Harmer Lab:Publications

Room 2123 Department of Plant Biology 1002 Life Sciences, One Shields Ave. University of California Davis Davis, CA 95616 Contact: slharmer at ucdavis.edu

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Publications Anver, S., Roguev, A., Zofall, M., Krogan, N.J., Grewal, S.I.S., and Harmer, S.L. (2014) Yeast X-Chromosome Associated Protein 5 (Xap5) Functions with H2A.Z to Suppress Aberrant Transcripts. EMBO reports. pii: e201438902. [1] Hsu, P.Y. and Harmer, S.L. (2014) Global profiling of the circadian transcriptome using microarrays. Methods in Molecular Biology. 1158:45-56 [2] Hsu, P.Y. and Harmer, S.L. (2013) Wheels within wheels: the plant circadian system. Trends in Plant Science [3] Hsu, P.Y., Devisetty, U.K., and Harmer, S.L. (2013) Cycling activators control the evening arm of the plant clock. eLife. 2:e00473. [4] Zemach, A., Kim, M.Y., Hsieh, P.-H., Coleman-Derr,D., Eshed-Williams, L., Thao, K, Harmer, S.L., and Zilberman, D. (2013) The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153(1):193-205 [5] Hu, W., Franklin, K.A., Sharrock, R.A., Jones, M.A., Harmer, S.L., and Lagarias, J.C. (2013) Unanticipated regulatory roles for Arabidopsis phytochromes revealed by null mutant analysis. Proceedings of the National Academy of the Sciences, 110(4) 1542-1547. [6] Hsu, P.Y. and Harmer, S.L. (2012) Circadian phase has profound effects on differential expression analysis. PLoS One, 7(11):e49853 [7] Jones, M.A., Williams, B.A., McNicol J., Simpson, C.G., Brown, J.W., and Harmer, S.L. (2012) Mutation of Arabidopsis SPLICEOSOMAL TIMEKEEPER LOCUS 1 causes circadian clock defects. Plant Cell, 24(10):4066-82 [8] Nozue, K., Harmer. S.L., and Maloof, J.N. (2011) Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PIF5 as a modulator of auxin signaling in Arabidopsis. Plant Physiology, 156(1): 357-372 [9] Rawat, R., Takahashi, N., Hsu, P.Y., Jones, M.A., Schwartz, J., Salemi, M.R., Phinney, B.S., and Harmer, S.L. (2011) REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock. PLoS Genetics, 7(3): e1001350. [10] Kerwin, R.E., Jimenez-Gomez, J.M., Fulop, D., Harmer, S.L., Maloof, J.N., Kliebenstein, D.J. (2011) Network QTL mapping of circadian clock outputs identifies metabolic pathway to clock linkages in Arabidopsis. Plant Cell, 23(2):471-85 [11] Jones, M.A., and Harmer, S.L. (2011) JMJD5 functions in concert with TOC1 in the Arabidopsis circadian system. Plant Signaling & Behavior 6(3): 1-4. [12] Jones, M.A., Covington, M.F., Ditacchio, L., Vollmers, C., Panda, S., Harmer, S.L. (2010) Jumonji domain protein JMJD5 functions in both the plant and human circadian systems. Proceedings of the National Academy of the Sciences 107(50): 21623-21628. [13] Ellison ,C.T., Vandenbussche, F., Van Der Straeten, D., Harmer, S.L. (2011) XAP5 CIRCADIAN TIMEKEEPER regulates ethylene responses in aerial tissues of Arabidopsis. Plant Physiology, 155(2):988-999. [14] Harmer, S.L. (2010). Plant biology in the fourth dimension. Plant Physiology, 154:467 - 470. [15] Rawat, R., Schwartz, J., Jones, M.A., Sairanen, I., Cheng, Y., Andersson, C.R., Zhao, Y., Ljung, K., and Harmer, S.L. (2009). REVEILLE1, a Myb-like transcription factor, integrates the circadian clock and auxin pathways. Proceedings of the National Academy of the Sciences 106(39) 16883-16888. [16] Harmer, S.L. (2009). The circadian system in higher plants. Annual Review of Plant Biology 60: 357 – 77. [17] Covington, M.F., Maloof, J.N., Straume, M., Kay, S.A., and Harmer, S.L. (2008). Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biology, 9(8):R130. [18] Martin-Tryon, E.L., and Harmer, S.L. (2008). XAP5 CIRCADIAN TIMEKEEPER coordinates light signals for proper timing of photomorphogenesis and the circadian clock in Arabidopsis. Plant Cell 20(5):1244-59. [19] Gong, W., He, K., Covington, M.F., Dinesh-Kumar, S.P., Snyder, M., Harmer, S.L., Zhu, X., and Deng, X.P. (2008). The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors. Molecular Plant, 1(1): 27 – 41. [20] Covington, M.F. and Harmer, S.L (2007) The circadian clock regulates auxin signaling and responses in Arabidopsis. PLoS Biology, 5(8): e227 [21] Nozue, K., Covington, M.F., Duek, P.D., Lorrain, S., Fankhauser, C., Harmer, S.L., and Maloof, J.N. (2007) Rhythmic growth explained by coincidence between internal and external cues. Nature, 448:358-61. [22] Walley, J.W., Coughlan, S., Hudson, M.E., Covington, M.F., Kaspi, R., Banu, G., Harmer, S.L., and Dehesh, K. (2007) Mechanical stress induces biotic and abiotic stress responses via a novel cis-element. PLoS Genetics, 3(10): e172. [23] Oliverio, K.A., Crepy, M., Martin-Tryon, E.L., Milich, R., Harmer, S.L., Putterill, J., Yanovsky, M., Casal, J.J. (2007) GIGANTEA regulates phytochrome A-mediated photomorphogenesis independently of its role in the circadian clock. Plant Physiology 144:495-502 [24] Martin-Tryon, E.L., Kreps, J.A., Harmer, S.L. (2007). GIGANTEA acts in blue light signaling and has biochemically separable roles in circadian clock and flowering time regulation. Plant Physiology 143:473-486. [25] Harmer, S. L. and Kay, S. A. (2005). Positive and negative factors confer phase-specific circadian regulation of transcription in Arabidopsis. Plant Cell 17:1926-1940. [26] Farre, E. M., Harmer, S. L., Harmon, F. G., Yanovsky, M. J., and Kay, S. A. (2005). Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock. Current Biology 15:47-54. [27] Harmer, S. L., Covington, M. F., Bläsing, O., and Stitt, M. (2005). Circadian regulation of global gene expression and metabolism. In: Endogenous Plant Rhythms, ed. Hall, A., and McWatters, H., Blackwell Publishing, pp.133-165 [28] Alabadi, D., Mas, P., Yanovsky, M., Harmer, S. L., and Kay, S. A. (2002). Critical role for CCA1 and LHY in maintaining circadian rhythmicity in Arabidopsis. Current Biology 12:757-761. [29] Harmer, S. L., Panda, S., and Kay, S. A. (2001). Molecular bases of circadian rhythms. Annual Review of Cell and Developmental Biology 17:215-253. [30] Harmer, S. L., Hogenesch, J. B., Straume, M., Chang, H. S., Han, B., Zhu, T., Wang, X., Kreps, J. A., and Kay, S. A. (2000). Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290:2110-2113. [31]