Identification of NMD regulated genes in Nicotiana benthamiana
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ABSTRACT:
PROVIDER: PRJNA429737 | ENA |
REPOSITORIES: ENA
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Project description:Nonsense mediated decay (NMD) is a translation termination coupled quality control system. NMD identifies and degrades aberrant mRNAs containing premature termination codons, thereby preventing the accumulation of detrimental truncated proteins. NMD also controls the expression of several normal mRNAs and non-coding transcripts. RNA-seq assays were conducted to identify the NMD regulated genes in Arabidopsis. However, NMD targets have not been studied in other plants. To identify the conserved NMD targets, we wanted to identify the NMD regulated genes in Nicotiana benthamiana model species. Virus induced gene silencing was used to inactivate UPF1 NMD key factor in N. benthamiana, and then comparative RNA-seq experiment was carried out using UPF1-silenced and control–silenced plants. We found that in N. benthamiana significantly more genes are controlled by NMD than in Arabidopsis and that, surprisingly few conserved NMD targets can be recognized. These results suggest that while the mechanism of NMD is highly conserved, the set of NMD controlled genes can be quickly changed in plants.
2019-07-01 | GSE109130 | GEO
Project description:Nicotiana benthamiana is a widely used organism for expression of foreign proteins. To increase protein abundance, overexpression promoters have been developed. However, several proteins cause negative effects on plant growth and development when they are overexpressed. Therefore, overexpression promoters cannot be widely used to generate transgenic plants that produce foreign proteins. In this study, we tried to find stress-inducible promoters which specifically express downstream genes when plants were exposed to stress conditions. By RNA-sequencing analysis of heat- and wound-treated plants, we found that NbHSP20 promoters can be used as a heat-inducible promoters to express foreign proteins in N. benthamiana.
2022-08-10 | GSE210621 | GEO
Project description:Small RNA expression from Nicotiana benthamiana leaves was profiled with the primary goal of ascertaining microRNA isoform diversity for known, conserved families. A secondary goal was to provide a baseline small RNA expression atlas for this species and tissue.
2014-02-10 | GSE48886 | GEO
Project description:Nicotiana benthamiana Genome sequencing
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Project description:In order to find the miRNAs, target genes and signaling pathways related to the dwarf phenotype induced by NlCSP1, 35S-NlCSP1 and 35S-GFP control were infiltrated into Nicotiana benthamiana. We analyzed the differentially expressed miRNAs in the infiltrated leaves (NlCSP1_Z/GFP_Z) and the upper uninfiltrated leaves (NlCSP1_O/GFP_O) of N. benthamiana. A total of 106 and 97 differentially expressed miRNAs were identified in NlCSP1_Z/GFP_Z and NlCSP1_O/GFP_O, respectively. KEGG annotation revealed a large number of differentially expressed miRNAs involved in plant hormone signal transduction, indicating that NlCSP1 changed the hormone signal pathway in N. benthamiana.
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Project description:Nicotiana benthamiana Raw sequence reads
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Project description:Nicotiana benthamiana Raw sequence reads
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