Genome-wide analysis of rice (<i>Oryza sativa</i> L. subsp. <i>japonica</i>) TATA box and Y Patch promoter elements

Civáň, Peter; Švec, Miroslav

doi:10.1139/g09-001

Cited by 40 publications

(35 citation statements)

References 14 publications

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“…The selected pHsp18 and pHsp82 promoter fragments retained the essential elements to drive heat shock induction in these tissues, and they performed as expected in GM plants. This is in agreement with previous publications where regulatory elements including the TATA box were in silico predicted in the two 5′ proximal regions [65], [66].…”

Section: Discussionsupporting

confidence: 93%

Production of Phytotoxic Cationic α-Helical Antimicrobial Peptides in Plant Cells Using Inducible Promoters

2014

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Synthetic linear antimicrobial peptides with cationic α-helical structures, such as BP100, have potent and specific activities against economically important plant pathogenic bacteria. They are also recognized as valuable therapeutics and preservatives. However, highly active BP100 derivatives are often phytotoxic when expressed at high levels as recombinant peptides in plants. Here we demonstrate that production of recombinant phytotoxic peptides in transgenic plants is possible by strictly limiting transgene expression to certain tissues and conditions, and specifically that minimization of this expression during transformation and regeneration of transgenic plants is essential to obtain viable plant biofactories. On the basis of whole-genome transcriptomic data available online, we identified the Os.hsp82 promoter that fulfilled this requirement and was highly induced in response to heat shock. Using this strategy, we generated transgenic rice lines producing moderate yields of severely phytotoxic BP100 derivatives on exposure to high temperature. In addition, a threshold for gene expression in selected tissues and stages was experimentally established, below which the corresponding promoters should be suitable for driving the expression of recombinant phytotoxic proteins in genetically modified plants. In view of the growing transcriptomics data available, this approach is of interest to assist promoter selection for specific purposes.

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Section: Discussionsupporting

confidence: 93%

Production of Phytotoxic Cationic α-Helical Antimicrobial Peptides in Plant Cells Using Inducible Promoters

2014

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“…To identify sequence elements that show TFBS enrichment, we next searched the promoters for specific upstream locations where these TFBS elements could be collectively enriched (see Methods: 3PEAT TSS Peak Prediction Model). We used a standard log-likelihood TFBS scanning technique to approximate DNA binding affinity along with a set of 200 known plant elements characterized in the literature (Grasser, 2006;Megraw et al, 2006;Bryne et al, 2008;Wingender, 2008;Civán and Svec, 2009;Yamamoto et al, 2009).…”

Section: The Location Of Transcription Initiation Can Be Accurately Mmentioning

confidence: 99%

“…To identify regions where transcription factor binding sequences are enriched with respect to the TSS, we started with a set of 203 TF positional weight matrices (PWMs) collected from a variety of sources (Grasser, 2006;Megraw et al, 2006;Bryne et al, 2008;Wingender, 2008;Civán and Svec, 2009;Yamamoto et al, 2009). While the PWMs used in this study were derived using experimentally supported data (rather than strictly computational approaches), PWMs are rarely a perfect characterization of TF binding domains or their sequence specificity.…”

Section: Peat Model Constructionmentioning

confidence: 99%

Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter Signatures

et al. 2014

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Understanding plant gene promoter architecture has long been a challenge due to the lack of relevant large-scale data sets and analysis methods. Here, we present a publicly available, large-scale transcription start site (TSS) data set in plants using a high-resolution method for analysis of 59 ends of mRNA transcripts. Our data set is produced using the paired-end analysis of transcription start sites (PEAT) protocol, providing millions of TSS locations from wild-type Columbia-0 Arabidopsis thaliana whole root samples. Using this data set, we grouped TSS reads into "TSS tag clusters" and categorized clusters into three spatial initiation patterns: narrow peak, broad with peak, and weak peak. We then designed a machine learning model that predicts the presence of TSS tag clusters with outstanding sensitivity and specificity for all three initiation patterns. We used this model to analyze the transcription factor binding site content of promoters exhibiting these initiation patterns. In contrast to the canonical notions of TATA-containing and more broad "TATA-less" promoters, the model shows that, in plants, the vast majority of transcription start sites are TATA free and are defined by a large compendium of known DNA sequence binding elements. We present results on the usage of these elements and provide our Plant PEAT Peaks (3PEAT) model that predicts the presence of TSSs directly from sequence.

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“…While many of these CPEs have been well studied in animals, studies in plants are not as extensive, leaving many elements that have only been identified computationally (Yamamoto et al, 2007a(Yamamoto et al, , 2011Civán and Svec, 2009;Bernard et al, 2010;Zuo and Li, 2011;Kumari and Ware, 2013). This is especially problematic considering that even some of the most well studied and conserved elements such as TATA and Inr show distinct consensus sequence differences in plants compared with their yeast and mammalian counterparts, making plant-specific consensus sequence identification an important priority in accurate promoter identification in plants (Kumari and Ware, 2013).…”

Section: The State Of the Core: Our Limited Knowledge Of Pol II Core mentioning

confidence: 99%

Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants

et al. 2016

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ORCID IDs: 0000-0001-6793-6151 (M.M.); 0000-0002-0105-6431 (S.A.F.)RNA Polymerase II (Pol II) regulatory cascades involving transcription factors (TFs) and their targets orchestrate the genetic circuitry of every eukaryotic organism. In order to understand how these cascades function, they can be dissected into small genetic networks, each containing just a few Pol II transcribed genes, that generate specific signal-processing outcomes. Small RNA regulatory circuits involve direct regulation of a small RNA by a TF and/or direct regulation of a TF by a small RNA and have been shown to play unique roles in many organisms. Here, we will focus on small RNA regulatory circuits containing Pol II transcribed microRNAs (miRNAs). While the role of miRNA-containing regulatory circuits as modular building blocks for the function of complex networks has long been on the forefront of studies in the animal kingdom, plant studies are poised to take a lead role in this area because of their advantages in probing transcriptional and posttranscriptional control of Pol II genes. The relative simplicity of tissue-and cell-type organization, miRNA targeting, and genomic structure make the Arabidopsis thaliana plant model uniquely amenable for small RNA regulatory circuit studies in a multicellular organism. In this Review, we cover analysis, tools, and validation methods for probing the component interactions in miRNA-containing regulatory circuits. We then review the important roles that plant miRNAs are playing in these circuits and summarize methods for the identification of small genetic circuits that strongly influence plant function. We conclude by noting areas of opportunity where new plant studies are imminently needed.

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Genome-wide analysis of rice (Oryza sativa L. subsp. japonica) TATA box and Y Patch promoter elements

Cited by 40 publications

References 14 publications

Production of Phytotoxic Cationic α-Helical Antimicrobial Peptides in Plant Cells Using Inducible Promoters

Production of Phytotoxic Cationic α-Helical Antimicrobial Peptides in Plant Cells Using Inducible Promoters

Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter Signatures

Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants

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