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The novel enhancer-blocking cis-element DDT is enriched in genes associated with long-term acclimation in Arabidopsis thaliana
Umeå University, Faculty of Science and Technology, Plant Physiology.
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Manuscript (Other academic)
URN: urn:nbn:se:umu:diva-5382OAI: diva2:144881
Available from: 2006-10-05 Created: 2006-10-05 Last updated: 2010-01-13Bibliographically approved
In thesis
1. Cold Acclimation: Dissecting the plant low temperature signaling pathway using functional genomics
Open this publication in new window or tab >>Cold Acclimation: Dissecting the plant low temperature signaling pathway using functional genomics
2006 (Swedish)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The physiological process of cold acclimation protects plants native to the temperate regions of the world from the deleterious effects of low and freezing temperatures. This is achieved by a series of transcriptional, regulatory, and metabolic changes that enable continued growth and survival. Within minutes of exposure to temperatures below ca. 10°C, a complex cascade of transcriptional events is initiated to accomplish these changes. The initial alarm phase favors the rapid induction of a library of stress proteins with protective functions (e.g. COR proteins). This is followed by a cold hardened phase, characterized by maximal freezing tolerance, which continues until either the stress is removed, or the plant's metabolic and/or developmental state can no longer support maximal resistance.

We have studied some of the important transcription factors and transcriptional changes associated with the initial alarm and later hardened phases of cold acclimation in the herbaceous annual Arabidopsis thaliana and the woody perennial Populus spp. We confirmed the functionality of the CBF-mediated signaling cascade in Poplar overexpressing AtCBF1, but noted that regulon composition and endogenous poplar CBF ortholog induction appeared to be tissue-specific. The lack of statistically significant DRE enrichment in the Poplar AtCBF1 regulons led us to investige cis-element abundance in the cold-associated transcription factor regulons of publicly available microarray data from Arabidopsis, leading to the development of a gene voting method of microarray analysis that we used to test for regulatory associations between transcription factors and their downstream cis-elements and gene targets. This analysis resulted in a new transcriptional model of the ICE1-mediated signaling cascade and implicated a role for phytochrome A. Application of this same method to microarray data from arabidopsis leaves developed at low temperature allowed us to identify a new cis-element, called DDT, which possessed enhancer-blocking function during the alarm stage of cold stress, but was enriched in the promoters of genes upregulated during the later cold hardened stages. As leaf growth and development at low temperature correlated with the enhancement freeze tolerance in Arabidopsis, we compared the transcriptomes of rapidly growing and fully grown poplar leaves at night (when both low temperatures and PhyA status might play important roles in nature), in the hopes of comparing this data with that of cold-treated leaves in the future. We identified the nocturnal mode of leaf growth in Populus deltoides as predominantly proliferative as opposed to expansive, and potentially linked to cellular carbohydrate status.

Place, publisher, year, edition, pages
Umeå: Fysiologisk botanik, 2006. 51 p.
cold acclimation, functional genomics, microarray, Populus tremula, Arabidopsis thaliana, gene voting, regulon, enhancer-blocking
National Category
urn:nbn:se:umu:diva-885 (URN)91-7264-188-6 (ISBN)
Public defence
2006-10-27, KB3B1, KBC, KBC, Umeå, 10:00 (English)
Available from: 2006-10-05 Created: 2006-10-05 Last updated: 2011-03-30Bibliographically approved

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