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2014

 

Jha, D. K. & Strahl, B. D. (2014) SET-ing the stage for DNA repair. Nat Struct Mol Biol. 5:655-657.

 

Wozniak, G. G. & Strahl, B. D. (2014) Catalysis-dependent stabilization of Bre1 fine-tunes histone H2B ubiquitylation to regulate gene transcription. Genes & Development. 28:1647-1652.

 

Shanle, E. K., Rothbart, S. B. & Strahl, B. D. (2014) Chromatin biochemistry enters the next generation of code ‘seq-ing’ Nature Methods. 11:799-800.

 

Jha, D. K. & Strahl, B. D. (2014) H3K36 methylation regulates chromatin remodeling and checkpoint activation after DSB. Nature Commun. 5:3965.

 

Greer, E. L., Beese-Sims, S. E., Spadafora, R., Rothbart, S. B., Badeaux, A. I., Strahl, B. D., Colaiácovo, M. P. & Shi, Y. A (2014) histone methylation network regulates transgenerational epigenetic memory in C. elegans. Cell Reports. 7:113-26.

 

Wozniak, G. G. & Strahl, B. D. (2014) Hitting the 'Mark': Interpreting Lysine Methylation in the Context of Active Transcription. BBA - Gene Regulatory Mechanisms. 10.1016/j.bbagrm.2014.03.002.

 

Rothbart S. B. & Strahl, B.D. (2014) Interpreting the language of histone and DNA modifications. BBA - Gene Regulatory Mechanisms. 10.1016/j.bbagrm.2014.03.001

 

Kim, H.-S., Mukhopadhyay, R., Rothbart, S. B., Silva, A. C., Vanoosthuyse, V., Radovani, E., Kislinger, T., Roguev, A., Ryan, C. J., Xu, J., Jahari, H., Hardwick, K., G., Greenblatt, J. F., Krogan, N. J., Fillingham, J., S., Strahl, B. D., Bouhassira, E., E., Edelmann, W. & Keogh, M.-C. Identification of a novel Bromodomain/Casein Kinase II/TAF-containing complex as a regulator of mitotic condensin function. Cell Reports. 6:1-14.

 

Klein, B. J., Piao, L., Xi, Yuanxin, Rincon-Arano, H., ROthbart, S. B., Larson, C., Wen, H., Zheng, X., Cortazar, M., Pena, P. V., Mangan, A., Bentley, D. L., Strahl, B. D., Groudine, M., Li, W., Shi, X., Kutateladze, T. G. (2014) The histone-H3K4-specific demethylase KDM5B binds to its substrate and product through distinct PHD dingers. Cell Reports. 6:1-11.

 

Dronamraju, R. & Strahl, B. D. (2014) A feed forward circuit comprising Spt6, Ctk1 and PAF regulates Pol II CTD phosphorylation and transcription elongation. Nucleic Acids Research. 42:870-881.

 

2013

Hattori, T., Taft, J., Swift, K., Luo, H., Witt, H., Slattery, M., Koide, A., Ruthenburg, A. J., Krajewski, K., Strahl, B. D., White, K. P., Farnham, P. J., Zhao, Y., Koide, S. (2013) Recombinant antibodies to histone posttranslational modifications. Nature Methods. 10:992-995.

 

McDaniel S. L. & Strahl, B. D. (2013) Stress-Free with Rpd3: A unique chromatin complex mediates the response to oxidative stress. Mol Cell Biol. 33:3726-3727.

 

Kinkelin, K., Wozniak, G. G., Rothbart, S. B., Lidschreiber, M., Strahl, B. D. & Cramer, P. Structures of RNA polymerase II complexes with Bye1, a chromatin-binding PHF3/DIDO1 homologue. (2013) Proc Natl Acad Sci USA. 110:15277-15282.

 

Gatchalian, J., Fütterer, A., Rothbart, S. B.,Tong, Q., Rincon-Arano, H., Sánchez de Diego, A. Groudine, M., Strahl, B. D., Martínez-A, C., van Wely, H. M. K. & Kutateladze, T. G. Dido3 PHD modulates cell differentiation and division. (2013) Cell Reports. 11:148-158.

 

Ali, M., Rincon-Arano, H., Zhao., W., Rothbart, S. B., Tong, Q., Parkhurst, S., Strahl, B. D., Deng, L.-W., Groudine, M., Kutateladze, T. G. (2013) Molecular basis for chromatin binding and regulation of MLL5. Proc Natl Acad Sci USA. 110:11296-11301.

 

Rothbart, S. B., Dickson, B. M., Ong, M. S., Krajewski, K., Houliston, S., Kireev, D. B., Arrowsmith, C. H. & Strahl, B. D. (2013) Multivalent histone engagement by the linked tandem Tudor and PHD domains of UHRF1 is required for the epigenetic inheritance of DNA methylation. Genes & Development. 27:1288-1298.

 

Law, J. A., Du, J., Hale, C. J., Feng, S., Krajewski, K., Strahl, B. D., Patel, D. J. & Jacobsen, S. E. (2013) SHH1 recruits RNA Polymerase-IV to RNA-directed DNA methylation targets. Nature. 498:385-389.

 

Cai, L., Rothbart, S. B., Lu, R., Xu, B., Tripathy, A., Chen, W.-Y., Zheng, D., Patel, D. J., Allis, C. D., Strahl, B. D., Song, J., Wang, G. G. (2013) An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting. Molecular Cell. 49:571-582.

 

2012

Ali, M., Yan, K., Lalonde, M.-E., Degerny, C., Rothbart, S. B., Strahl, B. D., Cote, J., Yang, X-.J. & Kutateladze, T., G. (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. 328-288.

 

Nishikori, S., Fuchs, S. M., Yasui, N., Wojcik, J., Koide, A., Strahl, B. D., Koide, S. A (2012) Broad ranges of affinity and specificty of anti-histone antibodies revealed by a quantitative peptide immunoprecipitation assay. J. Mol. Biol. 424:391-399.

 

Rothbart SB, Krajewski K, Nady N, Tempel W, Xue S, Badeaux AI, Barsyty-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. 19:1155-60.

 

Rizzardi LF, Dorn EE, Strahl BD, Cook JG (2012) H3K4 di-methylation promotes DNA replication origin function in Saccharomyces cerevisiae. Genetics. 192:371-384.

 

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, L-M, Krajewski K., Keogh M-C., Garcia, Strahl BD. (2012) Poly-acetylated chromatin signatures are preferred epitopes for site-specific histone H4 acetyl antibodies. Scientific Reports. 2:489.

 

Stolzenburg S, Rots MG, Beltran AS, Rivenbark AG, Yuan X, Strahl BD, Blancafort P. (2012) Targeted silencing of the oncogene transcription factor SOX2 in breast cancer. Nucleic Acid Research. 40, 6725-6740.

 

Rivenbark AG, Stolzenburg S, Yuan X, Strahl BD, Blancafort P. (2012) Epigenetic reprogramming of cancer cells by targeted DNA methylation. Epigenetics. 7, 1-11.

 

Fuchs SM, Kizer KO, Braberg H, Krogan N, Strahl BD. (2012) RNA polymerase II CTD phosphorylation regulates protein stability of the Set2 methyltransferase and histone H3 di- and trimethylation at lysine 36. J Biol Chem. 287, 3249-3256.

 

2011

Fuchs SM, Krajewski K, Miller V, Baker RW, Strahl BD. (2011) Influence of combinatorial histone modifications on antibody and effector protein recognition. Current Bio. 11, 53-58.

 

Gardner KE, Zhou L, Parra MA, Chen X, Strahl BD. (2011) Identification of lysine 37 of histone H2B as a novel site of methylation. PLoS ONE. 6:e16244.

 

Fuchs, S. M. & Strahl, B. D. (2011) Antibody recognition of histone post-translational modifications: emerging issues and future prospects. Epigenomics. 3:247-249.

 

Ramachandran S, Vogel L, Strahl BD, Dokholyan NV. (2011) Thermodynamic stability of protein-protein interaction is a necessary but not sufficient driving force for evolutionary concervation. PLoS Comput Biol. 7:e1001042.

 

Gardner KE, Allis CD, Strahl BD. (2011) OPERating ON chromatin, a colorful language where context matters. J. Mol Bio. 409, 36-46

 

Key Papers From 2009 and Earlier

 

Nakanishi S, Lee JS, Gardner KE, Gardner JM, Takahashi Y-H, Chandrasekharan MB, Sun Z-W, Osley MA, Strahl BD, Jaspersen SL, Shilatifard A. (2009) Histone H2BK123 monoubiquitination is the critical determinant for H3K4 and H3K79 trimethylation by COMPASS and Dot1. J of Cell Bio. 186, 371-377.


Lickwar C, Rao B, Shabalin A, Nobel A, Strahl BD, Lieb JD. (2009) The Set2/Rpd3S pathway suppresses cryptic transcription without regard to gene length or transcription frequency PLoS ONE. 4:e4886.

 

Fuchs SM, Laribee RN, Strahl BD. (2009) Protein modifications in transcription elongation. BBA - Gene Regulatory Mechanisms. 1789:26-36.

 

Youdell ML, Kizer KO, Kisseleva-Romanova E, Fuchs SM, Duro E, Strahl BD, Mellor J. (2008) Roles for Ctk1 and Spt6 in regulating the different methylation states of histone H3 lysine 36. Mol. Cell. Biol. 28, 4915-26.

 

Merker JD, Dominska M, Greenwell PW, Rinella E, Bouck DC, Shibata Y, Strahl BD, Mieczkowski P, Petes TD. (2008) The histone methylase Set2p and the histone deacetylase Rpd3p repress meiotic recombination at the HIS4 meiotic recombination hotspot in Saccharomyces cerevisiae. DNA Repair (Amst) 7, 1298-308.

 

Henikoff S, Strahl BD, Warburton PE. (2008) Epigenomics: a roadmap to chromatin. Science 322, 853.

 

Wyce A, Xiao T, Whelan KA, Kosman C, Walter W, Eick D, Hughes TR, Krogan NJ, Strahl BD, Berger SL. (2007) H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complex. Mol. Cell 27, 275-88.

 

Ashly G. Rivenbark & Brian D. Strahl (2007) Molecular biology. Unlocking cell fate. Science 318, 403-4

 

Laribee RN, Shibata Y, Mersman DP, Collins SR, Kemmeren P, Roguev A, Weissman JS, Briggs SD, Krogan NJ, Strahl BD. (2007) CCR4/NOT complex associates with the proteasome and regulates histone methylation. Proc. Natl. Acad. Sci. USA 104, 5836-41.

 

Morris SA, Rao B, Garcia BA, Hake SB, Diaz RL, Shabanowitz J, Hunt DF, Allis CD, Lieb JD, Strahl BD. (2007) Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification. J Biol Chem. 282, 7632-40.

 

Xiao T, Shibata Y, Rao B, Laribee RN, O'Rourke R, Buck MJ, Greenblatt JF, Krogan NJ, Lieb JD, Strahl BD. (2007) The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes. Mol Cell Biol. 27, 721-31.

 

Biswas D, Dutta-Biswas R, Mitra D, Shibata Y, Strahl BD, Formosa T, Stillman DJ. (2006) Opposing roles for Set2 and yFACT in regulating TBP binding at promoters. EMBO J. 25, 4479-89.

 

Laribee RN, Fuchs SM, Strahl BD. (2007) H2B ubiquitylation in transcriptional control: a FACT-finding mission. Genes Dev. 21, 737-43.

 

Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ, Boone C, Emili A, Weissman JS, Hughes TR, Strahl BD, Grunstein M, Greenblatt JF, Buratowski S, Krogan NJ. (2005) Cotranscriptional Set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123, 593-605.

 

Rao B, Shibata Y, Strahl BD, Lieb JD. (2005) Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide. Mol Cell Biol. 25, 9447-59.

 

Laribee RN, Krogan NJ, Xiao T, Shibata Y, Hughes TR, Greenblatt JF, Strahl BD. (2005) BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex. Curr Biol. 15, 1487-93.

 

Morris SA, Shibata Y, Noma K, Tsukamoto Y, Warren E, Temple B, Grewal SI, Strahl BD. (2005) Histone H3 K36 methylation is associated with transcription elongation in Schizosaccharomyces pombe. Eukaryot Cell. 4, 1446-54.

 

Kizer KO, Phatnani HP, Shibata Y, Hall H, Greenleaf AL, Strahl BD. (2005) A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. Mol Cell Biol. 25, 3305-16.

 

Xiao T, Kao CF, Krogan NJ, Sun ZW, Greenblatt JF, Osley MA, Brian D. Strahl. (2005) Histone H2B ubiquitylation is associated with elongating RNA polymerase II. Mol Cell Biol. 25, 637-51.

 

Lee CK, Shibata Y, Rao B, Brian D. Strahl, Lieb JD. (2004) Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat Genet. 36, 900-905.

 

Xiao T, Hall H, Kizer KO, Shibata Y, Hall MC, Borchers CH, Brian D. Strahl. (2003) Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev. 17, 654-63.

 

Briggs SD, Xiao T, Sun ZW, Caldwell JA, Shabanowitz J, Hunt DF, Allis CD, Brian D Strahl. (2002) Gene silencing: trans-histone regulatory pathway in chromatin. Nature 418, 498.

 

Brian D. Strahl & C. David Allis. (2000) The language of covalent histone modifications. Nature 403, 41-5

 

For complete information on papers from Brian Strahl's lab, follow this link to PubMed or Brian Strahl's google scholar page

 

 

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