READS - A Resource for Plant Non-coding Regulatory Sequence Analysis (original) (raw)
Related papers
Nucleic Acids Research, 2002
PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular promoter sequences. Links to the EMBL, TRANSFAC and MEDLINE databases are provided when available. Data about the transcription sites are extracted mainly from the literature, supplemented with an increasing number of in silico predicted data. Apart from a general description for specific transcription factor sites, levels of confidence for the experimental evidence, functional information and the position on the promoter are given as well. New features have been implemented to search for plant cis-acting regulatory elements in a query sequence. Furthermore, links are now provided to a new clustering and motif search method to investigate clusters of co-expressed genes. New regulatory elements can be sent automatically and will be added to the database after curation. The PlantCARE relational database is available via the World Wide Web at http://sphinx.rug.ac.be:8080/PlantCARE/.
Functional tagging of regulatory elements in the plant genome
Development, 1991
In comparison with animals, relatively few plant genes have been identified that have been shown to be under organ-, tissue-or cell-type-specific regulation. In this paper, we describe how the /J-glucuronidase (GUS) reporter gene (gusA or uidA), fused to a weak promoter (a truncated (-90 bp) CaMV35S promoter), can be used to identify tissue-specific markers in transgenic tobacco plants. The rationale was that the expression of gusA would be determined primarily by position effect. Quantitative analysis revealed that, of 184-90-gus transgenic plants, 73 % exhibited gusA gene activation in leaf tissue, and the level of GUS enzyme activity varied over a 300-fold range within the population. In comparison, transformation with a promoterless gusA gene resulted in GUS expression in 78 % of all plants analyzed (in leaf and/or root) and expression levels were threefold or more lower. Qualitative GUS analysis of single locus-90-gus transformants revealed differential expression in diverse tissues. The spatial pattern of GUS activity was unique to individual transformants, was a reflection of differential gusA gene transcription, and was stably transmissible to progeny. Evidence for preferential expression in roots not only of the-90-gus, but also the promoterless gusA gene is presented. The value of the-90 bp promoter-gusA sequence, which is termed an 'interposon', as a tool both to identify native enhancer sequences in situ and to investigate position effects in plants, is discussed.
PLoS ONE, 2013
On chromosome 4 in the Arabidopsis genome, two neighboring genes (calmodulin methyl transferase At4g35987 and senescence associated gene At4g35985) are located in a head-to-head divergent orientation sharing a putative bidirectional promoter. This 1258 bp intergenic region contains a number of environmental stress responsive and tissue specific cisregulatory elements. Transcript analysis of At4g35985 and At4g35987 genes by quantitative real time PCR showed tissue specific and stress inducible expression profiles. We tested the bidirectional promoter-function of the intergenic region shared by the divergent genes At4g35985 and At4g35987 using two reporter genes (GFP and GUS) in both orientations in transient tobacco protoplast and Agro-infiltration assays, as well as in stably transformed transgenic Arabidopsis and tobacco plants. In transient assays with GFP and GUS reporter genes the At4g35985 promoter (P85) showed stronger expression (about 3.5 fold) compared to the At4g35987 promoter (P87). The tissue specific as well as stress responsive functional nature of the bidirectional promoter was evaluated in independent transgenic Arabidopsis and tobacco lines. Expression of P85 activity was detected in the midrib of leaves, leaf trichomes, apical meristemic regions, throughout the root, lateral roots and flowers. The expression of P87 was observed in leaf-tip, hydathodes, apical meristem, root tips, emerging lateral root tips, root stele region and in floral tissues. The bidirectional promoter in both orientations shows differential up-regulation (2.5 to 3 fold) under salt stress. Use of such regulatory elements of bidirectional promoters showing spatial and stress inducible promoter-functions in heterologous system might be an important tool for plant biotechnology and gene stacking applications.
Biotic stress inducible promoters in crop plants- a review
2017
Promoter is a DNA sequence that regulates the expression of a particular gene. They are classified on the basis of their function and spatio-temporal expression into constitutive, tissue-specific or development-stage-specific and inducible promoters. Plant genes associated with defence responses are activated by stress-factors and these genes are known to be regulated by promoters or the upstream elements. Promoters induced by abiotic stress factors in plants are fairly well studied compared to biotic stresses. This review presented information generated on promoters and regulatory elements involved in defence gene expression due to insect damage, pathogen and nematode attack to crop plants, mechanism and their utilization in crop improvement through genetic engineering.
Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences
Bioinformatics, 2005
To better understand the regulatory networks that control plant gene expression, tools are needed to systematically analyze and visualize promoter regulatory sequences in Arabidopsis thaliana. We have developed the Athena database, which contains 30 067 predicted Arabidopsis promoter sequences and consensus sequences for 105 previously characterized transcription factor (TF) binding sites. Athena provides four novel tools to facilitate the analysis of promoter sequences: a promoter visualization tool to enable the rapid inspection of key regulatory sequences in multiple promoters; a TF binding site enrichment tool to identify statistically over-represented TF sites occurring in a user-selected subset of promoters; a data-mining tool to rapidly select promoter sequences containing the specified combination of TF binding sites; and a tool to display the distribution of TF binding site positions in a selected set of promoter sequences.
Cis-regulatory elements used to control gene expression in plants
Plant Cell, Tissue and Organ Culture (PCTOC), 2016
Plant biotechnology is a dynamically developing science, which comprises many fields of knowledge. Novel plant genetic engineering findings highly influence the improvement of industrial production. These findings mostly concern cis-regulatory elements, which are sequences controlling gene expression at all developmental stages. They comprise of promoters, enhancers, insulators and silencers, which are used to construct synthetic expression cassettes. Examples of most important cis-regulatory elements are reviewed in the present paper. Variability among core promoters content and distal promoter regions impedes evaluation of interactions between them during the artificial promoters construction. Synthetic promoters and artificial expression cassettes trigger a significant increase in gene expression level, better properties and quality of a product. Accumulating knowledge about gene promoters, cis sequences and their cooperating factors allows uniform expression systems and highly predictable results.
BMC Bioinformatics, 2003
The gene regulatory information is hardwired in the promoter regions formed by cis-regulatory elements that bind specific transcription factors (TFs). Hence, establishing the architecture of plant promoters is fundamental to understanding gene expression. The determination of the regulatory circuits controlled by each TF and the identification of the cisregulatory sequences for all genes have been identified as two of the goals of the Multinational Coordinated Arabidopsis thaliana Functional Genomics Project by the Multinational Arabidopsis Steering Committee (June 2002).
Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes
PLANT PHYSIOLOGY, 2003
The identification of promoters and their regulatory elements is one of the major challenges in bioinformatics and integrates comparative, structural, and functional genomics. Many different approaches have been developed to detect conserved motifs in a set of genes that are either coregulated or orthologous. However, although recent approaches seem promising, in general, unambiguous identification of regulatory elements is not straightforward. The delineation of promoters is even harder, due to its complex nature, and in silico promoter prediction is still in its infancy. Here, we review the different approaches that have been developed for identifying promoters and their regulatory elements. We discuss the detection of cis-acting regulatory elements using word-counting or probabilistic methods (so-called "search by signal" methods) and the delineation of promoters by considering both sequence content and structural features ("search by content" methods). As an example of search by content, we explored in greater detail the association of promoters with CpG islands. However, due to differences in sequence content, the parameters used to detect CpG islands in humans and other vertebrates cannot be used for plants. Therefore, a preliminary attempt was made to define parameters that could possibly define CpG and CpNpG islands in Arabidopsis, by exploring the compositional landscape around the transcriptional start site. To this end, a data set of more than 5,000 gene sequences was built, including the promoter region, the 5Ј-untranslated region, and the first introns and coding exons. Preliminary analysis shows that promoter location based on the detection of potential CpG/CpNpG islands in the Arabidopsis genome is not straightforward. Nevertheless, because the landscape of CpG/ CpNpG islands differs considerably between promoters and introns on the one side and exons (whether coding or not) on the other, more sophisticated approaches can probably be developed for the successful detection of "putative" CpG and CpNpG islands in plants.
Regulation of Gene Expression in Plants
In almost all of the areas of gene expression control except one, plant research has lagged considerably behind studies in yeast, insects and vertebrates. Advances in animal gene expression control have also benefited plant research, as we continue to find that much of the machinery and mechanisms controlling gene expression have been preserved in all eukaryotes. However, there are some interesting differences in gene structure and regulation between plants and animals. First, vertebrate genes can be quite large, often spanning tens of thousands of base pairs and usually separated by numerous large introns, whereas plant genes tend to be much smaller (averaging between 1–2 kb (kilobases) with fewer and smaller introns. Second, as we shall see in the following chapters, plant transcripts retain introns more often than do animal transcripts (30% of all genes in the model plant, Arabidopsis, compared to 10% in humans). Unfortunately, at this time we have only a few plant models for gene regulation, and only Arabidopsis, rice and poplar have been fully sequenced. Since Arabidopsis was the first plant genome to be fully sequenced, most of our information has come from studies of its transcriptome, and it is not known to what extent it truly represents other members of the plant kingdom. In addition, as our knowledge of factors influencing gene expression increases, so too, does our recognition that the current annotations in the gene databases will need to be updated to reflect new information as it appears in the literature. Finally, compared to animals, plants have evolved different signaling mechanisms, partly because plant hormones do not exactly function as do those in animals, and partly because plants must cope with environmental changes differently than animals, since they cannot physically escape their environments except possibly through reproduction. Therefore, plants have evolved very complex, interacting signaling pathways in response to developmental signals and biotic/abiotic stresses. All of these observations ultimately reflect some of the differences plants display in regulating gene expression compared to yeasts, insects and vertebrates. Although we have touched upon some of the differences between animal and plant control of gene expression here, it is equally important to recognize and appreciate the common mechanisms they share. For example, the basic transcriptional machinery via DNA-dependent RNA Polymerase II is virtually the same in plants and animals. Furthermore, some transcription factors, like myb and myc factors are similar in structure and function in both plants and animals. Plants and animals contain introns separating the coding regions of most genes and again, they utilize similar machinery to process the introns and form mature mRNAs. Since translation in all eukaryotes is basically the same, we see more similarities between plants and animals in this process, than differences. These mechanisms relate to mRNA structure, including sequences in the 5′ leader region and those in the 3′ untranslated region which influence the efficiency and selectivity of translation. It is hoped that the following chapters will expose the reader to some of the most recent, novel and fascinating examples of transcriptional and posttranscriptional control of gene expression in plants and, where appropriate, provide comparison to notable examples of animal gene regulation.