Rothbart Laboratory

Selected Publications

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


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

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 cellsJournal 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    

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  


Shanle EK, Rothbart SB, Strahl BD. 2014. Chromatin biochemistry enters the next generation of code ‘seq-ing.’ Nat Methods 11(8): 799-800.

Greer EL, Beese-Sims SE, Brookes E, Spadafora R, Zhu Y, Rothbart SB, Aristizabal-Corrales D, Chen S, Badeaux AI, Jin Q, Wang W, Strahl BD, Colaiácovo MP, Shi Y. 2014. A histone methylation network regulates transgenerational epigenetic memory in C. elegansCell Rep 7(1):113-126. 

Rothbart SB, Strahl BD. 2014. Interpreting the language of histone and DNA modificationsBBA-Gene Regul Mech 1839(8):627-643. 

Kim HS, *Mukhopadhyay R, *Rothbart SB, Silva AC, Vanoosthuyse V, Radovani E, Kislinger T, Roguev A, Colm JR, Xu J, Harlizawati J, Hardwick KG, Greenblatt JF, Krogan NJ, Fillingham J, Strahl BD, Bouhassira EE, Edelmann W, Keogh MC. 2014. Identification of a BET family Bromodomain/Casein Kinase II/TAF-containing complex as a regulator of mitotic condensin functionCell Rep 6(5):892-905. 
*Equal contribution

*Klein BJ, *Piao L, Xi Y, Rincon-Arano H, Rothbart SB, Peng D, Wen H, Larson C, Zhang X, Zheng X, Cortazar M, Pena PV, Mangan A, Bentley DL, Strahl BD, Groudine M, Li W, Shi X, Kutateladze TG. 2014 The histone-H3K4-specific demethylase KDM5B binds to its substrate and product through distinct PHD fingersCell Rep 6(2): 325-335. 
*Equal contribution


Kinkelin K, Wozniak GG, Rothbart SB, Lidschreiber M, Strahl BD, Cramer P. 2013. Structures of RNA polymerase II complexes with Bye1, a chromatin-binding PHF3/DIDO homologueProc Natl Acad Sci 110(38): 15277-15282. 

*Gatchalian J, *Fütterer A, Rothbart SB, Tong Q, Rincon-Arano H, Sánchez de Diego A, Groudine M, Strahl BD, Martínez-A C, van Wely K, Kutateladze TG. 2013. Dido3 PHD modulates cell differentiation and divisionCell Rep 4(1):148-158.
*Equal contribution

*Ali M, *Rincon-Arano H, Zhao W, Rothbart SB, Tong Q, Parkhurst S, Strahl BD, Deng L, Groudine M, Kutateladze TG. 2013. Molecular basis for chromatin binding and regulation of MLL5Proc Natl Acad Sci 110(28):11296-11301. 
*Equal contribution

Rothbart SB, *Dickson BM, *Ong MS, *Krajewski K, Houliston S, Kireev DB, Arrowsmith CH, Strahl BD. 2013. Multivalent histone engagement by the linked tandem Tudor and PHD domains of UHRF1 is required for the epigenetic inheritance of DNA methylationGenes Dev 27(11):1288-1298. 
*Equal contribution

*Cai L, *Rothbart SB, *Lu R, Xu B, Chen WY, Tripathy A, Rockowitz S, Zheng D, Patel DJ, Allis CD, Strahl BD, Song J, Wang GG. 2013. An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targetingMol Cell 49(3):571-582. 
*Equal contribution


Ali M, Yan K, Lalonde ME, Degerny C, Rothbart SB, Strahl BD, Cote J, Yang XJ, Kutateladze TG. 2012. Tandem PHD fingers of MORF/MOZ acetyltransferases display selectivity for acetylated histone H3 and are required for the association with chromatinJ Mol Biol 424(5):328-338. 

Rothbart SB, Krajewski K, Nady N, Tempel W, Xue S, Badeaux AI, Barsyte-Lovejoy D, Martinez JY, Bedford MT, Fuchs SM, Arrowsmith CH, Strahl BD. 2012. Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylationNat Struct Mol Biol 19(11):1155-1160. 

Rothbart SB, Krajewski K, Strahl BD, Fuchs SM. 2012. Peptide microarrays to interrogate the “histone code”Methods Enzymol 512:107-135. 

Rothbart SB, Lin S, Britton LM, Krajewski K, Keogh MC, Garcia BA, Strahl BD. 2012. Poly-acetylated chromatin signatures are preferred epitopes for site-specific histone H4 acetyl antibodiesSci Rep 2:489.