Glass Lab Publications

Publications

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

 

2023 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.

2022 Singh AK, Phillips M, Alkrimi S, Tonelli M, Boyson SP, Malone KL, Nix JC, Glass KCStructural 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.

2022 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

2022 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.

2022 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.

2022 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.

2021 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. PMID: 34638547

2021 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 KCCoordination of Di-Acetylated Histone Ligands by the ATAD2 Bromodomain. Int J Mol Sci. 2021 Aug 24;22(17). doi: 10.3390/ijms22179128.  PMID: 34502039

2021 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. PMID: 34298819

2020 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. PMID: 33084328.

2020 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.

2020 Obi JO, Lubula MY, Cornilescu G, Henrickson A, McGuire K, Evans CM, Phillips M, Boyson SP, Demeler B, Markley JL, Glass KCThe 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. PMID: 33554132

2019 Gay JC, Eckenroth BE, Evans CM, Langini C, Carlson S, Lloyd JT, Caflisch A, Glass KCDisulfide 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. PMID: 30520161.

2018 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.

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

2016 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 effectEpigenetics. 2016 Oct 2; 11(10) 740-749. doi: 10.1080/15592294.2016. 1226452. Epub 2016 Nov 1. PMID: 27588609, PMCID:  PMC5094623

2016 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 3J Biol Chem, 2016 Aug 26; 291(35):18326-41. doi: 10.1074/jbc.M115.690651.  Epub 2016 Jun 8. PMID: 27281824, PMCID:  PMC5000080

2015 Hassan HE, Carlson S, Abdallah I, Buttolph T, Glass KC, Fandy TE. Curcumin and dimethoxycurcumin induced epigenetic changes in leukemia cellsPham Research. 2015 Mar, 32(3):863-75, doi: 10.1016/j.febslet.2014.09.028. Epub 2014 Sep 4. PMID: 25186441

2014 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 Letters, 2014. 588(21):3844-54. soi: 10.1016/j.febslet.2014.09.028. Epub 2014 Sep 30. PMID: 25281266, PMCID:  PMC4252766

2014 Carlson S, Glass KCThe MOZ histone acetyltransferase in epigenetic signaling and diseaseJ Cel. Physiol. 2014 Nov; 229(11):1571-4, doi: 10.1002/jcp.24617. Review. PubMed PMID: 24633655; PMCID:  PMC4750494

2014 Lubula M, Poplawski A, Glass KC. Crystallization and preliminary X-ray diffraction analysis of the BRPF1 bromodomain in complex with its H2AK5ac and H4K12ac histone-peptide ligandsActa Crystallogr F Struct Biol Commun. 2014 Oct; 70(Pt 10):1389-93. doi: 10.1107/S2053230X14018433.  Epub 2024 Sep 25. PMID: 25286946, PMCID:  PMC4252766

2014 Poplawski A, Hu K, Lee W, Natesan S, Peng D, Carlson S, Shi X, Balaz S, Markley JL, Glass KCMolecular insights into the recognition of N-terminal histone modifications by the BRPF1 bromodomainJ Mol Biol. 2014 Apr 17; 426(8): 1661-1676. doi: 10.1016/j.jmb.2013.12.007. Epub 2013 Dec 12. PMID: 24333487, PMCID: PMC3969779

2013 Lalonde ME, Glass KC, Avakumov N, Joncas FH, Saksouk N, Paquet E, Holliday M, Tan S, Yang XJ, Kutateladze TG, Côté J. Exchange of associated factors directs a switch in HBO1 acetyltransferase histone tail specificityGenes Dev. 27(18):2009-24, 2013. PMID: 24065767

2013 Lee W, Hu K, Toneli M, Bahrami A, Neuhardt E, Glass KC, Markley JL. Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometersJ Magn Reson. 2013 Nov; 236:83-8. doi: 10.1016/j.jmr.2013.08.010. Epub 2013 Aug 30. PMID: 24091140, PMCID:  PMC3848185

2012 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 genomesCell Reports. 2012 Feb 23; 1(2):83-90, doi: 10.1016/j.celrep.2011.12.008. PMID: 22720264, PMCID:  PMC3377377

2012 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 proliferationMol Cell Biol. 2012 Feb; 32(3):689-703. doi:  10.1128/MCB.006455.11. Epub 2011 Dec 5. PMID: 22144582, PMCID:  PMC3266594

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

2010 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 domainJ Mol Biol. 2010 May 14; 398(4):489-96. doi: 10.1016/j/jmb.2010.03.024. Epub 2010 Mar 20. PMID: 20307547, PMCID: PMC2865857

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

2009 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 transformationMol Cell. 33:248-256, 2009. PMID: 19187765

2009 Saksouk N, Avvakumov N*, Champagne KS*, Hung T*, Doyon Y, Cayrou C, Paquet E, Ulla 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 tailMol Cell. 2009 Jan 30; 33:257-265. doi: 10.1016/j.molcel.2008.12.016. PMID: 19187766, PMCID: PMC2650391

2008 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 peptideProteins. 2008 Sep; 72: 1371-6. doi: 10/1--2/prot.22140. PMID: 18623064, PMCID:  PMC2756976

2008 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 suppressorJ Mol Biol. 2008 Jul 4; 380: 303-12. doi: 10.1016/j.jmb.2008.04.061. Epub 2008 May 2. PMID: 18533182; PMCID: PMC2576750

2007 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 recombinationNature. 2007 Dec 13; 450 (7172): 1106-10. doi: 10.1038/natgure06431. Epub 2007 Nov 21. PMID: 18033247, PMCID:  PMC2988437

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

2005 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 paralogJ Biol Chem. 2005 Oct 7; 280(40): 34096-34104. doi: 10.10774/jbc.M505041200. Epub 2024 Jul 28. PMID: 16051603

*These authors contributed equally to the work.

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

 

 

Dr. Karen Glass

E-mail: Karen.Glass@med.uvm.edu

Phone: (802)656-5760
Office Location: Firestone 362

 

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REFERENCES:

1. Cloud J. (2010).  Why Your DNA Isn't Your Destiny.  Time Magazine 172.

2. Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, et al. (2018).  How many human proteoforms are there?  Nat Chem Biol 14, 206-214.

3. Filippakopoulos P, Picaud S, Mangos M, Keates T, Lambert JP, Barsyte-Lovejoy D, et al. (2012).  Histone recognition and large-scale structural analysis of the human bromodomain family.  Cell 149, 214-231.

4. Lubula MY, Eckenroth BE, Carlson S, Poplawski A, Chruszcz M, Glass KC.  (2014).  Structural insighes into recognition of acetylated histone ligands by the BRPF1 bromodomain.  FEBS Lett.  

5. Poplawski A, Hu K, Lee W, Natesan S, Peng D, Carson S, Shi X, Balaz S, Markley JL, Glass KC.  (2014). Molecular insights into the recognition of N-terminal histone modifications by the BRPF1 bromodomain.  J Mol Biol  426, 1661-1676. 

6. Kitabayaski I, Aikawa Y, Yokoyamma A, Hosoda F, Nagi M, Kakazu N, et al. (2001).  Fusion of MOZ and p300 histone acetyltransferases in acute monotytic leukemia with a t(8;22)(p1;q13) chromosome translocation.  Leukemia 15, 89-94

7. Carpapeti M, Agular RC, Goldman JM, Cross NC.  (1998). A novel fusion between MOZ and the nuclear receptor coactivator TIF2 in acute myeloid leukemia.  Blood  91, 3127-3133.

8. Champagne KS, Saksouk N, Pena PV, Johnson K, Ullah M, Yang X, et al.  (2008).  The crystal structure of the ING5 PHD finger in complex with an H3K4me3 histone peptide.  Proteins  72, 1371-1376.

9. Lalonde ME, Avvakumov N, Glass KC, Joncas FH, Saksouk N, Holliday M, et al. (2013).  Exchange of associated factors directs a switch in HBO1 acetyletransferase histone tail specificity.  Genes Dev  27, 2009-2024.

10. Carlson S, Glass KC.  (2014).  The MOZ Histone Acetyltransferase in Epigenetic Signaling and Disease.  J Cell Physiol.

11.  Filippakopoulos P, KnappS.  (2014). Targeting bromodomains:  epigenetic readers of lysine acetylation.  Nat Rev Drug Discov 13, 337-356.