cis-Regulatory elements in plant cell signaling (original) (raw)
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A Genome-Scale Resource for the Functional Characterization of Arabidopsis Transcription Factors
Cell Reports, 2014
Extensive transcriptional networks play major roles in cellular and organismal functions. Transcript levels are in part determined by the combinatorial and overlapping functions of multiple transcription factors (TFs) bound to gene promoters. Thus, TF-promoter interactions provide the basic molecular wiring of transcriptional regulatory networks. In plants, discovery of the functional roles of TFs is limited by an increased complexity of network circuitry due to a significant expansion of TF families. Here, we present the construction of a comprehensive collection of Arabidopsis TFs clones created to provide a versatile resource for uncovering TF biological functions. We leveraged this collection by implementing a highthroughput DNA binding assay and identified direct regulators of a key clock gene (CCA1) that provide molecular links between different signaling modules and the circadian clock. The resources introduced in this work will significantly contribute to a better understanding of the transcriptional regulatory landscape of plant genomes.
PLANT PHYSIOLOGY, 2009
Analysis of gene expression data generated by high-throughput microarray transcript profiling experiments has demonstrated that genes with an overall similar expression pattern are often enriched for similar functions. This guilt-by-association principle can be applied to define modular gene programs, identify cis-regulatory elements, or predict gene functions for unknown genes based on their coexpression neighborhood. We evaluated the potential to use Gene Ontology (GO) enrichment of a gene's coexpression neighborhood as a tool to predict its function but found overall low sensitivity scores (13%-34%). This indicates that for many functional categories, coexpression alone performs poorly to infer known biological gene functions. However, integration of cis-regulatory elements shows that 46% of the gene coexpression neighborhoods are enriched for one or more motifs, providing a valuable complementary source to functionally annotate genes. Through the integration of coexpression data, GO annotations, and a set of known cis-regulatory elements combined with a novel set of evolutionarily conserved plant motifs, we could link many genes and motifs to specific biological functions. Application of our coexpression framework extended with cis-regulatory element analysis on transcriptome data from the cell cycle-related transcription factor OBP1 yielded several coexpressed modules associated with specific cis-regulatory elements. Moreover, our analysis strongly suggests a feed-forward regulatory interaction between OBP1 and the E2F pathway. The ATCOECIS resource (http:// bioinformatics.psb.ugent.be/ATCOECIS/) makes it possible to query coexpression data and GO and cis-regulatory element annotations and to submit user-defined gene sets for motif analysis, providing an access point to unravel the regulatory code underlying transcriptional control in Arabidopsis (Arabidopsis thaliana).
2017
Changing environmental conditions are limiting crop productivity and, hence, there is an urgent need to develop stress tolerant plants. Engineering of Cisregulatory elements (CREs) is an effective strategy to design such plants. Transcription factors (TFs) can be used effectively to manipulate gene expression. However, overlapping expression has been observed for several stress-responsive TFs. In order to design improved plants by Cis-engineering, we first need to understand the complex regulatory network of TFs and the cross-talk between them. Advances in systems biology have enabled us to visualize plants from a holistic view during the abiotic stress. The current review discusses major transcriptional regulatory networks involved in abiotic stress tolerance, and how a better understanding of these networks may help in designing stress-tolerant plants. Finally, the review mentions some potential approaches to generate stresstolerant crops to enhance crop productivity, which is the...
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/.
PLoS ONE, 2011
Transcriptional regulation is an important mechanism underlying gene expression and has played a crucial role in evolution. The number, position and interactions between cis-elements and transcription factors (TFs) determine the expression pattern of a gene. To identify functionally relevant cis-elements in gene promoters, a phylogenetic shadowing approach with a lipase gene (LIP1) was used. As a proof of concept, in silico analyses of several Brassicaceae LIP1 promoters identified a highly conserved sequence (LIP1 element) that is sufficient to drive strong expression of a reporter gene in planta. A collection of ca. 1,200 Arabidopsis thaliana TF open reading frames (ORFs) was arrayed in a 96-well format (RR library) and a convenient mating based yeast one hybrid (Y1H) screening procedure was established. We constructed an episomal plasmid (pTUY1H) to clone the LIP1 element and used it as bait for Y1H screenings. A novel interaction with an HD-ZIP (AtML1) TF was identified and abolished by a 2 bp mutation in the LIP1 element. A role of this interaction in transcriptional regulation was confirmed in planta. In addition, we validated our strategy by reproducing the previously reported interaction between a MYB-CC (PHR1) TF, a central regulator of phosphate starvation responses, with a conserved promoter fragment (IPS1 element) containing its cognate binding sequence. Finally, we established that the LIP1 and IPS1 elements were differentially bound by HD-ZIP and MYB-CC family members in agreement with their genetic redundancy in planta. In conclusion, combining in silico analyses of orthologous gene promoters with Y1H screening of the RR library represents a powerful approach to decipher cis-and trans-regulatory codes.
PLOS One, 2011
Background: Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day. Synchronized transcriptome cycling is driven through an extensive network of diurnal and clock-regulated transcription factors and their target cis-regulatory elements. Study of the cycling transcriptome in other plant species could thus help elucidate the similarities and differences and identify hubs of regulation common to monocot and dicot plants.
Identification of plant transcription factor target sequences
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2017
Regulation of gene expression depends on specific cis-regulatory sequences located in the gene promoter regions. These DNA sequences are recognized by transcription factors (TF) in a sequence-specific manner, and their identification could help to elucidate the regulatory networks that underlie plant physiological responses to developmental programs or to environmental adaptation. Here we review recent advances in high throughput methodologies for the identification of plant TF binding sites. Several approaches offer a map of the TF binding locations in vivo and of the dynamics of the gene regulatory networks. As an alternative, high throughput in vitro methods provide comprehensive determination of the DNA sequences recognized by TF. These advances are helping to decipher the regulatory lexicon and to elucidate transcriptional network hierarchies in plants in response to internal or external cues. Highlights Current status of the determination of transcription factor binding sites in planta is reviewed SELEX-seq and protein binding microarrays provide comprehensive in vitro determination of bound DNA sequences Elucidation of transcription networks benefits from in vivo and in vitro
A Functional Genomics Approach Reveals CHE as a Component of the Arabidopsis Circadian Clock
Science, 2009
Transcriptional feedback loops constitute the molecular circuitry of the plant circadian clock. In Arabidopsis , a core loop is established between CCA1 and TOC1. Although CCA1 directly represses TOC1 , the TOC1 protein has no DNA binding domains, which suggests that it cannot directly regulate CCA1 . We established a functional genomic strategy that led to the identification of CHE, a TCP transcription factor that binds specifically to the CCA1 promoter. CHE is a clock component partially redundant with LHY in the repression of CCA1 . The expression of CHE is regulated by CCA1, thus adding a CCA1/CHE feedback loop to the Arabidopsis circadian network. Because CHE and TOC1 interact, and CHE binds to the CCA1 promoter, a molecular linkage between TOC1 and CCA1 gene regulation is established.