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Items: 44

1.

Trabectedin Inhibits EWS-FLI1 and Evicts SWI/SNF from Chromatin in a Schedule Dependent Manner.

Harlow ML, Chasse MH, Boguslawski EA, Sorensen KM, Gedminas JM, Kitchen-Goosen SM, Rothbart SB, Taslim C, Lessnick SL, Peck AS, Madaj ZB, Bowman MJ, Grohar PJ.

Clin Cancer Res. 2019 Feb 5. pii: clincanres.3511.2018. doi: 10.1158/1078-0432.CCR-18-3511. [Epub ahead of print]

PMID:
30723142
2.

A DNA methylation reader complex that enhances gene transcription.

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.

Science. 2018 Dec 7;362(6419):1182-1186. doi: 10.1126/science.aar7854.

PMID:
30523112
3.

A functional proteomics platform to reveal the sequence determinants of lysine methyltransferase substrate selectivity.

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.

Sci Adv. 2018 Nov 28;4(11):eaav2623. doi: 10.1126/sciadv.aav2623. eCollection 2018 Nov.

4.

Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies.

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, Ruthenburg AJ.

Mol Cell. 2018 Oct 4;72(1):162-177.e7. doi: 10.1016/j.molcel.2018.08.015. Epub 2018 Sep 20.

PMID:
30244833
5.

Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns.

Javasky E, Shamir I, Gandhi S, Egri S, Sandler O, Rothbart SB, Kaplan N, Jaffe JD, Goren A, Simon I.

Genome Res. 2018 Oct;28(10):1455-1466. doi: 10.1101/gr.230300.117. Epub 2018 Aug 30.

PMID:
30166406
6.

Chromatin structure and its chemical modifications regulate the ubiquitin ligase substrate selectivity of UHRF1.

Vaughan RM, Dickson BM, Whelihan MF, Johnstone AL, Cornett EM, Cheek MA, Ausherman CA, Cowles MW, Sun ZW, Rothbart SB.

Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):8775-8780. doi: 10.1073/pnas.1806373115. Epub 2018 Aug 13.

7.

Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance.

Vaughan RM, Dickson BM, Cornett EM, Harrison JS, Kuhlman B, Rothbart SB.

Nucleic Acids Res. 2018 May 18;46(9):4405-4416. doi: 10.1093/nar/gky151.

8.

Structural basis for DNMT3A-mediated de novo DNA methylation.

Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L, Liu S, Ji D, Rothbart SB, Wang Y, Wang GG, Song J.

Nature. 2018 Feb 15;554(7692):387-391. doi: 10.1038/nature25477. Epub 2018 Feb 7.

9.

The Arginine Methyltransferase PRMT6 Regulates DNA Methylation and Contributes to Global DNA Hypomethylation in Cancer.

Veland N, Hardikar S, Zhong Y, Gayatri S, Dan J, Strahl BD, Rothbart SB, Bedford MT, Chen T.

Cell Rep. 2017 Dec 19;21(12):3390-3397. doi: 10.1016/j.celrep.2017.11.082.

10.

Analysis of Histone Antibody Specificity with Peptide Microarrays.

Cornett EM, Dickson BM, Rothbart SB.

J Vis Exp. 2017 Aug 1;(126). doi: 10.3791/55912.

11.

A D53 repression motif induces oligomerization of TOPLESS corepressors and promotes assembly of a corepressor-nucleosome complex.

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.

Sci Adv. 2017 Jun 2;3(6):e1601217. doi: 10.1126/sciadv.1601217. eCollection 2017 Jun.

12.

Histone peptide microarray screen of chromo and Tudor domains defines new histone lysine methylation interactions.

Shanle EK, Shinsky SA, Bridgers JB, Bae N, Sagum C, Krajewski K, Rothbart SB, Bedford MT, Strahl BD.

Epigenetics Chromatin. 2017 Mar 14;10:12. doi: 10.1186/s13072-017-0117-5. eCollection 2017.

13.

Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq.

Busby M, Xue C, Li C, Farjoun Y, Gienger E, Yofe I, Gladden A, Epstein CB, Cornett EM, Rothbart SB, Nusbaum C, Goren A.

Epigenetics Chromatin. 2016 Nov 4;9:49. eCollection 2016.

14.

A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4.

Dickson BM, de Waal PW, Ramjan ZH, Xu HE, Rothbart SB.

J Chem Phys. 2016 Oct 21;145(15):154113.

15.

Multivalent Chromatin Engagement and Inter-domain Crosstalk Regulate MORC3 ATPase.

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 TG.

Cell Rep. 2016 Sep 20;16(12):3195-3207. doi: 10.1016/j.celrep.2016.08.050.

16.

Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1.

Harrison JS, Cornett EM, Goldfarb D, DaRosa PA, Li ZM, Yan F, Dickson BM, Guo AH, Cantu DV, Kaustov L, Brown PJ, Arrowsmith CH, Erie DA, Major MB, Klevit RE, Krajewski K, Kuhlman B, Strahl BD, Rothbart SB.

Elife. 2016 Sep 6;5. pii: e17101. doi: 10.7554/eLife.17101.

17.

ArrayNinja: An Open Source Platform for Unified Planning and Analysis of Microarray Experiments.

Dickson BM, Cornett EM, Ramjan Z, Rothbart SB.

Methods Enzymol. 2016;574:53-77. doi: 10.1016/bs.mie.2016.02.002. Epub 2016 Mar 2.

18.

Substrate Specificity Profiling of Histone-Modifying Enzymes by Peptide Microarray.

Cornett EM, Dickson BM, Vaughan RM, Krishnan S, Trievel RC, Strahl BD, Rothbart SB.

Methods Enzymol. 2016;574:31-52. doi: 10.1016/bs.mie.2016.01.008. Epub 2016 Feb 16.

19.

Neuronal Stress Pathway Mediating a Histone Methyl/Phospho Switch Is Required for Herpes Simplex Virus Reactivation.

Cliffe AR, Arbuckle JH, Vogel JL, Geden MJ, Rothbart SB, Cusack CL, Strahl BD, Kristie TM, Deshmukh M.

Cell Host Microbe. 2015 Dec 9;18(6):649-58. doi: 10.1016/j.chom.2015.11.007.

20.

AMP-activated Protein Kinase (AMPK) Control of mTORC1 Is p53- and TSC2-independent in Pemetrexed-treated Carcinoma Cells.

Agarwal S, Bell CM, Rothbart SB, Moran RG.

J Biol Chem. 2015 Nov 13;290(46):27473-86. doi: 10.1074/jbc.M115.665133. Epub 2015 Sep 21.

21.

A Role for Widely Interspaced Zinc Finger (WIZ) in Retention of the G9a Methyltransferase on Chromatin.

Simon JM, Parker JS, Liu F, Rothbart SB, Ait-Si-Ali S, Strahl BD, Jin J, Davis IJ, Mosley AL, Pattenden SG.

J Biol Chem. 2015 Oct 23;290(43):26088-102. doi: 10.1074/jbc.M115.654459. Epub 2015 Sep 3.

22.

An Allosteric Interaction Links USP7 to Deubiquitination and Chromatin Targeting of UHRF1.

Zhang ZM, Rothbart SB, Allison DF, Cai Q, Harrison JS, Li L, Wang Y, Strahl BD, Wang GG, Song J.

Cell Rep. 2015 Sep 1;12(9):1400-6. doi: 10.1016/j.celrep.2015.07.046. Epub 2015 Aug 20.

23.

Molecular Insights into Inhibition of the Methylated Histone-Plant Homeodomain Complexes by Calixarenes.

Ali M, Daze KD, Strongin DE, Rothbart SB, Rincon-Arano H, Allen HF, Li J, Strahl BD, Hof F, Kutateladze TG.

J Biol Chem. 2015 Sep 18;290(38):22919-30. doi: 10.1074/jbc.M115.669333. Epub 2015 Jul 30.

24.

An Interactive Database for the Assessment of Histone Antibody Specificity.

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.

Mol Cell. 2015 Aug 6;59(3):502-11. doi: 10.1016/j.molcel.2015.06.022. Epub 2015 Jul 23.

25.

From histones to ribosomes: a chromatin regulator tangoes with translation.

Rothbart SB, Dickson BM, Strahl BD.

Cancer Discov. 2015 Mar;5(3):228-30. doi: 10.1158/2159-8290.CD-15-0073.

26.

An acetyl-methyl switch drives a conformational change in p53.

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.

Structure. 2015 Feb 3;23(2):322-31. doi: 10.1016/j.str.2014.12.010.

27.

Identification of a fragment-like small molecule ligand for the methyl-lysine binding protein, 53BP1.

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.

ACS Chem Biol. 2015 Apr 17;10(4):1072-81. doi: 10.1021/cb500956g. Epub 2015 Jan 28.

28.

Structural plasticity of methyllysine recognition by the tandem tudor domain of 53BP1.

Tong Q, Cui G, Botuyan MV, Rothbart SB, Hayashi R, Musselman CA, Singh N, Appella E, Strahl BD, Mer G, Kutateladze TG.

Structure. 2015 Feb 3;23(2):312-21. doi: 10.1016/j.str.2014.11.013. Epub 2015 Jan 8.

29.

Chromatin biochemistry enters the next generation of code 'seq-ing'.

Shanle EK, Rothbart SB, Strahl BD.

Nat Methods. 2014 Aug;11(8):799-800. doi: 10.1038/nmeth.3044. No abstract available.

30.

A histone methylation network regulates transgenerational epigenetic memory in C. elegans.

Greer EL, Beese-Sims SE, Brookes E, Spadafora R, Zhu Y, Rothbart SB, Aristizábal-Corrales D, Chen S, Badeaux AI, Jin Q, Wang W, Strahl BD, Colaiácovo MP, Shi Y.

Cell Rep. 2014 Apr 10;7(1):113-26. doi: 10.1016/j.celrep.2014.02.044. Epub 2014 Mar 27.

31.

Interpreting the language of histone and DNA modifications.

Rothbart SB, Strahl BD.

Biochim Biophys Acta. 2014 Aug;1839(8):627-43. doi: 10.1016/j.bbagrm.2014.03.001. Epub 2014 Mar 12. Review.

32.

Identification of a BET family bromodomain/casein kinase II/TAF-containing complex as a regulator of mitotic condensin function.

Kim HS, Mukhopadhyay R, Rothbart SB, Silva AC, Vanoosthuyse V, Radovani E, Kislinger T, Roguev A, Ryan CJ, Xu J, Jahari H, Hardwick KG, Greenblatt JF, Krogan NJ, Fillingham JS, Strahl BD, Bouhassira EE, Edelmann W, Keogh MC.

Cell Rep. 2014 Mar 13;6(5):892-905. doi: 10.1016/j.celrep.2014.01.029. Epub 2014 Feb 22.

33.

The histone-H3K4-specific demethylase KDM5B binds to its substrate and product through distinct PHD fingers.

Klein BJ, Piao L, Xi Y, Rincon-Arano H, Rothbart SB, Peng D, Wen H, Larson C, Zhang X, Zheng X, Cortazar MA, Peña PV, Mangan A, Bentley DL, Strahl BD, Groudine M, Li W, Shi X, Kutateladze TG.

Cell Rep. 2014 Jan 30;6(2):325-35. doi: 10.1016/j.celrep.2013.12.021. Epub 2014 Jan 9.

34.

Structures of RNA polymerase II complexes with Bye1, a chromatin-binding PHF3/DIDO homologue.

Kinkelin K, Wozniak GG, Rothbart SB, Lidschreiber M, Strahl BD, Cramer P.

Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):15277-82. doi: 10.1073/pnas.1311010110. Epub 2013 Sep 3.

35.

Dido3 PHD modulates cell differentiation and division.

Gatchalian J, Fütterer A, Rothbart SB, Tong Q, Rincon-Arano H, Sánchez de Diego A, Groudine M, Strahl BD, Martínez-A C, van Wely KH, Kutateladze TG.

Cell Rep. 2013 Jul 11;4(1):148-58. doi: 10.1016/j.celrep.2013.06.014. Epub 2013 Jul 3.

36.

Molecular basis for chromatin binding and regulation of MLL5.

Ali M, Rincón-Arano H, Zhao W, Rothbart SB, Tong Q, Parkhurst SM, Strahl BD, Deng LW, Groudine M, Kutateladze TG.

Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11296-301. doi: 10.1073/pnas.1310156110. Epub 2013 Jun 24.

37.

Multivalent histone engagement by the linked tandem Tudor and PHD domains of UHRF1 is required for the epigenetic inheritance of DNA methylation.

Rothbart SB, Dickson BM, Ong MS, Krajewski K, Houliston S, Kireev DB, Arrowsmith CH, Strahl BD.

Genes Dev. 2013 Jun 1;27(11):1288-98. doi: 10.1101/gad.220467.113.

38.

An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting.

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.

Mol Cell. 2013 Feb 7;49(3):571-82. doi: 10.1016/j.molcel.2012.11.026. Epub 2012 Dec 27.

39.

Tandem PHD fingers of MORF/MOZ acetyltransferases display selectivity for acetylated histone H3 and are required for the association with chromatin.

Ali M, Yan K, Lalonde ME, Degerny C, Rothbart SB, Strahl BD, Côté J, Yang XJ, Kutateladze TG.

J Mol Biol. 2012 Dec 14;424(5):328-38. doi: 10.1016/j.jmb.2012.10.004. Epub 2012 Oct 12.

40.

Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation.

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.

Nat Struct Mol Biol. 2012 Nov;19(11):1155-60. doi: 10.1038/nsmb.2391. Epub 2012 Sep 30.

41.

Peptide microarrays to interrogate the "histone code".

Rothbart SB, Krajewski K, Strahl BD, Fuchs SM.

Methods Enzymol. 2012;512:107-35. doi: 10.1016/B978-0-12-391940-3.00006-8.

42.

Poly-acetylated chromatin signatures are preferred epitopes for site-specific histone H4 acetyl antibodies.

Rothbart SB, Lin S, Britton LM, Krajewski K, Keogh MC, Garcia BA, Strahl BD.

Sci Rep. 2012;2:489. doi: 10.1038/srep00489. Epub 2012 Jul 3.

43.

Pemetrexed indirectly activates the metabolic kinase AMPK in human carcinomas.

Rothbart SB, Racanelli AC, Moran RG.

Cancer Res. 2010 Dec 15;70(24):10299-309. doi: 10.1158/0008-5472.CAN-10-1873.

44.

Therapeutics by cytotoxic metabolite accumulation: pemetrexed causes ZMP accumulation, AMPK activation, and mammalian target of rapamycin inhibition.

Racanelli AC, Rothbart SB, Heyer CL, Moran RG.

Cancer Res. 2009 Jul 1;69(13):5467-74. doi: 10.1158/0008-5472.CAN-08-4979. Epub 2009 Jun 23.

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