PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants

Chow, Chi Nga; Zheng, Han; Wu, Nai; Chien, Chia Hung; Huang, Hsien Da; Lee, Tzong-Yi; Chiang-Hsieh, Yi Fan; Hou, Ping; Yang, Tien Yi; Chang, Wen Chi

doi:10.1093/nar/gkv1035

Cited by 309 publications

(246 citation statements)

References 36 publications

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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%

“…The reliability of PlantPAN2.0 was ascertained as described by Chow et al [12]. The A. thaliana transcription factor (TF) binding sites used in PlantPAN2.0 were experimentally verified by high-throughput, in vitro protein binding microarray technology.…”

Section: Promoter Isolation and In Silico Analysismentioning

confidence: 99%

“…These matrices were supplemented with 548 up-to-date matrices from JASPAR, TRANSFAC (public release 7.0), and PLACE. Finally, 19 960 TFs and 1143 matrices of TF binding sites from 76 plant species were introduced into Plant-PAN2.0 [12]. Match™ software was used in PlantPAN2.0 to scan putative cis-acting sequences against its library of positional weight matrices.…”

Section: Promoter Isolation and In Silico Analysismentioning

confidence: 99%

“…As a result, the minFP value was estimated as a score that recognized the best 1% of hits. As the trained minFP is set as the cut-off profile in PlantPAN2.0, strict scanning results are obtained [12].…”

Section: Promoter Isolation and In Silico Analysismentioning

confidence: 99%

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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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Section: Promoter Isolation and In Silico Analysismentioning

confidence: 99%

Section: Promoter Isolation and In Silico Analysismentioning

confidence: 99%

Section: Promoter Isolation and In Silico Analysismentioning

confidence: 99%

Section: Promoter Isolation and In Silico Analysismentioning

confidence: 99%

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

et al. 2016

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“…Promoter sequences were retrieved from Sol Genomics Network (https://solgenomics.net/) and analyzed using PlantPAN 2.0 platform (http://plantpan2.itps.ncku.edu.tw/) (Chow et al, 2016) to identify the regulatory motifs.…”

Section: Gene Promoter Analysesmentioning

confidence: 99%

Phytochrome and phytohormone interplay in tomato: impacts on fruit physiology and quality traits

Bianchetti¹

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Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP‐TF and determination of its transcriptional effect

et al. 2020

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In plants, the phenylpropanoid pathway is responsible for the synthesis of a diverse array of secondary metabolites that include lignin monomers, flavonoids, and coumarins, many of which are essential for plant structure, biomass recalcitrance, stress defense, and nutritional quality. Our previous studies have demonstrated that Populus trichocarpa PtrEPSP‐TF, an isoform of 5‐enolpyruvylshikimate 3‐phosphate (EPSP) synthase, has transcriptional activity and regulates phenylpropanoid biosynthesis in Populus. In this study, we report the identification of single nucleotide polymorphism (SNP) of PtrEPSP‐TF that defines its functionality. Populus natural variants carrying this SNP were shown to have reduced lignin content. Here, we demonstrated that the SNP‐induced substitution of 142nd amino acid (PtrEPSP‐TFD142E) dramatically impairs the DNA‐binding and transcriptional activity of PtrEPSP‐TF. When introduced to a monocot species rice (Oryza sativa) in which an EPSP synthase isoform with the DNA‐binding helix‐turn‐helix (HTH) motif is absent, the PtrEPSP‐TF, but not PtrEPSP‐TFD142E, activated genes in the phenylpropanoid pathway. More importantly, heterologous expression of PtrEPSP‐TF uncovered five new transcriptional regulators of phenylpropanoid biosynthesis in rice. Collectively, this study identifies the key amino acid required for PtrEPSP‐TF functionality and provides a strategy to uncover new transcriptional regulators in phenylpropanoid biosynthesis.

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PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants

Cited by 309 publications

References 36 publications

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

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

Phytochrome and phytohormone interplay in tomato: impacts on fruit physiology and quality traits

Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP‐TF and determination of its transcriptional effect

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