Characterization of a T-DNA promoter trap line of Arabidopsis thaliana uncovers a cryptic bi-directional promoter

Pratibha, Pritu; Singh, Sunil Kumar; Sharma, Isha; Kumar, Ravi Shankar; Srinivasan, Raji; Bhat, S. R.; Ahuja, Paramvir Singh; Sreenivasulu, Yelam

doi:10.1016/j.gene.2013.04.031

Cited by 15 publications

(13 citation statements)

References 27 publications

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“…Development and screening of transferred DNA (T-DNA) promoter trap population of A. thaliana (ecotype Columbia) has been described earlier (Pratibha et al 2013). The line showing β-glucuronidase (GUS) expression in ovules (designated as GUS-650) was identified and used in this study for detailed analysis.…”

Section: Methodsmentioning

confidence: 99%

“…Among the various approaches, transfer DNA (T-DNA) promoter trap technique has emerged as the most powerful tool for identifying functional and cryptic promoters. In this approach, transgenics are generated using a T-DNA vector having a selectable marker gene under the control of a constitutive promoter, and a promoter-less reporter gene placed at the right border for visualizing the trapped promoter (Pratibha et al 2013). Transgenics are first selected on the basis of trait conferred by the selectable marker gene and then screened for the reporter gene expression.…”

Section: Introductionmentioning

confidence: 99%

“…Expression of the reporter gene in the transformant indicates that the T-DNA has trapped a promoter. Apart from tissuespecific, developmental stage-specific and stress-induced promoters, this approach has also led to the identification and isolation of several cryptic promoter elements (Okresz et al 1998;Foster et al 1994;Mollier et al 2000;Sivanandan et al 2005;Pratibha et al 2013). Cryptic promoters are pseudo or potential sequences capable of transcription of downstream gene, which are otherwise silent and not associated with any protein or RNA-coding gene (Lindsey et al 1993).…”

Section: Introductionmentioning

confidence: 99%

“…To date, several cryptic promoters have been reported including promoter elements specific for meristematic tissues like calli and root tips (Okresz et al 1998), guard cells (Plesch et al 2000) and roots (Mollier et al 2000;Sivanandan et al 2005). Recently, we have isolated and characterized an anther-specific cryptic bi-directional promoter in Arabidopsis (Pratibha et al 2013).…”

Section: Introductionmentioning

confidence: 99%

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Identification and Characterization of a T-DNA Promoter Trap Line of Arabidopsis thaliana Uncovers an Embryo Sac-Specific Bi-directional Promoter

et al. 2014

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The Arabidopsis thaliana promoter trap line showing uidA reporter gene expression specifically in mature embryo sacs was found to carry transfer DNA (T-DNA) insertion in the 5′ untranslated region (UTR) of At3g17150. At3g17140 and At3g17150 are a pair of head-tohead-oriented genes separated by a 668-bp intergenic region encoding for a putative pectin methyl esterase inhibitor protein. In the GUS-650 line, uidA reporter gene was inserted in head-to-head orientation to the At3g17140 gene. Presence of At3g17140 transcripts in the GUS-650 line indicated that T-DNA insertion did not affect this gene and the 668-bp intergenic region functions as a bi-directional promoter. The 672-bp fragment separating the uidA and At3g17140 genes was cloned and placed in forward or reverse orientation next to the uidA gene. Transgenic Arabidopsis plants carrying either of these constructs showed β-glucuronidase (GUS) activity in the ovules confirming that the 672-bp sequence is a bi-directional promoter specific to ovules. These results were also supported by the presence of cis-acting motifs such as TATA box, CAAT box, seed storage protein element (CAACAC), endosperm-specific elements (AACA), Skn-1 motif (GTCAT) and bZIP transcription factor binding element (ACGT) within the 672-bp sequence in both orientations. The significance of a promoter trap approach and the utility of such a promoter are discussed.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Identification and Characterization of a T-DNA Promoter Trap Line of Arabidopsis thaliana Uncovers an Embryo Sac-Specific Bi-directional Promoter

et al. 2014

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“…; Pratibha et al . ). These regulatory sequences might have once been active but lost functionality during evolutionary processes such as insertions and rearrangements, and these sequences could be functional when positioned upstream of genes.…”

Section: Promoter Trapping Screening Of Mutantsmentioning

confidence: 97%

Genetic resources offer efficient tools for rice functional genomics research

Fan

Hsing

et al. 2015

Plant Cell & Environment

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Rice is an important crop and major model plant for monocot functional genomics studies. With the establishment of various genetic resources for rice genomics, the next challenge is to systematically assign functions to predicted genes in the rice genome. Compared with the robustness of genome sequencing and bioinformatics techniques, progress in understanding the function of rice genes has lagged, hampering the utilization of rice genes for cereal crop improvement. The use of transfer DNA (T-DNA) insertional mutagenesis offers the advantage of uniform distribution throughout the rice genome, but preferentially in gene-rich regions, resulting in direct gene knockout or activation of genes within 20-30 kb up- and downstream of the T-DNA insertion site and high gene tagging efficiency. Here, we summarize the recent progress in functional genomics using the T-DNA-tagged rice mutant population. We also discuss important features of T-DNA activation- and knockout-tagging and promoter-trapping of the rice genome in relation to mutant and candidate gene characterizations and how to more efficiently utilize rice mutant populations and datasets for high-throughput functional genomics and phenomics studies by forward and reverse genetics approaches. These studies may facilitate the translation of rice functional genomics research to improvements of rice and other cereal crops.

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