Genome-Wide Patterns of Arabidopsis Gene Expression in Nature (original) (raw)
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The Plant Cell, 2013
The regulation of gene expression is crucial for an organism's development and response to stress, and an understanding of the evolution of gene expression is of fundamental importance to basic and applied biology. To improve this understanding, we conducted expression quantitative trait locus (eQTL) mapping in the Tsu-1 (Tsushima, Japan) × Kas-1 (Kashmir, India) recombinant inbred line population of Arabidopsis thaliana across soil drying treatments. We then used genome resequencing data to evaluate whether genomic features (promoter polymorphism, recombination rate, gene length, and gene density) are associated with genes responding to the environment (E) or with genes with genetic variation (G) in gene expression in the form of eQTLs. We identified thousands of genes that responded to soil drying and hundreds of main-effect eQTLs. However, we identified very few statistically significant eQTLs that interacted with the soil drying treatment (GxE eQTL). Analysis of genome reseq...
Plant Physiology and Biochemistry, 2001
Arabidopsis thaliana has been widely used as a model system, in various aspects of biological studies, such as genomics, genetics, cellular, developmental and molecular biology. In order to reveal the molecular events and regulatory networks controlling Arabidopsis development and responses to genetic and environmental changes, we designed and used a high-density oligonucleotide probe array (GeneChip) to profile global gene expression patterns. The Arabidopsis oligonucleotide probe array consists of probes from 8 300 unique Arabidopsis genes, which covers approximately one-third of the genome. Global transcription profiles of A. thaliana in various developmental stages, and their responses to different environments were generated using this microarray, and archived. Here, we analyze data sets derived from nineteen independent experiments. Constitutively and differentially expressed genes in seedlings, roots, leaves, inflorescences, flowers and siliques at different developmental stages were identified. Functions of these genes based on homologs were determined and categorized. Our results provide insight into the coordinated transcriptional regulation of the genes during plant growth and development. © 2001 Éditions scientifiques et médicales Elsevier SAS
Plant Cell, 2002
Numerous studies have shown that transcription factors are important in regulating plant responses to environmental stress. However, specific functions for most of the genes encoding transcription factors are unclear. In this study, we used mRNA profiles generated from microarray experiments to deduce the functions of genes encoding known and putative Arabidopsis transcription factors. The mRNA levels of 402 distinct transcription factor genes were examined at different developmental stages and under various stress conditions. Transcription factors potentially controlling downstream gene expression in stress signal transduction pathways were identified by observed activation and repression of the genes after certain stress treatments. The mRNA levels of a number of previously characterized transcription factor genes were changed significantly in connection with other regulatory pathways, suggesting their multifunctional nature. The expression of 74 transcription factor genes responsive to bacterial pathogen infection was reduced or abolished in mutants that have defects in salicylic acid, jasmonic acid, or ethylene signaling. This observation indicates that the regulation of these genes is mediated at least partly by these plant hormones and suggests that the transcription factor genes are involved in the regulation of additional downstream responses mediated by these hormones. Among the 43 transcription factor genes that are induced during senescence, 28 of them also are induced by stress treatment, suggesting extensive overlap responses to these stresses. Statistical analysis of the promoter regions of the genes responsive to cold stress indicated unambiguous enrichment of known conserved transcription factor binding sites for the responses. A highly conserved novel promoter motif was identified in genes responding to a broad set of pathogen infection treatments. This observation strongly suggests that the corresponding transcription factors play general and crucial roles in the coordinated regulation of these specific regulons. Although further validation is needed, these correlative results provide a vast amount of information that can guide hypothesis-driven research to elucidate the molecular mechanisms involved in transcriptional regulation and signaling networks in plants.
Transcriptome dynamics of Arabidopsis during sequential biotic and abiotic stresses
The Plant journal : for cell and molecular biology, 2016
In nature, plants have to cope with a wide range of stress conditions that often occur simultaneously or in sequence. To investigate how plants cope with multi-stress conditions, we analyzed the dynamics of whole-transcriptome profiles of Arabidopsis thaliana exposed to six sequential double stresses inflicted by combinations of (1) infection by the fungus Botrytis cinerea, (2) herbivory by Pieris rapae, and (3) drought stress. Each of these stresses induced specific expression profiles over time, in which one third of all differentially expressed genes was shared by at least two single stresses. Of these, 394 genes were differentially expressed during all three stress conditions, albeit often in opposite directions. When two stresses were applied in sequence, plants displayed transcriptome profiles that were very similar to the second stress, irrespective of the nature of the first stress. Nevertheless, significant first-stress-signatures could be identified in the sequential stres...
A gene expression map of Arabidopsis thaliana development
Nature …, 2005
Regulatory regions of plant genes tend to be more compact than those of animal genes, but the complement of transcription factors encoded in plant genomes is as large or larger than that found in those of animals 1 . Plants therefore provide an opportunity to study how transcriptional programs control multicellular development. We analyzed global gene expression during development of the reference plant Arabidopsis thaliana in samples covering many stages, from embryogenesis to senescence, and diverse organs. Here, we provide a first analysis of this data set, which is part of the AtGenExpress expression atlas. We observed that the expression levels of transcription factor genes and signal transduction components are similar to those of metabolic genes. Examining the expression patterns of large gene families, we found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.
Nucleic Acids Research, 2006
We present MultiGO, a web-enabled tool for the identification of biologically relevant gene sets from hierarchically clustered gene expression trees (http://ekhidna.biocenter.helsinki.fi/poxo/multigo). High-throughput gene expression measuring techniques, such as microarrays, are nowadays often used to monitor the expression of thousands of genes. Since these experiments can produce overwhelming amounts of data, computational methods that assist the data analysis and interpretation are essential. MultiGO is a tool that automatically extracts the biological information for multiple clusters and determines their biological relevance, and hence facilitates the interpretation of the data. Since the entire expression tree is analysed, MultiGO is guaranteed to report all clusters that share a common enriched biological function, as defined by Gene Ontology annotations. The tool also identifies a plausible cluster set, which represents the key biological functions affected by the experiment. The performance is demonstrated by analysing drought-, cold-and abscisic acid-related expression data sets from Arabidopsis thaliana. The analysis not only identified known biological functions, but also brought into focus the less established connections to defense-related gene clusters. Thus, in comparison to analyses of manually selected gene lists, the systematic analysis of every cluster can reveal unexpected biological phenomena and produce much more comprehensive biological insights to the experiment of interest.
Comparative transcriptome meta-analysis of Arabidopsis thaliana under drought and cold stress
PloS one, 2018
Multiple environmental stresses adversely affect plant growth and development. Plants under multiple stress condition trigger cascade of signals and show response unique to specific stress as well as shared responses, common to individual stresses. Here, we aim to identify common and unique genetic components during stress response mechanisms liable for cross-talk between stresses. Although drought and cold stress have been widely studied, insignificant information is available about how their combination affects plants. To that end, we performed meta-analysis and co-expression network comparison of drought and cold stress response in Arabidopsis thaliana by analyzing 390 microarray samples belonging to 29 microarray studies. We observed 6120 and 7079 DEGs (differentially expressed genes) under drought and cold stress respectively, using Rank Product methodology. Statistically, 28% (2890) DEGs were found to be common in both the stresses (i.e.; drought and cold stress) with most of ...
Extensive cis -Regulatory Variation Robust to Environmental Perturbation in Arabidopsis
The Plant Cell Online, 2014
cis-and trans-acting factors affect gene expression and responses to environmental conditions. However, for most plant systems, we lack a comprehensive map of these factors and their interaction with environmental variation. Here, we examined allele-specific expression (ASE) in an F1 hybrid to study how alleles from two Arabidopsis thaliana accessions affect gene expression. To investigate the effect of the environment, we used drought stress and developed a variance component model to estimate the combined genetic contributions of cis-and trans-regulatory polymorphisms, environmental factors, and their interactions. We quantified ASE for 11,003 genes, identifying 3318 genes with consistent ASE in control and stress conditions, demonstrating that cis-acting genetic effects are essentially robust to changes in the environment. Moreover, we found 1618 genes with genotype x environment (GxE) interactions, mostly cis x E interactions with magnitude changes in ASE. We found fewer trans x E interactions, but these effects were relatively less robust across conditions, showing more changes in the direction of the effect between environments; this confirms that trans-regulation plays an important role in the response to environmental conditions. Our data provide a detailed map of cis-and trans-regulation and GxE interactions in A. thaliana, laying the ground for mechanistic investigations and studies in other plants and environments.
A generic model of transcriptional regulatory networks: Application to plants under abiotic stress
2013 IEEE International Workshop on Genomic Signal Processing and Statistics, 2013
Understanding the relationships between transcription factors (TFs) and genes in plants under abiotic stress responses, tolerance and adaptation to adverse environments is very important in developing resilient crop varieties. While experimental methods to characterize stress responsive TFs and their targets are highly accurate, identification and characterization of the role of a given gene in a given stress response event are often laborious and time consuming. Computational approaches, on the other hand, offer a platform to identify new knowledge by integrating high throughput omics data and mathematical methods/models. In this research, we have developed a generic linear model of transcriptional regulatory networks (TRNs) and a companion algorithm to identify and to characterize stress responsive genes and their roles in a given stress response event. The proposed methodology was applied to plants, by using Arabidopsis thaliana as an example, under abiotic stress. Well known interactions were inferred as well as putative novel ones that may play important roles in plants under abiotic stress conditions as confirmed by statistical and literature evidences.
2021
Natural variation in gene expression plays a crucial role in evolution, natural selection and improved response to environmental cues. Expression divergence may be caused by localised polymorphisms within the gene or regulatory regions (cis) or induced by differences in regulatory factors (trans). The relative contribution of cis- and trans-regulatory variants can be quantified by genome-wide analysis of Allele-specific expression (ASE) with few F1 samples, unlike the conventional eQTL mapping methods. Differential allelic expression patterns between reciprocal crosses reflect the effect of parent-of-origin and genomic imprinting, while deviation in gene expression of hybrids from parentals reflects heterosis events. This project aims to define an optimal methodology for ASE analysis using RNA-seq data to quantify the effects of cis- and trans-regulatory variants on gene expression differences. To develop this protocol, we used simulated and sequenced RNA-Seq data from leaf tissue i...