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| Status |
Public on Nov 08, 2019 |
| Title |
Nicotiana tabacum degradome analysis using high definition adapters proves an efficient targeting method against the Tomato leaf curl New Delhi virus using artificial ta-siRNAs [sRNA-seq] |
| Organism |
Nicotiana tabacum |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
RNA interference (RNAi) is a conserved, RNA-mediated, regulatory mechanism in eukaryotes. In plants, it plays an important role in growth, development and resistance against viral infections. As a counter-defence, plant viruses, e.g. geminiviruses, encode RNAi suppressors, such as AC2, AC4 and AV2. To obtain Nicotiana tabacum virus resistant plants against Tomato leaf curl New Delhi virus (ToLCNDV), we employ the biogenesis pathway of a class of endogenous siRNAs, the trans-acting siRNAs (ta-siRNAs), by engineering artificial ta-siRNAs (ata-siRNAs) targeting the AC2 (TRiV-AC2) and AC4 (TRiV-AC4) RNAi suppressors using miRNA390 dual target sites. The mode of action of ta-siRNAs comprises of the cleavage of the target (similar to the miRNA targeting). Using degradome approaches, the abundance of the resulting 3' fragment of the cleaved transcript can be quantified and the precise localization of the cleavage on the target mRNA can be identified. We sequenced degradome libraries of Nicotiana tabacum plants infected with ToLCNDV which were treated with the ata-siRNA-AC2 construct; mock-treated plants were used as controls. Following quality checks, the abundance distributions of the degradation fragments were normalized. The transcripts with different cleavage patterns was the AC2, supporting the conclusion that an efficient cleavage of the target occurred, without significant off-target effects.
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| Overall design |
2 biological replicates of small RNA libraries, infiltrated with TRiV-AC2, were analysed.
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| Contributor(s) |
Singh A, Mohorianu I, Dalmay T, Mukherjee S, Dasgupta I |
| Citation(s) |
31513956 |
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| Submission date |
Aug 18, 2016 |
| Last update date |
Nov 11, 2019 |
| Contact name |
Archana Singh |
| E-mail(s) |
archana.bhubioinfo@gmail.com
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| Organization name |
Cambridge University
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| Department |
Plant Science
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| Street address |
Downing Street
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| City |
Cambridge |
| State/province |
England |
| ZIP/Postal code |
CB23EA |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL22345 |
Illumina HiSeq 2500 (Nicotiana tabacum) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE85819 |
Nicotiana tabacum degradome analysis using high definition adapters proves an efficient targeting method against the Tomato leaf curl New Delhi virus using artificial ta-siRNAs |
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| Relations |
| BioProject |
PRJNA339477 |
| SRA |
SRP082389 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE85816_RAW.tar |
40.2 Mb |
(http)(custom) |
TAR (of CSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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