Rothbart Laboratory

Selected Publications

For comprehensive lists of Dr. Rothbart’s publications please visit his Google Scholar page or his PubMed.


Slaughter MJ, Shanle EK, Khan A, Chua KF, Hong T, Boxer LD, Allis CD, Josefowicz SZ, Garcia BA, Rothbart SB, Strahl BD, Davis IJ. 2021. HDAC inhibition results in widespread alteration of the histone acetylation landscape and BRD4 targeting to gene bodies. Cell Rep 34(3):108638.


Vaughan RM, Kupai A, Rothbart SB. 2020. Chromatin regulation through ubiquitin and ubiquitin-like histone modifications. Trends Biochem Sci.

Franks JL, Martinez-Chacin RC, Wang X, Tiedemann RL, Bonacci T, Choudhury R, Bolhuis DL, Enrico TP, Mouery RD, Damrauer JS, Yan F, Harrison JS, Major MB, Hoadley KA, Suzuki A, Rothbart SB, Brown NG, Emanuele MJ. 2020. In silico APC/C substrate discovery reveals cell cycle-dependent degradation of UHRF1 and other chromatin regulators. PLoS Biol.

Fan H, Atiya HI, Wang Y, Pisanic TR, Wang TH, Shih IM, Foy KK, Frisbie L, Buckanovich RJ, Chomiak AA, Tiedemann RL, Rothbart SB, Chandler C, Shen H, Coffman LG. 2020. Epigenomic reprogramming toward mesenchymal-epithelial transition in ovarian-cancer-associated mesenchymal stem cells drives metastasis. Cell Rep.

Vaughan RM, Kupai A, Foley CA, Sagum CA, Tibben BM, Eden HE, Tiedemann RL, Berryhill CA, Patel V, Shaw KM, Krajewski K, Strahl BD, Bedford MT, Frye SV, Dickson BM, Rothbart SB. 2020. The histone and non-histone methyllysine reader activities of the UHRF1 tandem Tudor domain are dispensable for the propagation of aberrant DNA methylation patterning in cancer cells. Epigenetics Chromatin 13(1):44. 

Armache A, Yang S, Martínez de Paz A, Robbins LE, Durmaz C, Cheong JQ, Ravishankar A, Daman AW, Ahimovic DJ, Klevorn T, Yue Y, Arslan T, Lin S, Panchenko T, Hrit J, Wang M, Thudium S, Garcia BA, Korb E, Armache KJ, Rothbart SB, Hake SB, Allis CD, Li H, Josefowicz SZ. 2020. Histone H3.3 phosphorylation amplifies stimulation-induced transcription. Nature 583(7818):852–857.

Rothbart SB, Baylin SB. 2020. Epigenetic therapy for epithelioid sarcoma. Cell 181(2):211.

Dickson BM, Tiedemann RL, Chomiak AA, Cornett EM, Vaughan RM, Rothbart SB. 2020. A physical basis for quantitative ChIP-sequencing. J Biol Chem.
*Selected as an Editor’s Pick and featured on the cover

Kupai A, Vaughan RM, Dickson BM, Rothbart SB. 2020. A degenerate peptide library approach to reveal sequence determinants of methyllysine-driven protein interactions. Front Cell Dev Biol.


Colino-Sanguino Y, Cornett EM, Moulder D, Smith GC, Hrit J, Cordeiro-Spinetti E, Vaughan RM, Krajewski K, Rothbart SB*, Clark SJ*, Valdés-Mora F*. 2019. A read/write mechanism connects p300 Bromodomain function to H2A.Z acetylation. iScience S2589-0042(19)30434-1.
*Co-corresponding authors

Cornett E, Ferry L, Defossez PA, Rothbart SB. 2019. Lysine methylation regulators moonlighting outside the epigenome. Mol Cell.

Vaughan RM, Rothbart SB*, Dickson BM*. 2019. The finger loop of the SRA domain in the E3 ligase UHRF1 is a regulator of ubiquitin targeting and is required for maintaining DNA methylationJ Biol Chem.
*Co-corresponding authors

Zhang Y, Jang Y, Lee JE, Ahn J, Xu L, Holden MR, Cornett EM, Krajewski K, Klein BJ, Wang SP, Dou Y, Roeder RG, Strahl BD, Rothbart SB, Shi X, Ge K, Kutateladze TG. 2019. Selective binding of the PHD6 finger of MLL4 to histone H4K16ac links MLL4 and MOF. Nat Commun 10(1):2314.

Kong X*, Chen J*, Xie W*, Brown SM, Cai Y, Wu K, Fan D, Nie Y, Yegnasubramanian S, Tiedemann RL, Tao Y, Yen RWC, Topper MJ, Zahnow CA, Easwaran H, Rothbart SB#, Xia L#, Baylin SB#. 2019. Defining UHRF1 domains that support maintenance of human colon cancer DNA methylation and oncogenic properties. Cancer Cell.
*These authors contributed equally
#Co-corresponding authors
Selected as a paper of the month by National Institute of Environmental Health Sciences

Harlow ML*, Chassé MH*, Boguslawski EA, Sorensen KM, Gedminas MJ, Goosen JM, Rothbart SB, Taslim C, Lessnick SL, Peck A, Madaj ZB, Bowman MJ, Grohar PJ. 2019. Trabectedin inhibits EWS-FLI1 and evicts SWI/SNF from chromatin in a schedule-dependent manner. Clin Cancer Res.
*Equal contributions


Harris CJ, Scheibe M, Wongpalee SP, Liu W, Cornett EM, Vaughan RM, Li X, Chen W, Xue Y, Zhong Z, Yen L, Barshop WD, Rayatpisheh S, Gallego-Bartolome J, Groth M, Wang Z, Wohlschlegel JA, Du J, Rothbart SB, Butter F, Jacobsen SE. 2018. A DNA methylation reader complex that enhances gene transcription. Science 362(6419):1182–1186.

Cornett EM, Dickson BM, Krajewski K, Spellmon N, Umstead A, Vaughan RM, Shaw KM, Versluis PP, Cowles MW, Brunzelle J, Yang Z, Vega IE, Sun ZW, Rothbart SB. 2018. A functional proteomics platform to reveal the sequence determinants of lysine methyltransferase substrate selectivity. Sci Adv.

Shah RN, Grzybowski AT, Cornett EM, Johnstone AL, Dickson BM, Boone BA, Cheek MA, Cowles MW, Maryanski D, Meiners MJ, Tiedemann RL, Vaughan RM, Arora N, Sun ZW, Rothbart SB*, Keogh MC*, Ruthenberg AJ*. 2018. Examining the roles of H3K4 methylation states with systematically characterized antibodies. Mol Cell.
Video abstract
*Equal contributions

Javasky E, Shamir I, Gandhi S, Egri S, Sandler O, Rothbart SB, Kaplan N, Jaffe JD, Goren A, Simon I. 2018. Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns. Genome Res.

Vaughan RM, Dickson BM, Whelihan MF, Johnstone AL, Cornett EM, Cheek MA, Ausherman CA, Cowles MW, Sun ZW, Rothbart SB. 2018. Chromatin structure and its chemical modifications regulate the ubiquitin ligase substrate selectivity of UHRF1. Proc Natl Acad Sci U S A.

Vaughan RM, Dickson BM, Cornett EM, Harrison JS, Kuhlman B, Rothbart SB. 2018. Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance. Nuc Acids Res.

Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L, Liu S, Ji D, Rothbart SB, Wang Y, Wang GG, Song J. 2018. Structural basis for DNMT3A-mediated de novo DNA methylation. Nature.


Veland N, Hardikar S, Zhong Y, Gayatri S, Dan J, Strahl BD, Rothbart SB, Bedford MT, Chen T. 2017. The arginine methyltransferase PRMT6 regulates DNA methylation and contributes to global DNA hypomethylation in cancer. Cell Rep 21(2):3390–3397.

Cornett EM, Dickson BM, Rothbart SB. 2017. Analysis of histone antibody specificity with peptide microarrays. JoVE (126):doi: 10.3791/55912.

Ma H, Duan J, Ke J, He Y, Gu X, Xu TH, Yu H, Wang Y, Brunzelle JS, Jiang Y, Rothbart SB, Xu HE, Li J, Melcher K. 2017. A D53 repression motif induces oligomerization of TOPLESS copressors and promotes assembly of a corepressor-nucleosome complex. Sci Adv.

Shanle EK, Shinsky SA, Bridgers JB, Bae N, Sagum C, Krajewski K, Rothbart SB, Bedford MT, Strahl BD. 2017. Histone peptide microarray screen of chromo and Tudor domains defines new histone lysine methylation interactions. Epigenetics Chromatin 10:12.


Busby M, Xue C, Li C, Farjourn Y, Gienger E, Yofe I, Gladden A, Epstein CB, Cornett EM, Rothbart SB, Nusbaum C, Goren A. 2016. Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seqEpigenomics Chromatin 9:49.

Dickson BM, de Waal PW, Ramjan ZH, Xu HE, Rothbart SB. 2016. A fast, open source implementation of adaptive biasing potential uncovers a ligand design strategy from the chromatin regulator BRD4J Chem Phys 145:154113.

Strikoudis A, Lazaris C, Trimarchi T, Galvoa Neto AL, Yang Y, Ntziachristos P, Rothbart SB, Buckley S, Dolgalev I, Stadtfeld M, Strahl BD, Dynlacht BD, Tsirigos A, Iannia Aifantis. 2016. Regulation of transcriptional elongation in pluripotency and cell differentiation by the PHD-finger protein Phf5aNat Cell Biol 18(11):1127–1138.

Andrews FH, Tong Q, Sullivan KD, Cornett EM, Zhang Y, Ali M, Ahn J, Pandey A, Guo AH, Strahl BD, Costello JC, Espinosa JM, Rothbart SB, Kutateladze. 2016. Multivalent chromatin engagement and inter-domain crosstalk regulate MORC3 ATPaseCell Rep 16(12):3195–3207.

Harrison J, Cornett E, Goldfarb D, DaRosa P, Li Z, Yan F, Dickson B, Guo A, Cantu D, Kaustov L, Brown P, Arrowsmith C, Klevit R, Erie D, Major B, Krajewski K, Kulhman B, Strahl B, Rothbart SB. 2016. Hemi-methylated DNA regulates DN methylation inheritance through allosteric activation of H3 ubiquitylation for UHRF1. eLife.  

Cornett EM, Dickson BM, Vaughan RM, Krishnan S, Trievel RC, Strahl BD, Rothbart SB. 2016. Substrate specificity profiling of histone-modifying enzymes by peptide microarray. Methods Enzymol 574:31–52.

Dickson BM, Cornett EM, Ramjan Z, Rothbart SB. 2016. ArrayNinja: An open source platform for unified planning and analysis of microarray experiments. Methods Enzymol 574:53–57.


Agarwal S, Bell C, Rothbart SB, Moran RG. 2015. AMPK control of mTORC1 is p53- and TSC2-independent in pemetrexed-treated carcinoma cellsJ Biol Chem 290(46):27473–27486.

Cliffe AR, Arbuckle JH, Vogel JL, Geden MJ, Rothbart SB, Cusack CL, Kristie TM, Deshmukh M. 2015. Neuronal stress pathway mediating a histone methyl/phospho switch is required for herpes simplex virus reactivation. Cell Host Microbe. 18(6):649–658.

Zhang ZM, Rothbart SB, Allison DF, Cai Q, Harrison JS, Li L, Wang Y, Strahl BD, Wang GG, Song J. 2015. An allosteric interaction links USP7 to deubiquitination and chromatin targeting of UHRF1. Cell Rep 12(9):1400–1406.

Simon JM, Parker JS, Liu F, Rothbart SB, Ait-Si-Ali S, Strahl BD, Jin J, Davis IJ, Mosley AL, Pattenden SG. 2015. A role for widely interspaced zinc finger (WIZ) in retention of the G9a methyltransferase on chromatin. J Biol Chem. 290(43):26088–26102.  

Ali M, Daze KD, Strongin DE, Rothbart SB, Rincon-Arano H, Allen HF, Li J, Strahl BD, Hof F, Kutatladze TG. 2015. Molecular insight into inhibition of the methylated histone-plant homeodomain complexes by calixarenesJ Biol Chem. 10(4):10721081. 

Rothbart SB*, Dickson BM, Raab JR, Grzybowski AT, Krajewski K, Guo AH, Shanle EK, Josefowicz SZ, Fuchs SM, Allis CD, Magnuson TR, Ruthenburg AJ, Strahl BD*. 2015. An interactive database for the assessment of histone antibody specificityMol Cell. 59(3):502–511
*Equal contributions

Perfetti MT, Baughman BM, Dickson BM, Mu Y, Cui G, Mader P, Dong A, Norris JL, Rothbart SB, Strahl BD, Brown PJ, Janzen WP, Arrowsmith CH, Mer G, McBride KM, James LI, Frye SV. 2015. Identification of a fragment-like small molecule ligand for the methyl-lysine binding protein, 53BP1. ACS Chem Biol 10(4):1072—1081

Rothbart SB, Dickson BM, and Strahl BD. 2015. From histones to ribosomes: A chromatin regulator tangoes with translationCancer Discov 5(3):228–230

Tong Q, Mazur SJ, Rincon-Arano H, Rothbart SB, Kuznetsov DM, Cui G, Liu WH, Gete Y, Klein BJ, Jenkins L, Mer G, Kutateladze AG, Strahl BD, Groudine M, Appella E, Kutateladze TG. 2015. An acetyl-methyl switch drives a conformational change in p53Structure. 23(2):322-331

Tong Q, Cui G, Botuyan MV, Rothbart SB, Hayashi R, Musselman CA, Singh N, Appella E, Strahl BD, Mer G, Kutateladze TG. 2015. Structural plasticity of methyllysine recognition by the tandem Tudor domain of 53BP1. Structure. 23(2):312-322