Publications:

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)