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Jin, Ge; Davey, Maria C.; Ertl, John R.; Chen, Rui; Yu, Zhu-tian; Daniel, Steven G.; Becker, Wayne M.; Chen, Chong-Maw

doi:10.1023/a:1006034932322

Cited by 17 publications

(2 citation statements)

References 47 publications

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“…LS5 and LS7 have been reported to provide binding sites to TGA2 and TGA1 respectively in A. thaliana [ 61 , 80 ]. TGA1NTPR1A and AS1LIKECSHPRA are reported as as1-like elements in tobacco and cucumber [ 81 , 82 ] respectively. Similarly, PR2GCNT and WBOXNTCHN48 are reported to be present in stress- and developmentally-regulated pathogenesis-related acidic tobacco β-1,3-glucanase gene [ 83 ] and an ethylene inducible tobacco class1 chitinase48 gene [ 84 ] respectively.…”

Section: Resultsmentioning

confidence: 99%

Global nucleosome positioning regulates salicylic acid mediated transcription in Arabidopsis thaliana

et al. 2015

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BackgroundThe nucleosome positioning regulates the gene expression and many other DNA-related processes in eukaryotes. Genome-wide mapping of nucleosome positions and correlation of genome-wide nucleosomal remodeling with the changes in the gene expression can help us understanding gene regulation on genome level.ResultsIn the present study, we correlate the gene expression and the genomic nucleosomal remodeling in response to salicylic acid (SA) treatment in A. thaliana. We have mapped genome-wide nucleosomes by performing tiling microarray using 146 bp mononucleosomal template DNA. The average nucleosomal coverage is approximately 346 bp per nucleosome both under the control and the SA-treated conditions. The nucleosomal coverage is more in the coding region than in the 5′ regulatory regions. We observe approximately 50% nucleosomal remodeling on SA treatment where significant nucleosomal depletion and nucleosomal enrichment around the transcription start site (TSS) occur in SA induced genes and SA repressed genes respectively in response to SA treatment. Especially in the case of the SA-induced group, the nucleosomal remodeling over the minimal promoter in response to SA is especially significant in the Non-expresser of PR1 (NPR1)-dependent genes. A detailed investigation of npr1-1 mutant confirms a distinct role of NPR1 in the nucleosome remodeling over the core promoter. We have also identified several motifs for various hormonal responses; including ABRE elements in the remodeled nucleosomal regions around the promoter region in the SA regulated genes. We have further identified that the W-box and TGACG/C motif, reported to play an important role in SA-mediated induction, are enriched in nucleosome free regions (NFRs) of the promoter region of the SA induced genes.ConclusionsThis is the first study reporting genome-wide effects of SA treatment on the chromatin architecture of A. thaliana. It also reports significant role of NPR1 in genome-wide nucleosomal remodeling in response to SA.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0404-2) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Global nucleosome positioning regulates salicylic acid mediated transcription in Arabidopsis thaliana

et al. 2015

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“…This octamer sequence is found in the C4-type phosphoenolpyruvate carboxylase gene in maize and binds a light-inducible DNA-binding factor (MUF1) (46). The TGACG motif and variations have been identified in the promoters of a variety of plant genes, such as the auxin-regulated tobacco glutathione transferase genes Nt103-1 and Nt103-35 (47), the CaMV 35 S promoter (the activation sequence-1 element) (48,49), the octopine synthase gene (50), a wheat histone gene (14), a light-regulated TGA1 gene (51), a cucumber hpr-A gene (52), and a tobacco group 1 pathogenesis-related proteins (PR-1) gene (53).…”

Section: Figmentioning

confidence: 99%

Transcriptional Activation of the Rice Tungro Bacilliform Virus Gene Is Critically Dependent on an Activator Element Located Immediately Upstream of the TATA Box

Höhn

Fütterer³

2000

Journal of Biological Chemistry

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To investigate the transcriptional mechanisms of rice tungro bacilliform virus, we have systematically analyzed an activator element located immediately upstream of the TATA box in the rice tungro bacilliform virus promoter and its cognate trans-acting factors. Using electrophoretic mobility shift assays, we showed that rice nuclear proteins bind to the activator element, forming multiple specific DNA-protein complexes via protein-protein interactions. Copper-phenanthroline footprinting and DNA methylation interference analysis indicated that multiple DNA-protein complexes share a common binding site located between positions ؊60 to ؊39, and the proteins contact the activator element in the major groove. DNA UV cross-linking assays further showed that two nuclear proteins (36 and 33 kDa), found in rice cell suspension and shoot nuclear extracts, and one (27 kDa), present in root nuclear extracts, bind to this activator element. In protoplasts derived from a rice (Oryza sativa) suspension culture, the activator element is a prerequisite for promoter activity and its function is critically dependent on its position relative to the TATA box. Thus, transcriptional activation may function via interactions with the basal transcriptional machinery, and we propose that this activation is mediated by protein-protein interactions in a position-dependent mechanism.In eukaryotes, the transcription of protein-coding genes by RNA polymerase II is regulated via two distinct types of DNA sequences: core promoter elements, located near the transcription start site that are sufficient to direct the accurate initiation of transcription; and upstream promoter elements, which contain binding sites for sequence-specific transcriptional activator and/or repressor proteins (1, 2). Transcriptional activators stimulate transcription by recruiting the RNA polymerase II machinery to a core promoter and/or stabilizing the transcription-initiation complex (3-6). Activators have been proposed to directly or indirectly (through coactivators) interact with components of the basal transcription machinery in mammalian systems (3,7,8).Although the basal transcriptional machinery, also referred to as the polymerase II transcription initiation complex, has not been studied in plants as extensively as in mammalian, Drosophila, and yeast systems, TATA-binding proteins (TBPs), 1 TFIID, TFIIA, and RNA polymerase II subunits have been isolated from plants (9 -12). Moreover, a number of plant trans-acting factors have been identified (13). Little is known in plants about the molecular mechanisms of transcriptional activation. It has been shown that TGA1a, a transcription activator interacting with the activation sequence-1 element in the CaMV 35 S promoter (14), increases the rate of preinitiation complex formation (15, 16). The plant transcription factor GT-1 belongs to the class of trihelix DNA-binding proteins, and it binds to a promoter cis-element with the core DNA sequence 5Ј-GGTTAA found initially in light-regulated genes (17). Recently, it has bee...

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The Photorespiratory Pathway of Leaf Peroxisomes

Reumann

2002

Plant Peroxisomes

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Untitled

Cited by 17 publications

References 47 publications

Global nucleosome positioning regulates salicylic acid mediated transcription in Arabidopsis thaliana

Global nucleosome positioning regulates salicylic acid mediated transcription in Arabidopsis thaliana

Transcriptional Activation of the Rice Tungro Bacilliform Virus Gene Is Critically Dependent on an Activator Element Located Immediately Upstream of the TATA Box

The Photorespiratory Pathway of Leaf Peroxisomes

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