An Intergenic Region Shared by At4g35985 and At4g35987 in Arabidopsis thaliana Is a Tissue Specific and Stress Inducible Bidirectional Promoter Analyzed in Transgenic Arabidopsis and Tobacco Plants

Banerjee, Joydeep; Sahoo, Dipak Kumar; Dey, Nrisingha; Houtz, Robert L.; Maiti, Indu B.

doi:10.1371/journal.pone.0079622

Cited by 55 publications

(45 citation statements)

References 80 publications

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“…The quantitative real-time PCR analysis was performed following a previously published protocol (Banerjee et al 2013b) using GUS-specific forward (5′-d-TTACGTCCTGTAGAAACCCCA-3′) and reverse (5′-d-ACTGCCTGGCACAGCAAT TGC-3′) primers. The PCR reaction was performed with four replicates and was repeated with three biological samples.…”

Section: Rna Isolation and Quantitative Real-time Pcrmentioning

confidence: 99%

A Region Containing an as-1 Element of Dahlia Mosaic Virus (DaMV) Subgenomic Transcript Promoter Plays a Key Role in Green Tissue- and Root-Specific Expression in Plants

et al. 2014

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A subgenomic transcript (Sgt) promoter was isolated from the genomic clone of dahlia mosaic virus (DaMV), which is a double-stranded DNA virus of the Caulimoviridae family. The DaMVSgt promoter, which is linked to the heterologous β-glucuronidase (GUS) reporter gene, was characterized in transient protoplasts and in transgenic tobacco, as well as in Arabidopsis plants. The 5′-and 3′-deletion analysis of a 591-bp DaMVSgt promoter fragment indicated that a 441-bp promoter fragment (−372 to +69 from the transcription start site; TSS) was sufficient for maximal promoter activity. A 141-bp promoter fragment (−72 to +69 from TSS) was the minimal promoter region that also showed relatively strong activity. The three activation sequence-1 (as-1) elements and the border regions were primarily responsible for the promoter activity, as revealed by a finer internal deletion and mutation analysis of the cis-elements and of the immediate border sequence of the activation domain. Electrophoretic mobility shift assay (EMSA), supershift EMSA, DNase I footprinting, Southwestern blotting, and UV cross-linking studies demonstrated the binding of a tobacco transcription factor, TGA1a, that correlated with 2,4-dichlorophenylacetic acid (2,4D)-induced transcriptional activity of the DaMVSgt promoter. Histological GUS staining and the GUS enzymatic assay demonstrated that the 441-bp DaMVSgt4 promoter and 141-bp minimal DaMVSgt4F are 5.5 and 4.6 times, respectively, stronger than the CaMV 35S promoter. The minimal DaMVSgt4F promoter is more active than CaMV 35S in all types of green tissues and roots, without any detectable expression in reproductive tissues and seeds. The DaMVSgt4F promoter may be useful for transgene containment applications.

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Section: Rna Isolation and Quantitative Real-time Pcrmentioning

confidence: 99%

A Region Containing an as-1 Element of Dahlia Mosaic Virus (DaMV) Subgenomic Transcript Promoter Plays a Key Role in Green Tissue- and Root-Specific Expression in Plants

et al. 2014

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“…Similarly, plant BDPs function in the regulation of important agricultural traits131415161718. The transcription of bidirectional protein-coding gene pairs arranged with in a head-to-head orientation is controlled by bidirectional promoters (BDPs), which have been intensively investigated in eukaryotic genomes, ranging from yeast1920, Drosophila 21, and humans522 to plants2324.…”

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confidence: 99%

Functional characterization of open chromatin in bidirectional promoters of rice

Fang

Wang

et al. 2016

Sci Rep

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Bidirectional gene pairs tend to be highly coregulated and function in similar biological processes in eukaryotic genomes. Structural features and functional consequences of bidirectional promoters (BDPs) have received considerable attention among diverse species. However, the underlying mechanisms responsible for the bidirectional transcription and coexpression of BDPs remain poorly understood in plants. In this study, we integrated DNase-seq, RNA-seq, ChIP-seq and MNase-seq data and investigated the effect of physical DNase I hypersensitive site (DHS) positions on the transcription of rice BDPs. We found that the physical position of a DHS relative to the TSS of bidirectional gene pairs can affect the expression of the corresponding genes: the closer a DHS is to the TSS, the higher is the expression level of the genes. Most importantly, we observed that the distribution of DHSs plays a significant role in the regulation of transcription and the coexpression of gene pairs, which are possibly mediated by orchestrating the positioning of histone marks and canonical nucleosomes around BDPs. Our results demonstrate that the combined actions of chromatin structures with DHSs, which contain functional cis-elements for interaction with transcriptional machinery, may play an important role in the regulation of the bidirectional transcription or coexpression in rice BDPs. Our findings may help to enhance the understanding of DHSs in the regulation of bidirectional gene pairs.

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“…The biotic stress caused by Perono spora tabacina is accompanied by an increase in the AtP85 promoter activity in the Nicotiana benthamiana tobacco leaves (3 times). The AtP87 promoter activity was not studied in this experiment (Banerjee et al, 2013).…”

Section: Promoters Of Plants Sensitivementioning

confidence: 99%

Promoters of plant genes responsive to pathogen invasion

Smirnova

Кочетов

2015

Russ J Genet Appl Res

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Gene networks controlling the plant resistance to different phytopathogens are rather complex; hundreds of genes can be involved in them. Infection causes considerable changes at molecular genetic, bio chemical, physiological, and morphological levels both locally (in the place of invasion) and systemically. The reconstruction of gene networks that are responsible for plant defense against pathogenic bacteria, fungi, and viruses is required for the elucidation of the underlying molecular mechanisms as well as for the development of new approaches to crop improvement. The transcriptional activity of genes involved in the defense mech anisms usually increases in response to the infection; therefore, the characteristics of their promoters is an important source of information for the detection of transcription factors that control their activity and for the search for new genes involved in the pathogen response. The data on promoters are required for the cre ation of plants that are resistant to phytopathogens by gene engineering techniques. The data on promoters of pathogen sensitive genes with an experimentally verified expression pattern annotated in the TransGene Promoters (TGP) database are presented in the article. The TGP database can be used as a source of infor mation for interpretation of transcriptome data and when planning genetically engineered experiments directed towards increasing plant resistance to pathogens of different origins.

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An Intergenic Region Shared by At4g35985 and At4g35987 in Arabidopsis thaliana Is a Tissue Specific and Stress Inducible Bidirectional Promoter Analyzed in Transgenic Arabidopsis and Tobacco Plants

Cited by 55 publications

References 80 publications

A Region Containing an as-1 Element of Dahlia Mosaic Virus (DaMV) Subgenomic Transcript Promoter Plays a Key Role in Green Tissue- and Root-Specific Expression in Plants

A Region Containing an as-1 Element of Dahlia Mosaic Virus (DaMV) Subgenomic Transcript Promoter Plays a Key Role in Green Tissue- and Root-Specific Expression in Plants

Functional characterization of open chromatin in bidirectional promoters of rice

Promoters of plant genes responsive to pathogen invasion

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