Grégoire S, Cheishvili D, Salmon-Divon M, Dymov S, Topham L, Calderon V, Shir Y, Szyf M, Stone LS. Epigenetic signature of chronic low back pain in human T cells. Pain Rep. 2021 Nov 3;6(4):e960. doi: 10.1097/PR9.0000000000000960. PMID: 34746619; PMCID: PMC8568391.

Topham L, Gregoire S, Kang H, Salmon-Divon M, Lax E, Millecamps M, Szyf M, Stone L. The methyl donor S-adenosyl methionine reverses the DNA methylation signature of chronic neuropathic pain in mouse frontal cortex. Pain Rep. 2021 Jul 13;6(2):e944. doi: 10.1097/PR9.0000000000000944. PMID: 34278163; PMCID: PMC8280078.

Kawarai Y, Jang SH, Lee S, Millecamps M, Kang H, Gregoire S, Suzuki-Narita M, Ohtori S, Stone LS. Exercise attenuates low back pain and alters epigenetic regulation in intervertebral discs in a mouse model. Spine J. 2021 Nov;21(11):1938-1949. doi: 10.1016/j.spinee.2021.06.002. Epub 2021 Jun 9. PMID: 34116218.

Do WL, Nguyen S, Yao J, Guo X, Whitsel EA, Demerath E, Rotter JI, Rich SS, Lange L, Ding J, Van Den Berg D, Liu Y, Justice AE, Guan W, Horvath S, Assimes TL, Bhatti P, Jordahl K, Shadyab A, Valencia CI, Stein AD, Smith A, Staimez LR, Conneely K, Narayan KMV. Associations between DNA methylation and BMI vary by metabolic health status: a potential link to disparate cardiovascular outcomes. Clin Epigenetics. 2021 Dec 22;13(1):230. doi: 10.1186/s13148-021-01194-3. PubMed PMID: 34937574.

Polinski KJ, Purdue-Smithe A, Robinson SL, Zhao SK, Schliep KC, Silver RM, Guan W, Schisterman EF, Mumford SL, Yeung EH. Maternal caffeine intake and DNA methylation in newborn cord blood. Am J Clin Nutr. 2021 Oct 20;. doi: 10.1093/ajcn/nqab348. [Epub ahead of print] PubMed PMID: 34669932.

Keshawarz A, Joehanes R, Guan W, Huan T, DeMeo DL, Grove ML, Fornage M, Levy D, O'Connor G. Longitudinal change in blood DNA epigenetic signature after smoking cessation. Epigenetics. 2021 Oct 6;:1-12. doi: 10.1080/15592294.2021.1985301. [Epub ahead of print] PubMed PMID: 34570667.

Yeung EH, Mendola P, Sundaram R, Zeng X, Guan W, Tsai MY, Robinson SL, Stern JE, Ghassabian A, Lawrence D, O'Connor TG, Segars J, Gore-Langton RE, Bell EM. Conception by fertility treatment and offspring deoxyribonucleic acid methylation. Fertil Steril. 2021 Aug;116(2):493-504. doi: 10.1016/j.fertnstert.2021.03.011. Epub 2021 Apr 3. PubMed PMID: 33823999; PubMed Central PMCID: PMC8349775.

Dai J, Leung M, Guan W, Guo HT, Krasnow RE, Wang TJ, El-Rifai W, Zhao Z, Reed T. Whole-Genome Differentially Hydroxymethylated DNA Regions among Twins Discordant for Cardiovascular Death. Genes (Basel). 2021 Jul 29;12(8). doi: 10.3390/genes12081183. PubMed PMID: 34440357; PubMed Central PMCID: PMC8392630.


Seiler, S.L., Song, J.M., Kotandeniya, D., Chen,Y., Kono, T., Han, Q., Colwell, M., Auch, B., Sarver, A.,Upadhyaya, P., Ren, Y., Faulk, C., De Flora, S., La Maestra, S., Chen, Y., Kassie, F., Tretyakova, N.Y. Inhalation exposure to cigarette smoke and inflammatory agents induces epigenetic changes in the lung. Nature Scientific Reports. Sci Rep 10, 655 (2020) DOI: 10.1038/s41598-020-67502-8

Ghorohova, E., Martella, G., Motwani, N.,Tretyakova, N., Sundelin, B., and Motwani, H. (2020) DNA epigenetic marks are linked to embryo aberrations in amphipods. Nature Scientific Reports. Sci Rep 10, 655 (2020). DOI: 10.1038/s41598-020-57465-1

“Pharmacological Regulation and Functional Significance of Chromatin Binding by BET Tandem Bromodomains” M.D. Olp, H. Cui, W. C. K. Pomerantz*, B. C. Smith*, 2020, accepted.

Opportunity Knocks for Uncovering New Function of an Understudied Nucleosome Remodeling Complex Member, the Bromodomain PHD Finger Transcription factor, BPTF, † Huda Zahid, † Noelle M. Olson, William C. K. Pomerantz* 2020, submitted

“Autophagy Dependent Sensitization of Triple Negative Breast Cancer Models to Topoisomerase II Poisons by Inhibition of The Nucleosome Remodeling Factor” L. Tyutyunyk-Massey; Y, Sun; N. Da; H. Ngo; M. Dammalapati; A. Vaidyanathan; M. Singh; S. Haqqani; J. Haueis; R. Finnegan; D. Xiaoyan; S. Kirberger; P. Bos; D. Bandyopadhyay; W. C. K. Pomerantz; Y. Pommier; D. Gewirtz; J. W. Landry, 2020, in revisions

“Super Enhancer Regulation of Cytokine-Induced Chemokine Production in Alcoholic Hepatitis” M. Liu; S. Cao; J. Gao; J. P. Arab; H. Cui; Y. Gao; T. S. Sehrawat; F. H. Hamdan; M. Ventura-Cots; J. Argemi; W. C. K. Pomerantz, S. A. Johnsen; J.-H Lee; F. Gao; T. Ordog; P. Mathurin; A. Revzin; R. Bataller; H. Yan*; V. H. Shah* 2020, in revision

“Controlling Intramolecular Interactions in the Design of Selective, High-Affinity, Ligands for the CREBBP Bromodomain.”. M. Brand, Michael; J. Clayton; M. Moroglu; M. Schiedel; S. Picaud; J. Bluck A. Skwarska; A. K. N. Chan, C. M. C. Laurin; A. R. Scorah; K. F. L. See, T. P. C. Rooney; O. Fedorov;G. Perell; P. Kalra; W. A. Cortopassi; K. E. Christensen; R. I. Cooper; R. S. Paton; ,W. C. K. Pomerantz; P. C. Biggin, E. M. Hammond; P. Filippakopoulos; S. J. Conway.* 2020 submitted ChemRxiv. Preprint.

"Quantifying the selectivity of protein-protein and small molecule interactions with fluorinated tandem bromodomain reader proteins", Prakriti Kalra, Logan McGraw , Jennifer R. Kimbrough, Anil K. Pandey, Jonathan Solberg, Huarui Cui, Anand Divakaran, Kristen John, Jon E. Hawkinson, William C.K. Pomerantz*, ACS Chem. Biol. 2020 Accepted.

“Selective N-Terminal BET Bromodomain Inhibitors by Targeting Non-Conserved Residues and Structured Water Displacement” H. Cui; A. Divakaran: A. K. Pandey; J. A. Johnson; H. Zahid, Z. Hoell, M. Ellingosn, K. Shi; H. Aihara; D. A. Harki; W. C. K. Pomerantz* 2020, ChemRxiv. Preprint. , Angew. Chem. 2020 Accepted. DOI: 10.1002/anie.202008625

“P300 deletion in liver endothelial cells attenuates portal hypertension and fibrogenesis via inhibition of CCL2-mediated angiocrine signaling” J. Gao, B. Wei, M. Liu, P. Hirsova, T. S. Sehrawat, S. Cao, X. Hu, F. Xue , U. Yaqoob, N. Kang, H. Cui., W. C. K. Pomerantz, E. Kostallari * , V. H. Shah * Hepatology 2020 Accepted.

“Combined Protein- and Ligand-Observed NMR Workflow to Screen Fragment Cocktails against Multiple Proteins: A Case Study Using Bromodomains” J. A. Johnson, N. Olson, M. J. Tooker S. K. Bur and W. C.K. Pomerantz* Molecules 2020, 25, 3549. DOI: 10.3390/molecules25173949

“New Inhibitors for the BPTF Bromodomain Enabled by Structural Biology and Biophysical Assay Development,” P.D. Ycas, Huda Zahid, A. Chan, , Noelle M. Olson, Jorden A. Johnson, Siva K. Talluri, Ernst Schonbrunn, W. C. K. Pomerantz * Org and Biomol Chem. 2020 18, 5174-5182.

“NMR Analyses of Acetylated H2A.Z Isoforms Identify Differential Binding Interactions with the Bromodomains of the NURF and CERF Nucleosome Remodeling Complexes”, N.M. Olson, Samantha Kroc, J. A. Johnson, H. Zahid, P. D. Ycas 1 , A. Chan, J. Kimbrough, P. Kalra 1 , E. Scheonbrunn, W. C. K. Pomerantz * , Biochemistry, 59, 1871-1880. DOI: 10.1021/acs.biochem.0c00159


Seiler, C. L., Song, J. M., Fernandez, J., Abrahante, J. E., Kono, T. J. Y., Chen, Y., Ren, Y., Kassie, F., Tretyakova, N. (2019) Epigenetic changes in alveolar type II lung cells of A/J mice following intranasal treatment with lipopolysaccharide Chem. Res. Toxicol. 32 (5), pp 831-835. DOI: 10.1021/acs.chemrestox.9b00015

Ji, S., Park, D., Kropachev, K., Kolbanovskiy, M., Fu, I., Broyde, S., Essawy, M., Geacintov, N.E.,and Tretyakova, N. (2019) 5-Formylcytosine-induced DNA–peptide cross-links reduce transcription efficiency, but do not do cause transcription errors in human cells. Journal of Biological Chemistry, 294(48):18387-18397. DOI: 10.1074/jbc.RA119.009834

Erber, L., Luo, A. and Chen, Y. Targeted and Interactome Proteomics Revealed the Role of PHD2 in Regulating BRD4 Proline Hydroxylation. Mol. Cell. Proteomics 18(9):1772-1781 (2019) DOI: 10.1074/mcp.RA119.001535

Li, Y., Evers, J., Luo, A., Erber, L., Postler, Z. and Chen, Y. A Quantitative Chemical Proteomics Approach for Site-specific Stoichiometry Analysis of Ubiquitination. Angew Chem Int Ed Engl. 58(2):537-541 (2019) DOI: 10.1002/anie.201810569

Liping Dou, Fei Yan, Jiuxia Pang, Dehua Zheng, Dandan Li, Li Gao, Lijun Wang, Yihan Xu, Jinlong Shi, Qian Wang, Lei Zhou, Na Shen, Puja Singh, Lili Wang, Yonghui Li, Yvchi Gao, Tao Liu, Chongjian Chen, Aref Al-Kali, Mark R Litzow, Young-In Chi, Ann M Bode, Chunhui Liu, Haojie Huang, Daihong Liu, Guido Marcucci, Shujun Liu, Li Yu. Protein lysine 43 methylation by EZH1 promotes AML1-ETO transcriptional repression in leukemia. Nat Commun., 2019 Nov 7;10(1):5051 DOI: 10.1038/s41467-019-12960-6

“Applied biophysical methods in bromodomain drug discovery.” W.C.K. Pomerantz, J. Johnson, P. Ycas for Chemical Epigenetics, Springer editor Antonella Mai 2019 1-51.

“Evaluating the advantages of using 3D-enriched fragments for targeting bromodomains” J. A. Johnson, C. A. Nicolaou, H. Hu, W. C.K. Pomerantz,* 2019, 10, 1648-1654.

“Systematically Mitigating the p38α Activity of Triazole-based BET inhibitors” A. S. Carlson† , H. Cui† , A Divakaran, J. A. Johnson, R. M. Brunner, W. C. K. Pomerantz*, Joseph J. Topczewski* ACS Med. Chem. Lett. 2019, 9, 1296-1301. Highlighted in, “In this Issue, ACS Med.Chem. Lett”

“Selectivity, ligand deconstruction, and cellular activity analysis of a BPTF bromodomain inhibitor.” S E. Kirberger, P. D. Ycas, J. A. Johnson, C. Chen, M. F. Ciccone, R. W. L Woo, A. K. Urick, H. Zahid, K. Shi, H. Aihara, d S. McAllister, M. Kashani-Sabet, J. Shi, A. Dickson, f C. O. dos Santos,* W. C.K. Pomerantz* Org. Biomol. Chem. 2019 17, 2020-2027. DOI: 10.1039/c8ob02599a


Kotandeniya, D., Seiler, C., Fernandez, J., Pujari, S., Murphy, K., Tretyakova, N. (2018) Can 5-methylcytosine analogues with extended alkyl side chains guide DNA methylation? Chemical Communications 54(9), pp. 1061-1064. DOI: 10.1039/c7cc06867k

Seiler, C., Fernandez, J., Kotandeniya, D., Sham, Y., and Tretyakova, N. (2018) Maintenance DNA methyltransferase activity in the presence of oxidized forms of 5-methylcytosine: Structural basis for TET-mediated DNA demethylation. Biochemistry, 57 (42), pp 6061–6069. DOI: 10.1021/acs.biochem.8b00683

Yang, K., Park, D., Tretyakova, N., and Greenberg, M. (2018) Histone protein tails decrease N7-methyl-2'-deoxyguanosine depurination rates and yield DNA-protein crosslinks in nucleosome core particles. Proc. Natl. Acad. Sci. 115(48), pp E11212-E11220. DOI: 10.1073/pnas.1813338115

Hrit J, Goodrich L, Li C, Wang BA, Nie J, Cui X, Martin EA, Simental E, Fernandez J, Liu MY, Nery JR, Castanon R, Kohli RM, Tretyakova N, He C, Ecker JR, Goll M, Panning B. (2018) OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development. Elife. 7:e34870. DOI: 10.7554/eLife.34870

Lewis L, Chappell GA, Kobets T, O'Brian BE, Sangaraju D, Kosyk O, Bodnar W, Tretyakova N, Pogribny IP, Rusyn I. (2018) Sex-specific differences in genotoxic and epigenetic effects of 1,3-butadiene among mouse tissues. Arch. Toxicol. 93(3) 791-800. DOI: 10.1007/s00204-018-2374-x

Smestad J, Erber L, Chen Y and Maher LJ. Chromatin Succinylation Correlates with Active Gene Expression and Is Perturbed by Defective TCA Cycle Metabolism. iScience 2:63-75 (2018) DOI: 10.1016/j.isci.2018.03.012

Fei Yan, Aref Al-Kali, Zijie Zhang, Jun Liu, Jiuxia Pang, Na Zhao, Chuan He, Mark R Litzow, Shujun Liu. A dynamic N 6-methyladenosine methylome regulates intrinsic and acquired resistance to tyrosine kinase inhibitors. Cell Res. 2018 Nov;28(11):1062-1076 DOI: 10.1038/s41422-018-0097-4

Na Shen, Fei Yan, Jiuxia Pang, Zhe Gao, Aref Al-Kali, Christy L Haynes, Mark R Litzow, Shujun Liu. HDL-AuNPs-BMS Nanoparticle Conjugates as Molecularly Targeted Therapy for Leukemia. ACS Appl Mater Interfaces. 2018 May 2;10(17):14454-14462 DOI: 10.1021/acsami.8b01696

F Yan, N Shen, J X Pang, N Zhao, Y W Zhang, A M Bode, A Al-Kali, M R Litzow, B Li, S J Liu. A vicious loop of fatty acid-binding protein 4 and DNA methyltransferase 1 promotes acute myeloid leukemia and acts as a therapeutic target. Leukemia. 2018 Apr;32(4):865-873 DOI: 10.1038/leu.2017.307

“Design, Synthesis, and Characterization of a Fluorescence Polarization Pan-BET Bromodomain Probe” C. N. Paulson, X. Guan, A. M. Ayoub, A. Chan, R. M. Karim, W. C. K. Pomerantz, E. Schönbrunn, G.I. Georg,* J. E. Hawkinson, ACS Med Chem. Lett, 2018 9, 1223-29.

“Molecular Basis for the N-Terminal Bromodomain and Extra Terminal (BET) Family Selectivity of a Dual Kinase-Bromodomain Inhibitor ” A. Divakaran, S. K. Talluri, A. Ayoub, N. K. Mishra, H. Cui, J. C. Widen, N. Berndt, J. Zhu, A. S. Carlson, J. J. Topczewski, E. Schönbrunn, D. Harki, W. C. K. Pomerantz*, J. Med. Chem 2018, 61, 9316-34. DOI: 10.1021/acs.jmedchem.8b01248


Ji, S., Shao, H., Han, Q., Seiler, C., Tretyakova, N. (2017) Reversible DNA-protein cross-linking at epigenetic DNA marks. Angew Chem Int Ed Engl. 56(45), pp 14130-14134. DOI: 10.1002/anie.201708286

F Yan, N Shen, J Pang, N Zhao, B Deng, B Li, Y Yang, P Yang, J R Molina, S Liu. A regulatory circuit composed of DNA methyltransferases and receptor tyrosine kinases controls lung cancer cell aggressiveness. Oncogene. 2017 Dec 14;36(50):6919-6928 DOI: 10.1038/onc.2017.305

Na Shen, Fei Yan, Jiuxia Pang, Na Zhao, Naseema Gangat, Laichu Wu, Ann M Bode, Aref Al-Kali, Mark R Litzow, Shujun Liu. Inactivation of Receptor Tyrosine Kinases Reverts Aberrant DNA Methylation in Acute Myeloid Leukemia. Clin Cancer Res. 2017 Oct 15;23(20):6254-6266 DOI: 10.1158/1078-0432.CCR-17-0235

F Yan, N Shen, J X Pang, Y W Zhang, E Y Rao, A M Bode, A Al-Kali, D E Zhang, M R Litzow, B Li, S J Liu. Fatty acid-binding protein FABP4 mechanistically links obesity with aggressive AML by enhancing aberrant DNA methylation in AML cells. Leukemia. 2017 Jun;31(6):1434-1442 DOI: 10.1038/leu.2016.349

Jiuxia Pang, Na Shen, Fei Yan, Na Zhao, Liping Dou, Lai-Chu Wu, Christopher L Seiler, Li Yu, Ke Yang, Veronika Bachanova, Eric Weaver, Natalia Y Tretyakova, Shujun Liu. Thymoquinone exerts potent growth-suppressive activity on leukemia through DNA hypermethylation reversal in leukemia cells. Oncotarget. 2017 May 23;8(21):34453-34467 DOI: 10.18632/oncotarget.16431

“Specific acetylation patterns of H2A.Z interact directly with discrete bromodomains.” G. T. Perell, N. K. Mishra, B. Sudhamalla, P.D. Ycas, P. K. Islam, W. C. K. Pomerantz*, Biochemistry 2017, 56, 4607-15. DOI: 10.1021/acs.biochem.7b00648

“BET bromodomain inhibitors with one-step synthesis discovered from virtual screen.” A. Ayoub, L. M. L. Hawk, R.J. Herzig, J. Jiang, A. J. Wisniewski, C. T. Gee, P. Zhao, J. Zhu, N. Berndt, N. K. Offei-Addo, T. G. Scott, J. Qi, J. E. Bradner, T. R. Ward, E. Schönbrunn, G. I. Georg*, W. C. K. Pomerantz*, J. Med. Chem. 2017, 60, 4805-17. DOI: 10.1021/acs.jmedchem.6b01336

“Bptf maintains chromatin accessibility and the self-renewal capacity of mammary gland stem cells.” W. D. Frey, A. Chaudhry, P. F. Slepicka, A. M. Ouellette, S. E. Kirberger, W. C. K. Pomerantz, G. J. Hannon, and C. O. dos Santos*, Stem Cell Reports 2017, 9, 1-9. DOI: 10.1016/j.stemcr.2017.04.031


Fei Yan, Jiuxia Pang, Yong Peng, Julian R Molina, Ping Yang, Shujun Liu. Elevated Cellular PD1/PD-L1 Expression Confers Acquired Resistance to Cisplatin in Small Cell Lung Cancer Cells. PLoS One. 2016 Sep 9;11(9):e0162925 DOI: 10.1371/journal.pone.0162925

Chong W, Demerath EW, Pankow JS, Bressler J, Fornage M, Grove ML, Chen W, Guan W. 2016. Imputation of Missing Covariate Values in Epigenome-Wide Analysis of DNA Methylation Data. Epigenetics. 11:132-139. DOI: 10.1080/15592294.2016.1145328

Joehanes R*, Just AC*, Marioni RE*, Pilling LC*, Reynolds LM*, Mandaviya PR*, Guan W*, Xu T*, Elks CE*, Aslibekyan S*, Moreno-Macias H*, Smith JA*, Brody JA*, Dhingra R*, Yousefi P, Pankow JS, Kunze S, Shah SH, McRae AF, Lohman K, Sha J, Absher DM, Ferrucci L, Zhao W, Demerath EW, Bressler J, Grove ML, Huan T, Liu C, Mendelson MM, Yao C, Kiel DP, Peters A, Wang-Sattler R, Visscher PM, Wray NR, Starr JM, Ding J, Rodriguez CJ, Wareham NJ, Irvin MR, Zhi D, Barrdahl M, Vineis P, Ambatipudi S, Uitterlinden AG, Hofman A, Schwartz J, Colicino E, Hou L, Vokonas PS, Hernandez DG, Singleton AB, Bandinelli S, Turner ST, Ware EB, Smith AK, Klengel T, Binder EB, Psaty BM, Taylor KD, Gharib SA, Swenson BR, Liang L, DeMeo DL, O'Connor GT, Herceg Z, Ressler KJ, Conneely KN, Sotoodehnia N, Kardia SL, Melzer D, Baccarelli AA, van Meurs JB, Romieu I, Arnett DK, Ong KK, Liu Y, Waldenberger M, 2 Deary IJ, Fornage M, Levy D, London SJ. 2016. Epigenetic Signatures of Cigarette Smoking. Circ Cardiovasc Genet. 9:436-447. (co-first author) DOI: 10.1161/CIRCGENETICS.116.001506


X N Gao, F Yan, J Lin, L Gao, X L Lu, S C Wei, N Shen, J X Pang, Q Y Ning, Y Komeno, A L Deng, Y H Xu, J L Shi, Y H Li, D E Zhang, C Nervi, S J Liu, L Yu. AML1/ETO cooperates with HIF1α to promote leukemogenesis through DNMT3a transactivation. Leukemia. 2015 Aug;29(8):1730-40 DOI: 10.1038/leu.2015.56

Fei Yan, Na Shen, Jiuxia Pang, Julian R Molina, Ping Yang, Shujun Liu. The DNA Methyltransferase DNMT1 and Tyrosine-Protein Kinase KIT Cooperatively Promote Resistance to 5-Aza-2'-deoxycytidine (Decitabine) and Midostaurin (PKC412) in Lung Cancer Cells. J Biol Chem. 2015 Jul 24;290(30):18480-94 DOI: 10.1074/jbc.M114.633693

“Dual screening of BPTF and Brd4 using protein-observed fluorine NMR uncovers new bromodomain probe molecules.” A. K. Urick, L. M. L. Hawk, M. K. Cassel, N. K. Mishra, S. Liu, N. Adhikari, W. Zhang, C. O. dos Santos, J.L. Hall, W. C. K. Pomerantz*, ACS. Chem. Biol. 2015, 10, 2246-56. Hear the interview at the 5:30 mark:


F Yan, N Shen, J Pang, D Xie, B Deng, J R Molina, P Yang, S Liu. Restoration of miR-101 suppresses lung tumorigenesis through inhibition of DNMT3a-dependent DNA methylation. Cell Death Dis. 2014 Sep 11;5(9):e1413 DOI: 10.1038/cddis.2014.380

“Fluorinated aromatic amino acids are sensitive probes for bromodomain ligand interactions.” N. K. Mishra, A. K. Urick, S. W. Ember, E. Schönbrunn, W. C. Pomerantz*, ACS. Chem. Biol. 2014 9, 2755-60.