Department of Biochemistry

Publications

For latest updates on the lab’s recent papers and citation information, please see the link to My NCBI (link) or the comprehensive Google Scholar Citations Page (link)

Boyd JR, Gao C, Quinn K, Fritz A, Stein J, Stein G, Glass K, Frietze S. peaksat: an R package for ChIP-seq peak saturation analysis. BMC Genomics. 2023 Jan 25;24(1):43. doi: 10.1186/s12864-023-09109-7. PubMed PMID: 36698077; PubMed Central PMCID: PMC9878872.

Singh AK, Phillips M, Alkrimi S, Tonelli M, Boyson SP, Malone KL, Nix JC, Glass KC. Structural insights into acetylated histone ligand recognition by the BDP1 bromodomain of Plasmodium falciparum. Int J Biol Macromol. 2022 Dec 31;223(Pt A):316-326. doi: 10.1016/j.ijbiomac.2022.10.247. Epub 2022 Oct 31. PubMed PMID: 36328269; PubMed Central PMCID: PMC10093686.

Phillips M*, Malone KL*, Boyle BW, Montgomery C, Kressy IA, Joseph FM, Bright KM, Boyson SP, Chang S, Nix JC, Young NL, Jeffers V, Frietze SE, Glass KC. Impact of combinatorial histone modifications on acetyllysine recognition by the ATAD2 and ATAD2B bromodomains. BioRxiv. 2022 November; :2022.11.14.516501. doi: 10.1101/2022.11.14.516501.

Gao C, Glass KC, Frietze S. Functional networks of the human bromodomain-containing proteins. Front Bioinform. 2022;2:835892. doi: 10.3389/fbinf.2022.835892. eCollection 2022. PubMed PMID: 36304339; PubMed Central PMCID: PMC9580951.

Fritz AJ, El Dika M, Toor RH, Rodriguez PD, Foley SJ, Ullah R, Nie D, Banerjee B, Lohese D, Tracy KM, Glass KC, Frietze S, Ghule PN, Heath JL, Imbalzano AN, van Wijnen A, Gordon J, Lian JB, Stein JL, Stein GS. Epigenetic-Mediated Regulation of Gene Expression for Biological Control and Cancer: Cell and Tissue Structure, Function, and Phenotype. Results Probl Cell Differ. 2022;70:339-373. doi: 10.1007/978-3-031-06573-6_12. Review. PubMed PMID: 36348114; PubMed Central PMCID: PMC9753575.

El Dika M, Fritz AJ, Toor RH, Rodriguez PD, Foley SJ, Ullah R, Nie D, Banerjee B, Lohese D, Tracy KM, Glass KC, Frietze S, Ghule PN, Heath JL, Imbalzano AN, van Wijnen A, Gordon J, Lian JB, Stein JL, Stein GS. Epigenetic-Mediated Regulation of Gene Expression for Biological Control and Cancer: Fidelity of Mechanisms Governing the Cell Cycle. Results Probl Cell Differ. 2022;70:375-396. doi: 10.1007/978-3-031-06573-6_13. PubMed PMID: 36348115; PubMed Central PMCID: PMC9703624.

Parikh SJ, Kamat S, Phillips M, Boyson SP, Yarbrough T, Davie D, Zhang Q, Glass KC, Shah MB. Insights into the Genetic Variations of Human Cytochrome P450 2C9: Structural Analysis, Characterization and Comparison. Int J Mol Sci. 2021 Sep 22;22(19). doi: 10.3390/ijms221910206. PubMed PMID: 34638547; PubMed Central PMCID: PMC8508694.

Evans CM, Phillips M, Malone KL, Tonelli M, Cornilescu G, Cornilescu C, Holton SJ, Gorjánácz M, Wang L, Carlson S, Gay JC, Nix JC, Demeler B, Markley JL, Glass KC. Coordination of Di-Acetylated Histone Ligands by the ATAD2 Bromodomain. Int J Mol Sci. 2021 Aug 24;22(17). doi: 10.3390/ijms22179128. PubMed PMID: 34502039; PubMed Central PMCID: PMC8430952.

Boyson SP, Gao C, Quinn K, Boyd J, Paculova H, Frietze S, Glass KC. Functional Roles of Bromodomain Proteins in Cancer. Cancers (Basel). 2021 Jul 19;13(14). doi: 10.3390/cancers13143606. Review. PubMed PMID: 34298819; PubMed Central PMCID: PMC8303718.

Lloyd JT, McLaughlin K, Lubula MY, Gay JC, Dest A, Gao C, Phillips M, Tonelli M, Cornilescu G, Marunde MR, Evans CM, Boyson SP, Carlson S, Keogh MC, Markley JL, Frietze S, Glass KC. Structural Insights into the Recognition of Mono- and Diacetylated Histones by the ATAD2B Bromodomain. J Med Chem. 2020 Nov 12;63(21):12799-12813. doi: 10.1021/acs.jmedchem.0c01178. Epub 2020 Oct 21. PubMed PMID: 33084328; PubMed Central PMCID: PMC7884259.

Parikh SJ, Evans CM, Obi JO, Zhang Q, Maekawa K, Glass KC, Shah MB. Structure of Cytochrome P450 2C9*2 in Complex with Losartan: Insights into the Effect of Genetic Polymorphism. Mol Pharmacol. 2020 Nov;98(5):529-539. doi: 10.1124/molpharm.120.000042. Epub 2020 Sep 16. PubMed PMID: 32938720; PubMed Central PMCID: PMC7569312.

Obi JO, Lubula MY, Cornilescu G, Henrickson A, McGuire K, Evans CM, Phillips M, Boyson SP, Demeler B, Markley JL, Glass KC. The BRPF1 bromodomain is a molecular reader of di-acetyllysine. Curr Res Struct Biol. 2020;2:104-115. doi: 10.1016/j.crstbi.2020.05.001. Epub 2020 May 12. PubMed PMID: 33554132; PubMed Central PMCID: PMC7861561.

Gay JC, Eckenroth BE, Evans CM, Langini C, Carlson S, Lloyd JT, Caflisch A, Glass KC. Disulfide bridge formation influences ligand recognition by the ATAD2 bromodomain. Proteins. 2019 Feb;87(2):157-167. doi: 10.1002/prot.25636. Epub 2018 Dec 27. PubMed PMID: 30520161; PubMed Central PMCID: PMC6457126.

Doyle J, Glass KC, Racz M, Teng J. Student-directed interactive animation for learning cytochrome P450-mediated drug metabolism. Curr Pharm Teach Learn. 2018 Dec;10(12):1565-1573. doi: 10.1016/j.cptl.2018.08.021. Epub 2018 Oct 1. PubMed PMID: 30527821.

Lloyd JT, Glass KC. Biological function and histone recognition of family IV bromodomain-containing proteins. J Cell Physiol. 2018 Mar;233(3):1877-1886. doi: 10.1002/jcp.26010. Epub 2017 Jun 13. Review. PubMed PMID: 28500727; PubMed Central PMCID: PMC5683942.

Hassan HE, Keita JA, Narayan L, Brady SM, Frederick R, Carlson S, Glass KC, Natesan S, Buttolph T, Fandy TE. The combination of dimethoxycurcumin with DNA methylation inhibitor enhances gene re-expression of promoter-methylated genes and antagonizes their cytotoxic effect. Epigenetics. 2016 Oct 2;11(10):740-749. doi: 10.1080/15592294.2016.1226452. Epub 2016 Nov 1. PubMed PMID: 27588609; PubMed Central PMCID: PMC5094623.

Kim S, Natesan S, Cornilescu G, Carlson S, Tonelli M, McClurg UL, Binda O, Robson CN, Markley JL, Balaz S, Glass KC. Mechanism of Histone H3K4me3 Recognition by the Plant Homeodomain of Inhibitor of Growth 3. J Biol Chem. 2016 Aug 26;291(35):18326-41. doi: 10.1074/jbc.M115.690651. Epub 2016 Jun 8. PubMed PMID: 27281824; PubMed Central PMCID: PMC5000080.

Hassan HE, Carlson S, Abdallah I, Buttolph T, Glass KC, Fandy TE. Curcumin and dimethoxycurcumin induced epigenetic changes in leukemia cells. Pharm Res. 2015 Mar;32(3):863-75. doi: 10.1007/s11095-014-1502-4. Epub 2014 Sep 4. PubMed PMID: 25186441.

Lubula MY, Eckenroth BE, Carlson S, Poplawski A, Chruszcz M, Glass KC. Structural insights into recognition of acetylated histone ligands by the BRPF1 bromodomain. FEBS Lett. 2014 Nov 3;588(21):3844-54. doi: 10.1016/j.febslet.2014.09.028. Epub 2014 Sep 30. PubMed PMID: 25281266; PubMed Central PMCID: PMC4252766.

Carlson S, Glass KC. The MOZ histone acetyltransferase in epigenetic signaling and disease. J Cell Physiol. 2014 Nov;229(11):1571-4. doi: 10.1002/jcp.24617. Review. PubMed PMID: 24633655; PubMed Central PMCID: PMC4750494.

Lubula MY, Poplawaski A, Glass KC. Crystallization and preliminary X-ray diffraction analysis of the BRPF1 bromodomain in complex with its H2AK5ac and H4K12ac histone-peptide ligands. Acta Crystallogr F Struct Biol Commun. 2014 Oct;70(Pt 10):1389-93. doi: 10.1107/S2053230X14018433. Epub 2014 Sep 25. PubMed PMID: 25286946; PubMed Central PMCID: PMC4188086.

Poplawski A, Hu K, Lee W, Natesan S, Peng D, Carlson S, Shi X, Balaz S, Markley JL, Glass KC. Molecular insights into the recognition of N-terminal histone modifications by the BRPF1 bromodomain. J Mol Biol. 2014 Apr 17;426(8):1661-76. doi: 10.1016/j.jmb.2013.12.007. Epub 2013 Dec 12. PubMed PMID: 24333487; PubMed Central PMCID: PMC3969779.

Lee W, Hu K, Tonelli M, Bahrami A, Neuhardt E, Glass KC, Markley JL. Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers. JMagn Reson. 2013 Nov;236:83-8. doi: 10.1016/j.jmr.2013.08.010. Epub 2013 Aug 30. PubMed PMID: 24091140; PubMed Central PMCID: PMC3858185.

Yuan CC, Matthews AG, Jin Y, Chen CF, Chapman BA, Ohsumi TK, Glass KC, Kutateladze TG, Borowsky ML, Struhl K, Oettinger MA. Histone H3R2 symmetric dimethylation and histone H3K4 trimethylation are tightly correlated in eukaryotic genomes. Cell Rep. 2012 Feb 23;1(2):83-90. doi: 10.1016/j.celrep.2011.12.008. PubMed PMID: 22720264; PubMed Central PMCID: PMC3377377.

Avvakumov N, Lalonde ME, Saksouk N, Paquet E, Glass KC, Landry AJ, Doyon Y, Cayrou C, Robitaille GA, Richard DE, Yang XJ, Kutateladze TG, Côté J. Conserved molecular interactions within the HBO1 acetyltransferase complexes regulate cell proliferation. Mol Cell Biol. 2012 Feb;32(3):689-703. doi: 10.1128/MCB.06455-11. Epub 2011 Dec 5. PubMed PMID: 22144582; PubMed Central PMCID: PMC3266594.

Hom RA, Chang PY, Roy S, Musselman CA, Glass KC, Selezneva AI, Gozani O, Ismagilov RF, Cleary ML, Kutateladze TG. Molecular mechanism of MLL PHD3 and RNA recognition by the Cyp33 RRM domain. J Mol Biol. 2010 Jul 9;400(2):145-54. doi: 10.1016/j.jmb.2010.04.067. Epub 2010 May 8. PubMed PMID: 20460131; PubMed Central PMCID: PMC3204800.

Roy S, Musselman CA, Kachirskaia I, Hayashi R, Glass KC, Nix JC, Gozani O, Appella E, Kutateladze TG. Structural insight into p53 recognition by the 53BP1 tandem Tudor domain. J Mol Biol. 2010 May 14;398(4):489-96. doi: 10.1016/j.jmb.2010.03.024. Epub 2010 Mar 20. PubMed PMID: 20307547; PubMed Central PMCID: PMC2865857.

Champagne KS, Kutateladze TG. Structural insight into histone recognition by the ING PHD fingers. Curr Drug Targets. 2009 May;10(5):432-41. doi: 10.2174/138945009788185040. Review. PubMed PMID: 19442115; PubMed Central PMCID: PMC2740728.

Hung T, Binda O, Champagne KS, Kuo AJ, Johnson K, Chang HY, Simon MD, Kutateladze TG, Gozani O. ING4 mediates crosstalk between histone H3 K4 trimethylation and H3 acetylation to attenuate cellular transformation. Mol Cell. 2009 Jan 30;33(2):248-56. doi: 10.1016/j.molcel.2008.12.016. PubMed PMID: 19187765; PubMed Central PMCID: PMC2650391.

Saksouk N, Avvakumov N*, Champagne KS*, Hung T*, Doyon Y, Cayrou C, Paquet E, Ullah M, Landry AJ, Côté V, Yang XJ, Gozani O, Kutateladze TG, Côté J. HBO1 HAT complexes target chromatin throughout gene coding regions via multiple PHD finger interactions with histone H3 tail. Mol Cell. 2009 Jan 30;33(2):257-65. doi: 10.1016/j.molcel.2009.01.007. PubMed PMID: 19187766; PubMed Central PMCID: PMC2677731.

Champagne KS, Saksouk N, Peña PV, Johnson K, Ullah M, Yang XJ, Côté J, Kutateladze TG. The crystal structure of the ING5 PHD finger in complex with an H3K4me3 histone peptide. Proteins. 2008 Sep;72(4):1371-6. doi: 10.1002/prot.22140. PubMed PMID: 18623064; PubMed Central PMCID: PMC2756976.

Peña PV, Hom RA, Hung T, Lin H, Kuo AJ, Wong RP, Subach OM, Champagne KS, Zhao R, Verkhusha VV, Li G, Gozani O, Kutateladze TG. Histone H3K4me3 binding is required for the DNA repair and apoptotic activities of ING1 tumor suppressor. J Mol Biol. 2008 Jul 4;380(2):303-12. doi: 10.1016/j.jmb.2008.04.061. Epub 2008 May 2. PubMed PMID: 18533182; PubMed Central PMCID: PMC2576750.

Matthews AG, Kuo AJ, Ramón-Maiques S, Han S, Champagne KS, Ivanov D, Gallardo M, Carney D, Cheung P, Ciccone DN, Walter KL, Utz PJ, Shi Y, Kutateladze TG, Yang W, Gozani O, Oettinger MA. RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination. Nature. 2007 Dec 13;450(7172):1106-10. doi: 10.1038/nature06431. Epub 2007 Nov 21. PubMed PMID: 18033247; PubMed Central PMCID: PMC2988437.

Champagne KS, Piscitelli E, Francklyn CS. Substrate recognition by the hetero-octameric ATP phosphoribosyltransferase from Lactococcus lactis. Biochemistry. 2006 Dec 19;45(50):14933-43. doi: 10.1021/bi061802v. PubMed PMID: 17154531; PubMed Central PMCID: PMC2567060.

Champagne KS, Sissler M, Larrabee Y, Doublié S, Francklyn CS. Activation of the hetero-octameric ATP phosphoribosyl transferase through subunit interface rearrangement by a tRNA synthetase paralog. J Biol Chem. 2005 Oct 7;280(40):34096-104. doi: 10.1074/jbc.M505041200. Epub 2005 Jul 28. PubMed PMID: 16051603.

Bovee ML, Champagne KS, Demeler B, Francklyn CS. The quaternary structure of the HisZ-HisG N-1-(5'-phosphoribosyl)-ATP transferase from Lactococcus lactis. Biochemistry. 2002 Oct 1;41(39):11838-46. doi: 10.1021/bi020243z. PubMed PMID: 12269828; NIHMSID:NIHMS453032.

*These authors contributed equally to the work.

** Please note name change in 2009 from Champagne KS to Glass KC.