Mo CY, Birdwell LD, Kohli RM. Specificity determinants for autoproteolysis of LexA, a key regulator of bacterial SOS mutagenesis. Biochemistry. 2014 May 20. doi: 10.1021/bi500026e (PMID: 24779472)
Nabel CS, Schutsky EK, Kohli RM. Molecular targeting of mutagenic AID and APOBEC deaminases. Cell Cycle. 2014. doi: 10.4161/cc.27036 (PMID: 24241207)
Kohli RM, Zhang Y. TET enzymes, TDG and the dynamics of DNA demethylation. Nature. 2013 Oct 24. doi: 10.1038/nature12750 (PMID: 24153300)
Nabel CS, Lee JW, Wang LC, Kohli RM. Nucleic acid determinants for selective deamination of DNA over RNA by activation-induced deaminase. Proc Natl Acad Sci USA. 2013 Aug 27. doi: 10.1073/pnas.1306345110 (PMID: 23942124)
Nabel CS, Jia H, Ye Y, Shen L, Goldschmidt HL, Stivers JT, Zhang Y, Kohli RM. AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation. Nat Chem Biol. 2012 Sep. doi: 10.1038/nchembio.1042 (PMID: 22772155)
Nabel CS, Manning SA, Kohli RM. The curious chemical biology of cytosine: deamination, methylation, and oxidation as modulators of genomic potential. ACS Chem Biol. 2012 Jan 20. doi: 10.1021/cb2002895 (PMID:22004246)
Nabel CS, Kohli RM. Molecular biology. Demystifying DNA demethylation. Science. 2011 Sep 2. doi: 10.1126/science.1211917 (PMID: 21885763)
Kohli RM. Grand challenge commentary: The chemistry of a dynamic genome. Nat Chem Biol. 2010 Dec. doi: 10.1038/nchembio.471 (PMID: 21079591)
Kohli RM, Maul RW, Guminski AF, McClure RL, Gajula KS, Saribasak H, McMahon MA, Siliciano RF, Gearhart PJ, Stivers JT. Local sequence targeting in the AID/APOBEC family differentially impacts retroviral restriction and antibody diversification. J Biol Chem. 2010 Dec 24. doi: 10.1074/jbc.M110.177402 (PMID: 20929867)
Kohli RM, Abrams SR, Gajula KS, Maul RW, Gearhart PJ, Stivers JT. A portable hot spot recognition loop transfers sequence preferences from APOBEC family members to activation-induced cytidine deaminase. J Biol Chem. 2009 Aug 21. doi: 10.1074/jbc.M109.025536 (PMID: 19561087)