616.234.5000

Publications

Rothbart Laboratory

Selected Publications

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

2017

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.     Article

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.      PubMed

2016

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-seq. Epigenomics Chromatin 9:49.       Article

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 BRD4. J Chem Phys 145:154113.      Article

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 Phf5a. Nat Cell Biol 18(11):1127–1138.     Article

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 ATPase. Cell Rep 16(12):3195–3207.       Article

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.      Article

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.       PubMed

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.       PubMed       Article

2015

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

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.    PubMed

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.     PubMed 

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.    PubMed

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 calixarenes. J Biol Chem. 10(4):10721081.    PubMed

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 specificity. Mol Cell. 59(3):502–511        PubMed

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          PubMed

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

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 p53. Structure. 23(2):322-331 PubMed

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   PubMed

2014

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

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. PubMed     Article

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

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 function. Cell Rep 6(5):892-905. PubMed     Article
*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 fingers. Cell Rep 6(2): 325-335. PubMed     Article
*Equal contribution

2013

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 homologue. Proc Natl Acad Sci 110(38): 15277-15282. PubMed     Article

*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 division. Cell Rep 4(1):148-158. PubMed     Article
*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 MLL5. Proc Natl Acad Sci 110(28):11296-11301. PubMed     Article
*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 methylation. Genes Dev 27(11):1288-1298. PubMed     Article
*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 targeting. Mol Cell 49(3):571-582. PubMed     Article
*Equal contribution

2012

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 chromatin. J Mol Biol 424(5):328-338. PubMed     Article

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 methylation. Nat Struct Mol Biol 19(11):1155-1160. 
PubMed
     Article

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

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 antibodies. Sci Rep 2:489. PubMed     Article