Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network

<p>Abstract</p> <p>Background</p> <p>Analyses of gene expression data from microarray experiments has become a central tool for identifying co-regulated, functional gene modules. A crucial aspect of such analysis is the integration of data from different experiments and different laboratories. How to weigh the contribution of different experiments is an important point influencing the final outcomes. We have developed a novel method for this integration, and applied it to genome-wide data from multiple Arabidopsis microarray experiments performed under a variety of experimental conditions. The goal of this study is to identify functional globally co-regulated gene modules in the Arabidopsis genome.</p> <p>Results</p> <p>Following the analysis of 21,000 Arabidopsis genes in 43 datasets and about 2 × 10⁸gene pairs, we identified a globally co-expressed gene network. We found clusters of globally co-expressed Arabidopsis genes that are enriched for known Gene Ontology annotations. Two types of modules were identified in the regulatory network that differed in their sensitivity to the node-scoring parameter; we further showed these two pertain to general and specialized modules. Some of these modules were further investigated using the <it>Genevestigator </it>compendium of microarray experiments. Analyses of smaller subsets of data lead to the identification of condition-specific modules.</p> <p>Conclusion</p> <p>Our method for identification of gene clusters allows the integration of diverse microarray experiments from many sources. The analysis reveals that part of the <it>Arabidopsis </it>transcriptome is globally co-expressed, and can be further divided into known as well as novel functional gene modules. Our methodology is general enough to apply to any set of microarray experiments, using any scoring function.</p

EBE, an AP2/ERF Transcription Factor Highly Expressed in Proliferating Cells, Affects Shoot Architecture in Arabidopsis

We report about ERF BUD ENHANCER (EBE; At5g61890), a transcription factor that affects cell proliferation as well as axillary bud outgrowth and shoot branching in Arabidopsis (Arabidopsis thaliana). EBE encodes a member of the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor superfamily; the gene is strongly expressed in proliferating cells and is rapidly and transiently up-regulated in axillary meristems upon main stem decapitation. Overexpression of EBE promotes cell proliferation in growing calli, while the opposite is observed in EBE-RNAi lines. EBE overexpression also stimulates axillary bud formation and outgrowth, while repressing it results in inhibition of bud growth. Global transcriptome analysis of estradiolinducible EBE overexpression lines revealed 48 EBE early-responsive genes, of which 14 were up-regulated and 34 were downregulated. EBE activates several genes involved in cell cycle regulation and dormancy breaking, including D-type cyclin CYCD3;3, transcription regulator DPa, and BRCA1-ASSOCIATED RING DOMAIN1. Among the down-regulated genes were DORMANCYASSOCIATED PROTEIN1 (AtDRM1), AtDRM1 homolog, MEDIATOR OF ABA-REGULATED DORMANCY1, and ZINC FINGER HOMEODOMAIN5. Our data indicate that the effect of EBE on shoot branching likely results from an activation of genes involved in cell cycle regulation and dormancy breaking.Fil: Mehrnia, Mohammad. Institut Max Planck Fur Molekulare Physiologie; AlemaniaFil: Balazadeh, Salma. Institut Max Planck Fur Molekulare Physiologie; Alemania. University of Potsdam. Institute of Biochemistry and Biology; AlemaniaFil: Zanor, María Inés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Instituto de Biología Molecular y Celular de Rosario; Argentina. Institut Max Planck Fur Molekulare Physiologie; AlemaniaFil: Mueller Roeber, Bernd. Institut Max Planck Fur Molekulare Physiologie; Alemania. University of Potsdam, Institute of Biochemistry and Biology; Alemani

Rocks in the auxin stream : wound-induced auxin accumulation and ERF115 expression synergistically drive stem cell regeneration

Plants are known for their outstanding capacity to recover from various wounds and injuries. However, it remains largely unknown how plants sense diverse forms of injury and canalize existing developmental processes into the execution of a correct regenerative response. Auxin, a cardinal plant hormone with morphogen-like properties, has been previously implicated in the recovery from diverse types of wounding and organ loss. Here, through a combination of cellular imaging and in silico modeling, we demonstrate that vascular stem cell death obstructs the polar auxin flux, much alike rocks in a stream, and causes it to accumulate in the endodermis. This in turn grants the endodermal cells the capacity to undergo periclinal cell division to repopulate the vascular stem cell pool. Replenishment of the vasculature by the endodermis depends on the transcription factor ERF115, a wound-inducible regulator of stem cell division. Although not the primary inducer, auxin is required to maintain ERF115 expression. Conversely, ERF115 sensitizes cells to auxin by activating ARF5/MONOPTEROS, an auxin-responsive transcription factor involved in the global auxin response, tissue patterning, and organ formation. Together, the wound-induced auxin accumulation and ERF115 expression grant the endodermal cells stem cell activity. Our work provides a mechanistic model for wound-induced stem cell regeneration in which ERF115 acts as a wound-inducible stem cell organizer that interprets wound-induced auxin maxima

Cell type boundaries organize plant development

In plants the dorsoventral boundary of leaves defines an axis of symmetry through the centre of the organ separating the top (dorsal) and bottom (ventral) tissues. Although the positioning of this boundary is critical for leaf morphogenesis, how the boundary is established and how it influences development remains unclear. Using live-imaging and perturbation experiments we show that leaf orientation, morphology and position are pre-patterned by HD-ZIPIII and KAN gene expression in the shoot, leading to a model in which dorsoventral genes coordinate to regulate plant development by localizing auxin response between their expression domains. However we also find that auxin levels feedback on dorsoventral patterning by spatially organizing HD-ZIPIII and KAN expression in the shoot periphery. By demonstrating that the regulation of these genes by auxin also governs their response to wounds, our results also provide a parsimonious explanation for the influence of wounds on leaf dorsoventrality.The EMM laboratory is supported by funds from the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation (through grant GBMF3406). The research leading to these results received funding from the Australian Research Council (MGH) and European Research Council under the European Union’s Seventh Framework Programme (FP/2007–2013)/ERC Grant Agreement n. 261081 (MGH), as well as the People Programme (Marie Curie Actions) under REA grant agreement n. 255089 (PS). The work was also supported by: the European Molecular Biology Laboratory (XY, MPC, CO, PS, NB, HR and MGH); the EMBL International PhD Programme (XY, NB and MPC); Gatsby Charitable Foundation (GAT3395/PR4) (HJ) and Swedish Research Council (VR2013-4632) (HJ)

Plant Development and Organogenesis: From Basic Principles to Applied Research

The way plants grow and develop organs significantly impacts the overall performance and yield of crop plants. The basic knowledge now available in plant development has the potential to help breeders in generating plants with defined architectural features to improve productivity. Plant translational research effort has steadily increased over the last decade due to the huge increase in the availability of crop genomic resources and Arabidopsis-based sequence annotation systems. However, a consistent gap between fundamental and applied science has yet to be filled. One critical point often brought up is the unreadiness of developmental biologists on one side to foresee agricultural applications for their discoveries, and of the breeders to exploit gene function studies to apply to candidate gene approaches when advantageous on the other. In this book, both developmental biologists and breeders make a special effort to reconcile research on the basic principles of plant development and organogenesis with its applications to crop production and genetic improvement. Fundamental and applied science contributions intertwine and chase each other, giving the reader different but complementary perspectives from only apparently distant corners of the same world

Integrative statistical methods for decoding molecular responses to insect herbivory in Nicotiana attenuata

This work focuses on the development of statistical methods to select features (genes and metabolites) exhibiting induced local and systemic defense responses to insect attack in Nicotiana attenuata along with the extraction of additional information regarding their timing of action. To characterize the dynamics of activation in time and space of herbivory-induced responses, I designed a framework by combining methods previously developed for feature selection and extraction to identify activated network motifs. These motifs are the set of features that are differentially perturbed in local and systemic tissues in response to herbivory. The extraction of multifactorial statistical information in terms of time response variable simultaneously captured the dynamic response of a gene/metabolite in more than one tissue and therefore helped in identifying tissue-specific activation of biochemical pathways during herbivory, their transition points and shared patterns of regulation with other physiological processes and gene-metabolite interactions at the level of isolated motifs. I utilized this framework to evaluate the transcriptional and metabolic dynamics in the roots to investigate their role in aboveground stress responses. I discovered an emergent property of an inversion in root-specific semidiurnal (12h) rhythms in response to simulated leaf herbivory. In addition, I illustrated the benefits of our statistical framework, used for generating spatio-temporally resolved transcriptional/metabolic maps, by visualizing the chronology of the activation of pathways central to signaling, tolerance and defense in N. attenuata. The research described in this thesis, in addition to being valuable in deciphering dynamic responses to insect attack in a whole plant context, lays the foundation for future analyses in which statistical modeling of these networks assisted with experimental data could predict the logical rules governing these dynamic interactions

The self-organization of plant microtubules inside the cell volume yields their cortical localization, stable alignment, and sensitivity to external cues.

Many cell functions rely on the ability of microtubules to self-organize as complex networks. In plants, cortical microtubules are essential to determine cell shape as they guide the deposition of cellulose microfibrils, and thus control mechanical anisotropy of the cell wall. Here we analyze how, in turn, cell shape may influence microtubule behavior. Building upon previous models that confined microtubules to the cell surface, we introduce an agent model of microtubules enclosed in a three-dimensional volume. We show that the microtubule network has spontaneous aligned configurations that could explain many experimental observations without resorting to specific regulation. In particular, we find that the preferred cortical localization of microtubules emerges from directional persistence of the microtubules, and their interactions with each other and with the stiff wall. We also identify microtubule parameters that seem relatively insensitive to cell shape, such as length or number. In contrast, microtubule array anisotropy depends on local curvature of the cell surface and global orientation follows robustly the longest axis of the cell. Lastly, we find that geometric cues may be overcome, as the network is capable of reorienting toward weak external directional cues. Altogether our simulations show that the microtubule network is a good transducer of weak external polarity, while at the same time, easily reaching stable global configurations