PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups

Chang, Wen Chi; Lee, Tzong-Yi; Huang, Hsien Da; Huang, His Yuan; Pan, Rong

doi:10.1186/1471-2164-9-561

Cited by 260 publications

(195 citation statements)

References 54 publications

(71 reference statements)

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“…Our method is useful for genome-wide studies of gene transcriptional regulation in plants. To our knowledge, previous computational methods for plant CRM identification are often restricted to a small group of genes (Vandepoele et al, 2006) or require TFBS cooccurrence in short regions (#200 bp; Steffens et al, 2005;Chang et al, 2008). In addition, these methods often consider combinations of only two cisregulatory sequences at a time.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, compared with a large number of computational CRM studies on animals mentioned above, only a couple of computational CRM studies in plants exist. These studies often focus on the identification of two to three TFs that are potentially working together to regulate target genes (Steffens et al, 2005;Vandepoele et al, 2006;Chang et al, 2008;Michael et al, 2008). Therefore, it is not clear how widespread CRMs are in plants, which multiple TFs likely coordinate the transcriptional regulation of their target genes, and how these TF combinations are shared by different plant species.…”

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confidence: 99%

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Thousands of Cis-Regulatory Sequence Combinations Are Shared by Arabidopsis and Poplar

Ding

2012

Plant Physiology

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The identification of cis-regulatory modules (CRMs) can greatly advance our understanding of gene regulatory mechanisms. Despite the existence of binding sites of more than three transcription factors (TFs) in a CRM, studies in plants often consider only the cooccurrence of binding sites of one or two TFs. In addition, CRM studies in plants are limited to combinations of only a few families of TFs. It is thus not clear how widespread plant TFs work together, which TFs work together to regulate plant genes, and how the combinations of these TFs are shared by different plants. To fill these gaps, we applied a frequent patternmining-based approach to identify frequently used cis-regulatory sequence combinations in the promoter sequences of two plant species, Arabidopsis (Arabidopsis thaliana) and poplar (Populus trichocarpa). A cis-regulatory sequence here corresponds to a DNA motif bound by a TF. We identified 18,638 combinations composed of two to six cis-regulatory sequences that are shared by the two plant species. In addition, with known cis-regulatory sequence combinations, gene function annotation, gene expression data, and known functional gene sets, we showed that the functionality of at least 96.8% and 65.2% of these shared combinations in Arabidopsis are partially supported, under a false discovery rate of 0.1 and 0.05, respectively. Finally, we discovered that 796 of the 18,638 combinations might relate to functions that are important in bioenergy research. Our work will facilitate the study of gene transcriptional regulation in plants.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Thousands of Cis-Regulatory Sequence Combinations Are Shared by Arabidopsis and Poplar

Ding

2012

Plant Physiology

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“…For BABA treatment, an SA-dependent pathway has been well described in Arabidopsis plants; however, to the best of our knowledge, no such study showing evidence for SA-dependent signalling in tomato has been published. Therefore, we analysed the promoter regions of BABA-upregulated transcripts spanning about 1000 bp before the start codon using the PlantPAN program (Chang et al, 2008) in the tomato transcription factor library. In the majority of BABA-upregulated transcripts, the sequence for the transcription factor ERELEE4 containing an ETresponsive element was identified (Table S2).…”

Section: Overlap Of Upregulated Genes Among Baba- Oligandrin-and Patmentioning

confidence: 99%

Diverse responses of wild and cultivated tomato to BABA, oligandrin andOidium neolycopersiciinfection

Satková

Starý

Plešková

et al. 2016

Ann Bot

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Background and Aims Current strategies for increased crop protection of susceptible tomato plants against pathogen infections include treatment with synthetic chemicals, application of natural pathogen-derived compounds or transfer of resistance genes from wild tomato species within breeding programmes. In this study, a series of 45 genes potentially involved in defence mechanisms was retrieved from the genome sequence of inbred reference tomato cultivar Solanum lycopersicum 'Heinz 1706'. The aim of the study was to analyse expression of these selected genes in wild and cultivated tomato plants contrasting in resistance to the biotrophic pathogen Oidium neolycopersici, the causative agent of powdery mildew. Plants were treated either solely with potential resistance inducers or by inducers together with the pathogen.Methods The resistance against O. neolycopersici infection as well as RT-PCR-based analysis of gene expression in response to the oomycete elicitor oligandrin and chemical agent b-aminobutyric acid (BABA) were investigated in the highly susceptible domesticated inbred genotype Solanum lycopersicum 'Amateur' and resistant wild genotype Solanum habrochaites.Key Results Differences in basal expression levels of defensins, germins, b-1,3-glucanases, heveins, chitinases, osmotins and PR1 proteins in non-infected and non-elicited plants were observed between the highly resistant and susceptible genotypes. Moreover, these defence genes showed an extensive up-regulation following O. neolycopersici infection in both genotypes. Application of BABA and elicitin induced expression of multiple defence-related transcripts and, through different mechanisms, enhanced resistance against powdery mildew in the susceptible tomato genotype.Conclusions The results indicate that non-specific resistance in the resistant genotype S. habrochaites resulted from high basal levels of transcripts with proven roles in defence processes. In the susceptible genotype S. lycopersicum 'Amateur', oligandrin-and BABA-induced resistance involved different signalling pathways, with BABAtreated leaves displaying direct activation of the ethylene-dependent signalling pathway, in contrast to previously reported jasmonic acid-mediated signalling for elicitins.

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“…Amplified DNA fragments were TOPO-TA cloned into a pCR®II-TOPO® vector (Life Technologies, USA) and sequenced. The obtained sequence was searched for cis-active elements, tandem repeats, CpG/CpNpG islands and microRNA binding sites using PlantPAN and PlantPAN 2.0 [11,12]. TSSP software and RegSite Plant DB, (Softberry Inc., USA) were employed to localize TATA-box and transcription initiation site (TIS).…”

Section: Promoter Isolation and In Silico Analysismentioning

confidence: 99%

Isolation and characterization of a copalyl diphosphate synthase gene promoter from Salvia miltiorrhiza

et al. 2016

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The promoter, 5' UTR, and 34-nt 5' fragments of protein encoding region of the Salvia miltiorrhiza copalyl diphosphate synthase gene were cloned and characterized. No tandem repeats, miRNA binding sites, or CpNpG islands were observed in the promoter, 5' UTR, or protein encoding fragments. The entire isolated promoter and 5' UTR is 2235 bp long and contains repetitions of many cis-active elements, recognized by homologous transcription factors, found in Arabidopsis thaliana and other plant species. A pyrimidine-rich fragment with only 6 non-pyrimidine bases was localized in the 33-nt stretch from nt 2185 to 2217 in the 5' UTR. The observed cis-active sequences are potential binding sites for trans-factors that could regulate spatio-temporal CPS gene expression in response to biotic and abiotic stress conditions. Obtained results are initially verified by in silico and co-expression studies based on A. thaliana microarray data.The quantitative RT-PCR analysis confirmed that the entire 2269-bp copalyl diphosphate synthase gene fragment has the promoter activity.Quantitative RT-PCR analysis was used to study changes in CPS promoter activity occurring in response to the application of four selected biotic and abiotic regulatory factors; auxin, gibberellin, salicylic acid, and high-salt concentration.

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PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups

Cited by 260 publications

References 54 publications

Thousands of Cis-Regulatory Sequence Combinations Are Shared by Arabidopsis and Poplar

Thousands of Cis-Regulatory Sequence Combinations Are Shared by Arabidopsis and Poplar

Diverse responses of wild and cultivated tomato to BABA, oligandrin andOidium neolycopersiciinfection

Isolation and characterization of a copalyl diphosphate synthase gene promoter from Salvia miltiorrhiza

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