TobEA: an atlas of tobacco gene expression from seed to senescence.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Transcriptomics has resulted in the development of large data sets and tools for the progression of functional genomics and systems biology in many model organisms. Currently there is no commercially available microarray to allow such expression studies in Nicotiana tabacum (tobacco). RESULTS: A custom designed Affymetrix tobacco expression microarray was generated from a set of over 40k unigenes and used to measure gene expression in 19 different tobacco samples to produce the Tobacco Expression Atlas (TobEA). TobEA provides a snap shot of the transcriptional activity for thousands of tobacco genes in different tissues throughout the lifecycle of the plant and enables the identification of the biological processes occurring in these different tissues. 772 of 2513 transcription factors previously identified in tobacco were mapped to the array, with 87% of them being expressed in at least one tissue in the atlas. Putative transcriptional networks were identified based on the co-expression of these transcription factors. Several interactions in a floral identity transcription factor network were consistent with previous results from other plant species. To broaden access and maximise the benefit of TobEA a set of tools were developed to provide researchers with expression information on their genes of interest via the Solanaceae Genomics Network (SGN) web site. The array has also been made available for public use via the Nottingham Arabidopsis Stock Centre microarray service. CONCLUSIONS: The generation of a tobacco expression microarray is an important development for research in this model plant. The data provided by TobEA represents a valuable resource for plant functional genomics and systems biology research and can be used to identify gene targets for both fundamental and applied scientific applications in tobacco

Low-temperature-specific effects of PHYTOCHROME C on the circadian clock in Arabidopsis suggest that PHYC underlies natural variation in biological timing

Author contributions KDE and AJM designed the study. FG characterised the gn7 deletion in the Scott lab (Figure 5a). PFD analysed PHY protein content in the gn7 line (Figure 5b). KDE performed all other experiments and data analysis. AJM assembled the data, removed them from Wenden et al. Plant Journal 2011 after peer review to comply with an editorial request for greater focus, and prepared this paper. Acknowledgements We are grateful to Rod Scott and the late Garry Whitelam for supporting early work on gn7, and to Dr. James Lynne (Horticulture Research International, Wellesbourne) for REML analysis.The circadian clock is a fundamental feature of gene regulation and cell physiology in eukaryotes and some prokaryotes, and an exemplar gene regulatory network in Systems Biology. The circadian system in Arabidopsis thaliana is complex in part due to its photo-transduction pathways. Analysis of natural genetic variation between Arabidopsis accessions Cape Verde Islands (Cvi-0) and Landsberg erecta (Ler) identified a major, temperature-specific Quantitative Trait Locus (QTL) on chromosome V that altered the circadian period of leaf movement (Edwards et al., Genetics, 2005). We tested Near-Isogenic Lines (NILs) to confirm that Ler alleles at this PerCv5c QTL lengthened the circadian period at 12°C, with little effect at higher temperatures. The PHYTOCHROME C gene lies within the QTL interval, and contains multiple sequence variants. Plants carrying either a T-DNA-insertion into PHYC or a deletion of PHYC also lengthened circadian period under white light, except at 27°C. phyB and phyABE mutants lengthened period only at 12°C. These results extend recent data showing PhyC effects in red light, confirming the number of photoreceptor proteins implicated in the plant circadian system at eleven. The connection between light input mechanisms and temperature effects on the clock is reinforced. Natural genetic variation within PHYC is likely to underlie the PerCv5c QTL. Our results suggest that functional variation within the PHYC-Ler haplotype group might contribute to the evolution of the circadian system and possibly to clock-related phenotypes such as flowering time. These results have previously passed peer-review, so we provide them in this citable preprint

Quantitative analysis of regulatory flexibility under changing environmental conditions

The circadian clock controls 24-h rhythms in many biological processes, allowing appropriate timing of biological rhythms relative to dawn and dusk. Known clock circuits include multiple, interlocked feedback loops. Theory suggested that multiple loops contribute the flexibility for molecular rhythms to track multiple phases of the external cycle. Clear dawn- and dusk-tracking rhythms illustrate the flexibility of timing in Ipomoea nil. Molecular clock components in Arabidopsis thaliana showed complex, photoperiod-dependent regulation, which was analysed by comparison with three contrasting models. A simple, quantitative measure, Dusk Sensitivity, was introduced to compare the behaviour of clock models with varying loop complexity. Evening-expressed clock genes showed photoperiod-dependent dusk sensitivity, as predicted by the three-loop model, whereas the one- and two-loop models tracked dawn and dusk, respectively. Output genes for starch degradation achieved dusk-tracking expression through light regulation, rather than a dusk-tracking rhythm. Model analysis predicted which biochemical processes could be manipulated to extend dusk tracking. Our results reveal how an operating principle of biological regulators applies specifically to the plant circadian clock

Circadian clock components control daily growth activities by modulating cytokinin levels and cell division-associated gene expression in <i>Populus</i> trees

Trees are carbon dioxide sinks and major producers of terrestrial biomass with distinct seasonal growth patterns. Circadian clocks enable the coordination of physiological and biochemical temporal activities, optimally regulating multiple traits including growth. To dissect the clock's role in growth, we analysed Populus tremula x P. tremuloides trees with impaired clock function due to down-regulation of central clock components. late elongated hypocotyl (lhy-10) trees, in which expression of LHY1 and LHY2 is reduced by RNAi, have a short free-running period and show disrupted temporal regulation of gene expression and reduced growth, producing 30-40% less biomass than wild-type trees. Genes important in growth regulation were expressed with an earlier phase in lhy-10, and CYCLIN D3 expression was misaligned and arrhythmic. Levels of cytokinins were lower in lhy-10 trees, which also showed a change in the time of peak expression of genes associated with cell division and growth. However, auxin levels were not altered in lhy-10 trees, and the size of the lignification zone in the stem showed a relative increase. The reduced growth rate and anatomical features of lhy-10 trees were mainly caused by misregulation of cell division, which may have resulted from impaired clock function

Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model

Circadian clocks generate 24-h rhythms that are entrained by the day/night cycle. Clock circuits include several light inputs and interlocked feedback loops, with complex dynamics. Multiple biological components can contribute to each part of the circuit in higher organisms. Mechanistic models with morning, evening and central feedback loops have provided a heuristic framework for the clock in plants, but were based on transcriptional control. Here, we model observed, post-transcriptional and post-translational regulation and constrain many parameter values based on experimental data. The model's feedback circuit is revised and now includes PSEUDO-RESPONSE REGULATOR 7 (PRR7) and ZEITLUPE. The revised model matches data in varying environments and mutants, and gains robustness to parameter variation. Our results suggest that the activation of important morning-expressed genes follows their release from a night inhibitor (NI). Experiments inspired by the new model support the predicted NI function and show that the PRR5 gene contributes to the NI. The multiple PRR genes of Arabidopsis uncouple events in the late night from light-driven responses in the day, increasing the flexibility of rhythmic regulation

Guided conjugate Bayesian clustering for uncovering rhythmically expressed genes

Background: An increasing number of microarray experiments produce time series of expression levels for many genes. Some recent clustering algorithms respect the time ordering of the data and are, importantly, extremely fast. The focus of this paper is the development of such an algorithm on a microarray data set consisting of 22,810 genes of the plant Arabidopsis thaliana measured at 13 time points over two days. Circadian rhythms control the timing of various physiological and metabolic processes and are regulated by genes acting in feedback loops. The aim is to cluster and classify the expression profiles in order to identify genes potentially involved in, and regulated by, the circadian clock. Results: A greedy search over time series of expression levels (where series are compared pairwise, the two most similar put in the same cluster and so forth) will get a fast result but will only explore a very limited number of the possible partitions of the profiles. We propose an improved, deterministic method based on a multi-step application of a conjugate Bayesian clustering algorithm. It allows the entire space to be searched more fully and intelligently. The values of the summary statistics are used to not only score clusters of genes, but also to guide the search of the vast partition space. By following this procedure, we are able to cluster genes that are known to be rhythmically expressed with genes of previously unknown function; thus suggesting potentially interesting targets for future experiments

Efficient utility-based clustering over high dimensional partition spaces

Because of the huge number of partitions of even a moderately sized dataset, even when Bayes factors have a closed form, in model-based clustering a comprehensive search for the highest scoring (MAP) partition is usually impossible. However, when each cluster in a partition has a signature and it is known that some signatures are of scientific interest whilst others are not, it is possible, within a Bayesian framework, to develop search algorithms which are guided by these cluster signatures. Such algorithms can be expected to find better partitions more quickly. In this paper we develop a framework within which these ideas can be formalized. We then briefly illustrate the efficacy of the proposed guided search on a microarray time coursed at a set where the clustering objective is to identify clusters of genes with different types of circadian expression profiles

Circadian gene expression under different light treatments by transcriptome profiling on microarrays

NASCARRAYS-196Most eukaryotic and some prokaryotic organisms regulate their metabolic and physiological behaviour with an internal 24h 'circadian clock'. Around 6% of the Arabidopsis thaliana genome was estimated to be regulated on a transcriptional level by this clock, with various phases of peak expression throughout the daily cycle (Harmer et al., 2000). The phase and period of the internal clock is entrained by changes in light and temperature so that the clock cycles in resonance with the external environment. The temporal co-ordination provided by the clock allows organisms to anticipate and respond to the predictable environmental changes in the day/night cycle. This resonance with the external environment is believed to impart organisms with a selective advantage (Ouyang et al., 1998).Using Affymetrix micro-arrays we hope to further our knowledge of the mechanisms of the clock to help in our attempts at modelling the molecular oscillator of Arabidopsis and understanding how the clock's phase relates to fitness. Firstly we will reduce the complexity of the clock by growing seedlings under monochromatic far-red light. Under white light conditions, light signals are input to the clock via the five phytochrome and two cryptochrome photoreceptors, whereas under far-red conditions light is input solely via Phytochrome A (PHYA). Secondly, we will alter the length of the day/night cycle, away from 24 hours, by growing seedlings under different white light/dark T-cycles (T=20h and T=28h). In both sets of experiments a time course of samples will be taken over the first and/or second circadian cycle from seedlings released into constant far-red or white light, following entrainment to light/dark cycles