The whole transcriptome RNA-seq analysis of poco1, a mitochondrial PPR protein mutant in Arabidopsis thaliana
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Hossein Emami
PROVIDER: E-MTAB-8912 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2017-05-12 | E-MTAB-5080 | biostudies-arrayexpress
Project description:We constructed a small RNA cDNA library, using small RNA fraction with a length of 19-29 bases, and we performed deep sequencing of the cDNA library. R. conorii subsp. conorii strain Malish 7 was cultivated on XTC cells for 3 days at 28M-BM-0C. RNA enriched with small RNA fractions was further extracted and cDNA was synthesized.
2013-03-02 | E-GEOD-27647 | biostudies-arrayexpress
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2014-01-01 | E-GEOD-48661 | biostudies-arrayexpress
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2012-12-31 | E-GEOD-40735 | biostudies-arrayexpress
Project description:Background: Introduction of a transgene that transcribes RNA homologous to an endogenous gene in the plant genome can induce silencing of both genes, a phenomenon termed cosuppression. Cosuppression was first discovered in transgenic petunia plants transformed with the CHS-A gene encoding chalcone synthase, in which nonpigmented sectors in flowers or completely white flowers are produced. Some of the flower-color patterns observed in transgenic petunias having CHS-A cosuppression resemble those in existing nontransgenic varieties. Although the mechanism by which white sectors are generated in nontransgenic petunia is known to be due to RNA silencing of the CHS-A gene as in cosuppression, whether the same trigger(s) and/or pattern of RNA degradation are involved in these phenomena has not been known. Here, we addressed this question using deep-sequencing and bioinformatic analyses of small RNAs. Results: We analyzed short interfering RNAs (siRNAs) produced in nonpigmented sectors of petal tissues in transgenic petunia plants that have CHS-A cosuppression and a nontransgenic petunia variety Red Star, that has naturally occurring CHS-A RNA silencing. In both silencing systems, 21-nt and 22-nt siRNAs were the most and the second-most abundant size classes, respectively. CHS-A siRNA production was confined to exon 2, indicating that RNA degradation through the RNA silencing pathway occurred in this exon. Common siRNAs were detected in cosuppression and naturally occurring RNA silencing, and their ranks based on the number of siRNAs in these plants were correlated with each other. Noticeably, highly abundant siRNAs were common in these systems. Phased siRNAs were detected in multiple phases at multiple sites, and some of the ends of the regions that produced phased siRNAs were conserved. Conclusions: The features of siRNA production found to be common to cosuppression and naturally occurring silencing of the CHS-A gene indicate mechanistic similarities between these silencing systems especially in the biosynthetic processes of siRNAs including cleavage of CHS-A transcripts and subsequent production of secondary siRNAs in exon 2. The data also suggest that these events occurred at multiple sites, which can be a feature of these silencing phenomena. Small RNAs isolated from petal tissues in two petunia lines were analyzed.
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