{"id":12,"date":"2019-10-09T12:34:42","date_gmt":"2019-10-09T19:34:42","guid":{"rendered":"http:\/\/labs.wsu.edu\/wyrick\/?page_id=12"},"modified":"2019-10-09T12:34:42","modified_gmt":"2019-10-09T19:34:42","slug":"publications","status":"publish","type":"page","link":"https:\/\/labs.wsu.edu\/wyrick\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"
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Publications<\/h1>\n<\/p><\/div>\n<\/section>\n
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Chromatin and DNA repair<\/strong><\/h2>\n

1.<\/b>\u00a0Mao, P., Wyrick, J.J., Roberts, S.A., and Smerdon, M.J. (2017) UV-Induced DNA Damage and Mutagenesis in Chromatin.\u00a0Photochem Photobiol.\u00a0<\/b>93:216-228.<\/p>\n

2.<\/b>\u00a0Mao, P. and Wyrick, J. J. (2017) Emerging Roles for Histone Modifications in DNA Excision Repair.\u00a0FEMS Yeast Research<\/b>\u00a0(in press).<\/p>\n

3.<\/b>\u00a0Kong, M., Liu, L., Chen, X., Driscoll, K.I., Mao, P., Bohm, S., Kad, N.M., Watkins, S.C., Bernstein, K.A., Wyrick, J.J., Min, J.H., and Van Houten, B. (2016) Single-molecule imaging reveals that Rad4 (XPC) employs a dynamic DNA damage recognition process.\u00a0Molecular Cell<\/b>\u00a064:376-387.<\/p>\n

4.<\/b>\u00a0Mao, P., Smerdon, M.J., Roberts, S.A., and Wyrick, J.J. (2016) Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution.\u00a0Proc Natl Acad Sci USA<\/b>\u00a0113:9057-9062.<\/p>\n

5.<\/b>\u00a0Mao, P., Kyriss, M. N. M., Hodges, A. J., Duan, M., Morris, R. T., Lavine, M. D., Topping, T. B., Gloss, L. M., and Wyrick, J. J. (2016) A Basic Domain in the Histone H2B N-terminal Tail is Important for Nucleosome Assembly by FACT.\u00a0Nucleic Acids Res.<\/b>\u00a044:9142-9152.<\/p>\n

6.<\/b>\u00a0Rodriguez, Y., Hinz, J. M., Laughery, M. F., Wyrick, J. J., and Smerdon, M. J. (2016) Site-specific Acetylation of Histone H3 Decreases Polymerase \u03b2 Activity on Nucleosome Core Particles in vitro.\u00a0J. Biol. Chem.<\/b>\u00a0291:11434-11445.<\/p>\n

7.<\/b>\u00a0Wyrick, J. J. and Roberts, S. A. (2015) Genomic approaches to DNA repair and mutagenesis.\u00a0DNA repair<\/b>\u00a036:146-155.<\/p>\n

8.<\/b> Meas, R., Smerdon, M. J. & Wyrick, J. J. (2015) The amino-terminal tails of histones H2A and H3 coordinate efficient base excision repair, DNA damage signaling and postreplication repair in Saccharomyces cerevisiae.\u00a0Nucleic Acids Res.<\/b>\u00a043:4990-5001.<\/p>\n

9.<\/b>\u00a0Hodges, A. J., Gallegos, I. J., Laughery, M. F., Meas, R., Tran, L. & Wyrick, J. J. Histone Sprocket Arginine Residues Are Important for Gene Expression, DNA Repair, and Cell Viability in Saccharomyces cerevisiae.\u00a0Genetics<\/b>\u00a0200, 795-806, (2015). PMCID: PMC4512544.<\/p>\n

10.<\/b>\u00a0Zavala, A. G., Morris, R. T., Wyrick, J. J. and Smerdon, M. J. (2014) High Resolution Characterization of CPD Hotspot Formation in Human Fibroblasts,\u00a0Nucleic Acids Res.<\/b>\u00a042: 893-905.<\/p>\n

11.<\/b>\u00a0Wyrick, J. J., Kyriss, M. N., and Davis, W. B. (2012) Ascending the nucleosome face: recognition and function of structured domains in the histone H2A-H2B dimer.\u00a0Biochim Biophys Acta 1819:892-901.<\/b><\/p>\n

12.<\/b> Kyriss, M.N., Jin, Y., Gallegos, I.J., Sanford, J.A., and Wyrick, J.J. (2010) Novel functional residues in the core domain of histone H2B regulate yeast gene expression and silencing and affect the response to DNA damage.\u00a0Mol. Cell. Biol.<\/b>\u00a030:3503-3518.<\/p>\n

13.<\/b> Zheng, S., Wyrick, J.J., Reese, J.C. (2010) Novel trans-tail regulation of H2B ubiquitylation and H3K4 methylation by the N-terminus of histone H2A.\u00a0Mol Cell Biol.<\/b>\u00a030:3635-45.<\/p>\n

14.<\/b> Nag, R., Kyriss, M., Smerdon, J.W., Wyrick, J.J., Smerdon, M.J. (2010) A cassette of N-terminal amino acids of histone H2B are required for efficient cell survival, DNA repair and Swi\/Snf binding in UV irradiated yeast.\u00a0Nucleic Acids Res.<\/b>\u00a038:1450-1460.<\/p>\n

15.<\/b> Jin, Y., Rodriguez, A.M., Wyrick, J.J. (2009) Genetic and Genome-wide Analysis of Simultaneous Mutations in Acetylated and Methylated Lysine Residues in Histone H3 in Saccharomyces cerevisiae.\u00a0Genetics<\/b>\u00a0181:461-472.<\/p>\n

16.<\/b> Chaudhuri, S., Wyrick, J.J., Smerdon, M.J. (2009) Histone H3 Lys79 Methylation is Required for Efficient Nucleotide Excision Repair in a Silenced Locus of Saccharomyces cerevisiae.\u00a0Nucleic Acids Res.<\/b>\u00a037:1690-1700.<\/p>\n

17.<\/b> Wyrick, J.J. and Parra, M.A. (2009) The role of histone H2A and H2B post-translational modifications in transcription: A genomic perspective.\u00a0Biochim Biophys Acta.<\/b>\u00a01789:37-44.<\/p>\n

18.<\/b> Parra, M.A. and Wyrick, J.J. (2007) Regulation of gene transcription by the histone H2A N-terminal domain.\u00a0Mol. Cell. Biol.<\/b>\u00a027:7641-7648.<\/p>\n

19.<\/b> Jin, Y., Rodriguez, A.M., Stanton, J.D., Kitazono, A.A., and Wyrick, J.J. (2007) Simultaneous mutation of methylated lysine residues in histone H3 causes enhanced gene silencing, cell cycle defects, and cell lethality in S. cerevisiae.\u00a0Mol. Cell. Biol.<\/b>\u00a027:6832-6841.<\/p>\n

20.<\/b> Wood, A., Shukla, A., Schneider, J., Lee, J.S., Stanton, J.D., Dzuiba, T., Swanson, S.K., Florens, L., Washburn, M.P., Wyrick, J., Bhaumik, S.R., Shilatifard, A (2006) Ctk complex mediated regulation of histone methylation by COMPASS.\u00a0Mol Cell Biol<\/b>\u00a027:709-720.<\/p>\n

21.<\/b>\u00a0Parra, M.A., Kerr, D., Fahy, D., Pouchnik, D.J., and Wyrick, J.J. (2006) Deciphering the Roles of the Histone H2B N-terminal domain in Genome-wide Transcription.\u00a0Mol Cell Biol<\/b>\u00a026:3842-3852..<\/p>\n

22.<\/b>\u00a0Martin, A.M., Pouchnik, D.J., Walker, J.L., and Wyrick, J.J. (2004) Redundant Roles for Histone H3 N-Terminal Lysine Residues in Subtelomeric Gene Repression in\u00a0Saccharomyces cerevisiae<\/i>.\u00a0Genetics<\/b>167:1123-1132.<\/p>\n

23.<\/b>\u00a0Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerger, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., Zeitlinger, J., Jennings, E.G., Murray, H.L., Gordon, D.B., Ren, B., Wyrick, J.J., Tagne, J.B., Volkert, T.L., Fraenkel, E., Gifford, D.K., Young, R.A. (2002) Transcriptional Regulatory Networks in Saccharomyces cerevisiae.\u00a0Science<\/i>298: 799-804.<\/p>\n

24.<\/b>\u00a0Wyrick, J.J. and Young, R.A. (2002) Deciphering Gene Expression Regulatory Networks.\u00a0Curr Opin Genet Dev<\/i>\u00a012: 130-6.<\/p>\n

25.<\/b>\u00a0Wyrick, J.J.*, Aparicio, J.G.*, Chen, T., Barnett, J.D., Jennings, E.G., Young, R.A., Bell, S.P., and Aparicio, O.M. (2001) Genome-Wide Distribution of ORC and MCM proteins in S. cerevisiae: High-Resolution Mapping of Replication Origins.\u00a0Science<\/i>\u00a0294: 2357-2360.
\n*Authors made equal contributions.<\/i><\/p>\n

26.<\/b>\u00a0Simon, I., Barnett, J., Hannett, N., Harbison, C.T., Rinaldi, N.J., Volkert, T.L., Wyrick, J.J., Zeitlinger, J., Gifford, D.K., Jaakkola, T.S., and Young, R.A. (2001) Serial Regulation of Transcriptional Regulators in the Yeast Cell Cycle.\u00a0Cell<\/i>\u00a0106: 697-708.<\/p>\n

27.<\/b>\u00a0Ren, B.*, Robert, F.*, Wyrick, J.J.*, Aparicio, O., Jennings, E.J., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., Volkert, T.L., Wilson, C.J., Bell, S.P., and Young, R.A. (2000) Genome-wide Location and Function of DNA-binding Proteins.\u00a0Science<\/i>\u00a0290: 2306-2309.
\n*Authors made equal contributions.<\/i><\/p>\n

28.<\/b>\u00a0Wyrick, J.J., Holstege, F.C.P., Jennings, E.G., Causton, H.C., Shore, D., Grunstein, M., Lander, E.S., Young, R.A., (1999) Chromosomal Landscape of Nucleosome-dependent Gene Expression and Silencing in Yeast.\u00a0Nature<\/i>402:418-421.<\/p>\n

29.<\/b>\u00a0Holstege, F.C.P., Jennings, E.G., Wyrick, J.J., Lee T., Hengartner, C.J., Green, M.R., Golub, T.R., Lander, E.S., and Young, R.A. (1998) Dissecting the Regulatory Circuitry of a Eukaryotic Genome.\u00a0Cell<\/i>\u00a095: 717-728.<\/p>\n

30.<\/b>\u00a0Lee, T., Wyrick, J.J., Koh, S.S., Jennings, E.G., Gadbois, E.L., and Young, R.A. (1998) Interplay of Positive and Negative Regulators in Transcription Initiation by RNA Polymerase II Holoenzyme.\u00a0Mol. Cell. Biol.<\/i>18: 4455-4462.<\/p>\n

 <\/p>\n

CRISPR\/Cas9<\/strong><\/h2>\n

1.<\/b>\u00a0Hinz, J.M., Laughery, M.F., and Wyrick, J.J. (2016) Nucleosomes Selectively Inhibit Cas9 Off-target Activity at a Site Located at the Nucleosome Edge.\u00a0J Biol Chem<\/b>\u00a0291:24851-24856.<\/p>\n

2.<\/b>\u00a0Kong, M., Liu, L., Chen, X., Driscoll, K.I., Mao, P., Bohm, S., Kad, N.M., Watkins, S.C., Bernstein, K.A., Wyrick, J.J., Min, J.H., and Van Houten, B. (2016) Single-molecule imaging reveals that Rad4 (XPC) employs a dynamic DNA damage recognition process.\u00a0Molecular Cell<\/b>\u00a064:376-387.<\/p>\n

3.<\/b>\u00a0Hinz, J.M., Laughery, M.F., and Wyrick, J.J. (2015) Nucleosomes Inhibit Cas9 Endonuclease Activity in Vitro.\u00a0Biochemistry<\/b>\u00a054:7063-7066.<\/p>\n

4.<\/b> Laughery, M.F., Hunter, T., Brown, A., Hoopes, J., Ostbye, T., Shumaker, T., Wyrick, J.J. (2015) New vectors for simple and streamlined CRISPR-Cas9 genome editing in Saccharomyces cerevisiae.\u00a0Yeast<\/b>\u00a032:711-720.<\/p>\n

 <\/p>\n

Plant and Yeast Bioinformatics<\/b><\/h2>\n

1.<\/b>\u00a0Morris, R.T., Doroshenk, K.A., Crofts, A.J., Lewis, N., Okita, T.W., Wyrick, J.J. (2011) RiceRBP: A database of experimentally identified RNA-binding proteins in Oryza sativa L. Plant Science 180:204-11.<\/p>\n

2.<\/b>\u00a0Doroshenk, K.A., Crofts A.J., Washida, H., Satoh-Cruz, M., Crofts, N., Sugino, A., Okita, T.W., Morris, R.T., Wyrick, J.J., Fukuda, M., Kumamaru, T., and Satoh, H. (2010) Characterization of the rice glup4 mutant suggests a role for the small GTPase Rab5 in the biosynthesis of carbon and nitrogen storage reserves in developing endosperm. Breeding Science 60:556-567.<\/p>\n

3.<\/b>\u00a0Morris, R.T., O’Connor, T.R., and Wyrick, J.J. (2010) Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae. Bioinformatics 26:168-174.<\/p>\n

4.<\/b>\u00a0Doroshenk, K.A., Crofts, A.J., Morris, R.T., Wyrick, J.J., Okita, T.W. (2009) Proteomic analysis of cytoskeleton-associated RNA binding proteins in developing rice seed. J Proteome Res. 8:4641-4653.<\/p>\n

5.<\/b>\u00a0Morris, R.T., O’Connor, T.R., and Wyrick, J.J. (2008) Osiris: an integrated promoter database for Oryza sativa L. Bioinformatics 24:2915-2917.<\/p>\n

6.<\/b>\u00a0O’Connor, T.R. and Wyrick, J.J. (2007) ChromatinDB: a database of genome-wide histone modification patterns for\u00a0Saccharomyces cerevisiae<\/i>.\u00a0Bioinformatics<\/i>\u00a0(in press).<\/p>\n

7.<\/b>\u00a0O’Connor, T.R., Dyreson, C., and Wyrick, J.J. (2005) Athena: a resource for rapid visualization and systematic analysis of\u00a0Arabidopsis<\/i>\u00a0promoter sequences.\u00a0Bioinformatics<\/i>\u00a021:4411-4413.<\/p>\n

 <\/p>\n

Issued Patents:<\/h3>\n

1.<\/b>\u00a0Wyrick, J.J., Young, R.A., Ren, B., and Robert, F. “Chromosome-wide analysis of protein-DNA interactions,” US patent# 6,410,243; June 25, 2002.<\/p>\n

2.<\/b>\u00a0Wyrick, J., Young, R.A., Ren, B., Robert, F., Simon, I. “Genome-wide location and function of DNA binding proteins,” US 7,470,507; December 30, 2008.<\/p>\n

3.<\/b>\u00a0Wyrick, J., Young, R.A., Ren, B., Robert, F., Simon, I. “Genome wide location and function of DNA binding proteins,” US 7,575,869; August 18, 2009.<\/p>\n<\/p><\/div>\n

<\/div>\n<\/section>\n","protected":false},"excerpt":{"rendered":"

Publications<\/p>\n

Chromatin and DNA repair<\/strong><\/h2>\n

1.\u00a0Mao, P., Wyrick, J.J., Roberts, S.A., and Smerdon, M.J. (2017) UV-Induced DNA Damage and Mutagenesis in Chromatin.\u00a0Photochem Photobiol.\u00a093:216-228.<\/p>\n

2.\u00a0Mao, P. and Wyrick, J. J. (2017) Emerging Roles for Histone Modifications in DNA Excision Repair.\u00a0FEMS Yeast Research\u00a0(in press).<\/p>\n

3.\u00a0Kong, M., Liu, L., Chen, X., Driscoll, K.I., Mao, P., Bohm, S., Kad, N.M., Watkins, S.C., Bernstein, K.A., Wyrick, J.J., Min, J.H., and Van Houten, B. (2016) Single-molecule imaging reveals that Rad4 (XPC) employs a dynamic DNA damage recognition process.\u00a0Molecular Cell\u00a064:376-387.<\/p>\n

4.\u00a0Mao, P., Smerdon, M.J., Roberts, S.A., and Wyrick, J.J. (2016) Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution.\u00a0Proc … » More …<\/span><\/a><\/p>\n","protected":false},"author":14798,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-builder.php","meta":[],"wsuwp_university_location":[],"wsuwp_university_org":[],"_links":{"self":[{"href":"https:\/\/labs.wsu.edu\/wyrick\/wp-json\/wp\/v2\/pages\/12"}],"collection":[{"href":"https:\/\/labs.wsu.edu\/wyrick\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.wsu.edu\/wyrick\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.wsu.edu\/wyrick\/wp-json\/wp\/v2\/users\/14798"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.wsu.edu\/wyrick\/wp-json\/wp\/v2\/comments?post=12"}],"version-history":[{"count":1,"href":"https:\/\/labs.wsu.edu\/wyrick\/wp-json\/wp\/v2\/pages\/12\/revisions"}],"predecessor-version":[{"id":13,"href":"https:\/\/labs.wsu.edu\/wyrick\/wp-json\/wp\/v2\/pages\/12\/revisions\/13"}],"wp:attachment":[{"href":"https:\/\/labs.wsu.edu\/wyrick\/wp-json\/wp\/v2\/media?parent=12"}],"wp:term":[{"taxonomy":"wsuwp_university_location","embeddable":true,"href":"https:\/\/labs.wsu.edu\/wyrick\/wp-json\/wp\/v2\/wsuwp_university_location?post=12"},{"taxonomy":"wsuwp_university_org","embeddable":true,"href":"https:\/\/labs.wsu.edu\/wyrick\/wp-json\/wp\/v2\/wsuwp_university_org?post=12"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}