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Room 2123
Department of Plant Biology
1002 Life Sciences, One Shields Ave.
University of California Davis
Davis, CA 95616

Contact: slharmer at

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Many organisms, including some prokaryotes and most eukaryotes, possess an internal timer or circadian clock that allows them to regulate their physiology to better adapt to our continually changing world. These circadian clocks generate roughly 24 hour rhythms in physiology and behavior that are maintained even in the absence of environmental cues. Although the molecular components of circadian clocks are not conserved across higher taxa, in all organisms studied these clocks are cell autonomous oscillators and in diverse eukaryotes are composed of complex transcriptional networks. As rooted organisms living in a continually changing world, plants are masters at withstanding environmental variation. The circadian clock is key: it both ensures the optimal timing of daily and seasonal events to cope with predictable stresses and regulates myriad signaling pathways to optimize responses to environmental cues. The study of circadian rhythms in plants thus presents a wide range of fascinating questions with real-world applications: What is the molecular nature of the circadian clock; that is, how can a cell keep time? What aspects of physiology are under circadian regulation? What are the mechanistic links between the clock network and other signaling pathways? Why does a functional circadian clock provide an adaptive advantage? The Harmer lab is using Arabidopsis thaliana and sunflower to address these important questions. We use forward and reverse genetics, genomics, biochemistry, and physiological studies to better understand the nature of the plant clock and how it helps shape plant responses to the environment.


Lab Members

Undergrad & high school interns

  • Dalena (Nhu) Chu
  • Emma Goguen
  • Navdeep Kaur
  • Rohan Konnur
  • Kellie Sluga
  • Winnifred Toy
  • Timothy Youngblood
  • Michael Zook

Former Members


Recent 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. (2013) Wheels within wheels: the plant circadian system. Trends in Plant Science [2]
  • Hsu, P.Y., Devisetty, U.K., and Harmer, S.L. (2013) Cycling activators control the evening arm of the plant clock. eLife. 2:e00473. [3]
  • 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 [4]
  • 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. [5]
  • Hsu, P.Y. and Harmer, S.L. (2012) Circadian phase has profound effects on differential expression analysis. PLoS One, 7(11):e49853 [6]
  • 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 [7]
  • 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 [8]
  • 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. [9]
  • 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 [10]
  • see complete list...


Blackman Lab
Jones Lab
Lagarias Lab
Maloof Lab
Montemurro Lab
Yanovsky Lab

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