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Arabidopsis thaliana

ABSTRACT: Endogenous small RNAs from Arabidopsis thaliana wild-type, dcl4 mutant and dcl4 mutant expressing nuclear or cytoplasmic DCL4

PROVIDER: PRJNA301359 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2927776.fastq.gz	Fastqsanger.gz
	SRR2927777.fastq.gz	Fastqsanger.gz
	SRR2927778.fastq.gz	Fastqsanger.gz
	SRR2927779.fastq.gz	Fastqsanger.gz

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Endogenous small RNAs from Arabidopsis thaliana wild-type, dcl4 mutant and dcl4 mutant expressing nuclear or cytoplasmic DCL4

Project description:Parallel RNA silencing pathways regulate gene expression in plants, either by transcriptional gene silencing via RNA-dependent DNA methylation (RdDM), or by post-transcriptional silencing targeting mRNAs. Both pathways rely on distinct Dicer-like proteins to cleave double-stranded RNA into small-interfering RNAs. Experiments to determine the subcellular localization of Dicer-like proteins in Arabidopsis revealed that DCL4 is predominantly expressed as a transcriptional start site isoform that encodes a cytoplasmic protein. A second, longer DCL4 transcript isoform encodes a nuclear-localization signal and its expression is repressed by DNA methylation. Consequently this isoform is induced when promoter methylation decreases due to infection with a bacterial pathogen or during silique development. Nuclear DCL4 produces unique populations of small RNAs, called DCL4NLS isoform-dependent siRNAs (disiRNAs), which function via a post-transcriptional silencing effector, but whose precursors are generated by the RdDM pathway. Arabidopsis cells can thus respond to genome methylation changes by modulating DCL4 localization, which in turn recruits PTGS factors to reinforce RNA silencing.

2016-11-14 | GSE74731 | GEO

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Project description:Small RNAs in the Physcomitrella dcl4 mutant

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Project description:High-throughput sequencing of Arabidopsis thaliana endogenous small RNAs by 454 pyrosequencing. Keywords: high-throughput sequencing

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Arabidopsis thaliana

Project description:High-throughput pyrosequencing of endogenous small RNAs from Arabidopsis thaliana wild-type and ddm1 mutant.

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Project description:Here we profiled small RNAs from whole cell, cytoplasmic and nuclear extracts from three-week-old Arabidopsis seedlings. We unexpectedly found that nuclear functional hc-siRNAs are predominantly present in the cytoplasm. Samples from Arabidopsis thaliana whole cell, cytoplasmic and nuclear extracts with 3 replicates for each. 9 samples in all.

2012-07-12 | E-GEOD-36500 | biostudies-arrayexpress

Virus-derived siRNAs in Arabidopsis thaliana

Project description:We investigated the role of A. thaliana RDRs in the RNAi-mediated viral immunity by using a mutant of cucumber mosaic virus (CMV) that does not express the VSR protein 2b. CMV contains three positive-strand genomic RNAs and the 2b protein encoded by RNA2 is essential for infection by suppressing antiviral silencing initiated by either DCL4 or DCL2. Our results demonstrate an essential role for the amplification of viral siRNAs by either RDR1 or RDR6 in antiviral silencing. Further analyses, including Illumina sequencing of more than 3.5 million viral siRNAs, indicated target specificity of the two antiviral RDRs.

2010-01-20 | GSE19965 | GEO

Arabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology

Project description:To determine the extent to which the major small RNA pathways functions across the Arabidopsis thaliana genome, small RNA populations from several tissues of wild-type (wt) and mutant plants were amplified by RT-PCR and sequenced using high-throughput 454 sequencing technology. Keywords: small RNAs, high-throughput sequencing Amplicons were prepared by 5' and 3' adaptor ligation and RT-PCR using small RNA fractions from inflorescence tissue (containing stage 1-12 flowers) of wt Col-0 plants, mutants with defects in each DCL gene (dcl1-7, dcl2-1, dcl3-1, dcl4-2), and mutants with defects in each RDR gene for which a function has been established (rdr1-1, rdr2-1, rdr6-15). Amplicons from whole seedlings (3 day post-germinations) were prepared from Col-0 and rdr6-15 plants. Small RNA preparations from leaf samples of Col-O that were either uninoculated or inoculated by Pseudomonas syringae pv tomato (DC3000hrcC) for 1 hr and 3 hr were also sequenced.

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Arabidopsis thaliana

Project description:High-throughput SOLEXA sequencing of endogenous small RNAs from Arabidopsis thaliana wild-type

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Arabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology

2007-02-01 | GSE6682 | GEO

Accumulation of the coumarin scopolin under abiotic stress conditions is mediated by the Arabidopsis thaliana THO/TREX complex

Project description:Secondary metabolites are involved in the plant stress response. Among these are scopolin and its active form scopoletin, which are coumarin derivatives associated with reactive oxygen species scavenging and pathogen defence. Here we show that in Arabidopsis thaliana, scopolin accumulation can be induced in the root by osmotic stress and in the leaf by low temperature stress. A genetic screen for altered scopolin levels in Arabidopsis thaliana identified a mutant compromised for scopolin accumulation in response to stress; the lesion was present in a homologue of THO1, the product of which contributes to the THO/TREX complex. The THO/TREX complex contributes to RNA silencing, supposedly by trafficking precursors of small RNAs. Mutants carrying defective THO and RDR6 genes were impaired with respect to scopolin accumulation in response to stress, suggesting a mechanism based on RNA silencing like the transacting small interfering RNA pathway which requires THO/TREX and RDR6 function.

2018-02-05 | MTBLS389 | MetaboLights

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