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Arabidopsis thaliana

ABSTRACT: Comparative sRNA-Seq analysis of TCV-infected wildtype and dcl1-9 mutant Arabidopsis thaliana

PROVIDER: PRJNA336060 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3992490.fastq.gz	Fastqsanger.gz
	SRR3992491.fastq.gz	Fastqsanger.gz
	SRR3992492.fastq.gz	Fastqsanger.gz
	SRR3992493.fastq.gz	Fastqsanger.gz
	SRR3992484.fastq.gz	Fastqsanger.gz

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Comparative transcriptome analysis of TCV-infected wildtype and dcl1-9 mutant Arabidopsis thaliana

Project description:Belonging to the Carmovirus family, Turnip crinkle virus (TCV) is a positive-strand RNA virus that can infect Arabidopsis. Most Arabidopsis ecotypes are highly susceptible to TCV, except for the TCV resistant line Di-17 derived from ecotype Dijon. Previous studies showed that many of the stress related genes have changed significantly after TCV infection. Besides the virus-triggered genes, small RNAs also play critical roles in plant defense by triggering either transcriptional and/or post-transcriptional gene silencing. In this study, TCV-infected wildtype Arabidopsis thaliana and dcl1-9 mutant plants were subjected to transcriptome and small RNA analysis to investigate the role of DCL1 in virus defense network.

2017-01-11 | GSE85067 | GEO

Comparative sRNA-Seq analysis of TCV-infected wildtype and dcl1-9 mutant Arabidopsis thaliana

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Arabidopsis thaliana

Project description:Comparative transcriptome analysis of TCV-infected wildtype and dcl1-9 mutant Arabidopsis thaliana

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Comparative mRNA and sRNA transcriptome analysis of TCV-infected wildtype and dcl1-9 mutant Arabidopsis thaliana

Project description:Comparative mRNA and sRNA transcriptome analysis of TCV-infected wildtype and dcl1-9 mutant Arabidopsis thaliana

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Differential expression of microRNAs in wildtype versus DCL1 mutants in Arabidopsis thaliana

Project description:Small RNA libraries of wildtype Arabidopsis thaliana and its mutant Dicer-like 1 (Dcl1) were constructed and sequenced for miRNA identification and expression analysis. The mutant data was used to validate novel miRNA predictions (from miRCat2 (Paicu et al. 2017), miRCat (Moxon et al. 2008), miRPlant (An et al. 2014) and miReap (http://mireap.sourceforge.net/)), by calculating the log fold change between the mutant and the wildtype samples.

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Project description:In Arabidopsis thaliana, four different DICER-LIKE (DCL) proteins have distinct, but partially overlapping functions in the biogenesis of microRNAs (miRNAs) and small interfering RNAs (siRNAs) from longer, non-coding precursor RNAs. To analyze the impact of different components of the small RNA (sRNA) biogenesis machinery on the transcriptome, we subjected dcl and other mutants impaired in sRNA biogenesis to whole-genome tiling array analysis. We compared both protein-coding genes and noncoding transcripts, including most pri-miRNAs, in two tissues and several stress conditions. We discovered distinct effects of dcl1, hyl1 and se mutations on the transcriptome, as well as a number of common genes affected in dcl1 and dcl2 dcl3 dcl4 triple mutants. Our results furthermore suggest that the DCL1 is not only involved in miRNA action, but can also contribute to silencing of certain transposons, apparently through an effect on DNA methylation. Together, our findings contribute to the knowledge of both specialization and overlap between different RNA silencing pathways.

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Project description:Differential expression of microRNAs in wildtype versus DCL1 mutants in Arabidopsis thaliana

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