|
|
|
 |
Circadian clock, temperature sensing and light signaling in plants. Transcriptional networks. Plant genome structure and annotation. Bioinformatics.My lab’s research focuses on understanding the architecture of transcriptional networks, how environmental signals are integrated into these networks and the evolution of these networks. We utilize molecular genetic, developmental, and physiological tools in conjunction with genomic, bioinformatic, and systems biology approaches to understand how transcriptional networks respond to the circadian clock and diurnal changes in light and temperature. Diurnal and circadian transcriptional networks. The circadian clock, thermocycles or photocycles regulate 90% of the transcriptome in the model dicot plant, Arabidopsis thaliana. At least part of this global transcriptional regulation can be attributed to three cis-regulatory elements/modules controlling morning, evening and midnight expression. However, histone modifications and DNA methylation play a role in global expression regulation. These modifications are being investigated using whole genome approaches coupled with mutant analysis. Conservation of diurnal and circadian transcriptional networks. The circadian clock has evolved to provide an adaptive advantage through anticipation of daily changes in the local environment. The conservation of the circadian clock across phyla coupled with the power of diurnal/circadian gene expression time courses to identify co-regulated genes makes it a robust system to study the evolution of transcriptional networks. Currently, diurnal and circadian cis-regulatory networks are being dissected using comparative genomic and phylogenetic footprinting approaches from plants to animals with sequenced genomes. Identifying the plant temperature sensor. It is not currently known how plants sense ambient changes in temperature. Expression studies and mutant analysis have implicated the circadian clock, chloroplasts, and the cold acclimation pathway in ambient temperature sensing. Current research focuses on characterizing new temperature sensing mutants. Exploiting natural variation to identify new circadian clock, light signaling and temperature sensing mechanisms. Hundreds of Arabidopsis accessions displaying varying responses to the environment have been collected by the community and provide a wealth of natural variation for gene discovery. In addition to identifying novel genes by QTL mapping, the genetic/genomic backgrounds of different accessions provide fresh insight into molecular mechanisms. Developing Brachypodium distachyon as a model system for biofuels and turf grasses. Brachypodium distachyon is a small selfing diploid grass with a rapid life cycle (~4 weeks), simple growth requirements, compact genome (~320 Mbp), transformability, emerging molecular tools, accession collections and evolutionary relationship to temperate cereals, forage and turf grasses, and potential biofuel crops, such as switchgrass (Panicum virgatum L.) and Miscanthus x giganteus. Brachypodium distachyon is being sequenced by JGI-DOE (2007-8) and I will develop it as a model to understand how grasses respond and integrate environmental signals that control growth. Selected PublicationsMichael TP, Mockler TC, Breton G, Byer A, Hazen SP, Yanovsky M, Kay S, Chory J. (2007) Network discovery pipeline elucidates conserved time of day specific cis-regulatory modules. Submitted. Michael TP, Chory J. (2007) The low temperature signaling pathway and the circadian clock mediate ambient temperature integration in Arabidopsis thaliana. In preparation. Balasubramanian S, Sureshkumar S, Agrawal M, Michael TP, Wessinger C, Maloof JN, Clark R, Warthmann N, Chory J, Weigel D. (2006) The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. Nature Genetics. 38(6): 711-5. Mockler TC, Yu X, Shalitin D, Parikh D, Michael TP, Liou J, Huang J, Smith Z, Alonso JM, Ecker JR, Chory J, Lin C. (2004) Regulation of flowering time in Arabidopsis by K homology domain proteins. Proc Natl Acad Sci. 101(34): 12759-64. Michael TP, Salomé PA, Yu HJ, Spencer TR, Sharp EL, McPeek MA, Alonso JM, Ecker JR, McClung CR. (2003) Enhanced fitness conferred by naturally occurring variation in the circadian clock. Science. 302(5647): 1049-53. Michael TP, McClung CR. (2003) Enhancer trapping reveals widespread circadian clock transcriptional control in Arabidopsis. Plant Physiology. 132(2): 629-39. Michael TP, Salomé PA, McClung CR. (2003) Two Arabidopsis circadian oscillators can be distinguished by differential temperature sensitivity. Proc Natl Acad Sci. 100(11): 6878-83. Michael TP, McClung CR. (2002) Phase-specific circadian clock regulatory elements in Arabidopsis. Plant Physiology. 130(2): 627-38. Salomé PA, Michael TP, Kearns EV, Fett-Neto AG, Sharrock RA, McClung CR. (2002) The out of phase 1 mutant defines a role for PHYB in circadian phase control in Arabidopsis. Plant Physiology. 129(4): 1674-85. McClung CR, Salomé PA, Michael TP. The Arabidopsis Circadian System. 2002. The Arabidopsis Book, eds. C.R. Somerville and E.M. Meyerowitz, American Society of Plant Biologists, Rockville, MD, doi/10.1199/tab.0009. |
|
