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Items: 22

1.

Facile target validation in an animal model with intracellularly expressed monobodies.

Gupta A, Xu J, Lee S, Tsai ST, Zhou B, Kurosawa K, Werner MS, Koide A, Ruthenburg AJ, Dou Y, Koide S.

Nat Chem Biol. 2018 Jul 16. doi: 10.1038/s41589-018-0099-z. [Epub ahead of print]

PMID:
30013062
2.

Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm.

Yang XH, Nadadur RD, Hilvering CR, Bianchi V, Werner M, Mazurek SR, Gadek M, Shen KM, Goldman JA, Tyan L, Bekeny J, Hall JM, Lee N, Perez-Cervantes C, Burnicka-Turek O, Poss KD, Weber CR, de Laat W, Ruthenburg AJ, Moskowitz IP.

Elife. 2017 Dec 27;6. pii: e31683. doi: 10.7554/eLife.31683.

3.

Quantitative and Structural Assessment of Histone Methyllysine Analogue Engagement by Cognate Binding Proteins Reveals Affinity Decrements Relative to Those of Native Counterparts.

Chen Z, Notti RQ, Ueberheide B, Ruthenburg AJ.

Biochemistry. 2018 Jan 23;57(3):300-304. doi: 10.1021/acs.biochem.7b00926. Epub 2017 Nov 10.

PMID:
29111671
4.

Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription.

Werner MS, Sullivan MA, Shah RN, Nadadur RD, Grzybowski AT, Galat V, Moskowitz IP, Ruthenburg AJ.

Nat Struct Mol Biol. 2017 Jul;24(7):596-603. doi: 10.1038/nsmb.3424. Epub 2017 Jun 19.

5.

Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation.

Hattori T, Lai D, Dementieva IS, Montaño SP, Kurosawa K, Zheng Y, Akin LR, Świst-Rosowska KM, Grzybowski AT, Koide A, Krajewski K, Strahl BD, Kelleher NL, Ruthenburg AJ, Koide S.

Proc Natl Acad Sci U S A. 2016 Feb 23;113(8):2092-7. doi: 10.1073/pnas.1522691113. Epub 2016 Feb 9.

6.

Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes.

Werner MS, Ruthenburg AJ.

Cell Rep. 2015 Aug 18;12(7):1089-98. doi: 10.1016/j.celrep.2015.07.033. Epub 2015 Aug 6.

7.

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.

8.

Calibrating ChIP-Seq with Nucleosomal Internal Standards to Measure Histone Modification Density Genome Wide.

Grzybowski AT, Chen Z, Ruthenburg AJ.

Mol Cell. 2015 Jun 4;58(5):886-99. doi: 10.1016/j.molcel.2015.04.022. Epub 2015 May 21.

9.

Traceless semisynthesis of a set of histone 3 species bearing specific lysine methylation marks.

Chen Z, Grzybowski AT, Ruthenburg AJ.

Chembiochem. 2014 Sep 22;15(14):2071-5. doi: 10.1002/cbic.201402313. Epub 2014 Aug 22.

10.

Recombinant antibodies to histone post-translational modifications.

Hattori T, Taft JM, Swist KM, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Krajewski K, Strahl BD, White KP, Farnham PJ, Zhao Y, Koide S.

Nat Methods. 2013 Oct;10(10):992-5. doi: 10.1038/nmeth.2605. Epub 2013 Aug 18.

11.

Does activation of the anti proton, rather than concertedness, determine the stereochemistry of base-catalyzed 1,2-elimination reactions? Anti stereospecificity in E1cB eliminations of β-3-trifluoromethylphenoxy esters, thioesters, and ketones.

Mohrig JR, Beyer BG, Fleischhacker AS, Ruthenburg AJ, John SG, Snyder DA, Nyffeler PT, Noll RJ, Penner ND, Phillips LA, Hurley HL, Jacobs JS, Treitel C, James TL, Montgomery MP.

J Org Chem. 2012 Mar 16;77(6):2819-28. doi: 10.1021/jo300053w. Epub 2012 Feb 24.

PMID:
22321002
12.

The United States of histone ubiquitylation and methylation.

Werner M, Ruthenburg AJ.

Mol Cell. 2011 Jul 8;43(1):5-7. doi: 10.1016/j.molcel.2011.06.015.

13.

Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions.

Ruthenburg AJ, Li H, Milne TA, Dewell S, McGinty RK, Yuen M, Ueberheide B, Dou Y, Muir TW, Patel DJ, Allis CD.

Cell. 2011 May 27;145(5):692-706. doi: 10.1016/j.cell.2011.03.053. Epub 2011 May 19.

14.

Multiple interactions recruit MLL1 and MLL1 fusion proteins to the HOXA9 locus in leukemogenesis.

Milne TA, Kim J, Wang GG, Stadler SC, Basrur V, Whitcomb SJ, Wang Z, Ruthenburg AJ, Elenitoba-Johnson KS, Roeder RG, Allis CD.

Mol Cell. 2010 Jun 25;38(6):853-63. doi: 10.1016/j.molcel.2010.05.011. Epub 2010 Jun 10.

15.

Multivalent engagement of chromatin modifications by linked binding modules.

Ruthenburg AJ, Li H, Patel DJ, Allis CD.

Nat Rev Mol Cell Biol. 2007 Dec;8(12):983-94. Review.

16.

How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers.

Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ.

Nat Struct Mol Biol. 2007 Nov;14(11):1025-1040. doi: 10.1038/nsmb1338. Epub 2007 Nov 5. Review.

17.

Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark.

Ruthenburg AJ, Allis CD, Wysocka J.

Mol Cell. 2007 Jan 12;25(1):15-30. Review.

18.

Regulation of MLL1 H3K4 methyltransferase activity by its core components.

Dou Y, Milne TA, Ruthenburg AJ, Lee S, Lee JW, Verdine GL, Allis CD, Roeder RG.

Nat Struct Mol Biol. 2006 Aug;13(8):713-9. Epub 2006 Jul 30.

PMID:
16878130
19.

Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex.

Ruthenburg AJ, Wang W, Graybosch DM, Li H, Allis CD, Patel DJ, Verdine GL.

Nat Struct Mol Biol. 2006 Aug;13(8):704-12. Epub 2006 Jul 9.

20.

Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA.

Losey HC, Ruthenburg AJ, Verdine GL.

Nat Struct Mol Biol. 2006 Feb;13(2):153-9. Epub 2006 Jan 15.

PMID:
16415880
21.

Nucleotide-dependent domain movement in the ATPase domain of a human type IIA DNA topoisomerase.

Wei H, Ruthenburg AJ, Bechis SK, Verdine GL.

J Biol Chem. 2005 Nov 4;280(44):37041-7. Epub 2005 Aug 12.

22.

A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias.

Ruthenburg AJ, Graybosch DM, Huetsch JC, Verdine GL.

J Biol Chem. 2005 Jul 15;280(28):26177-84. Epub 2005 May 15.

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