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Arabidopsis thaliana

ABSTRACT: Small RNA-seq of ago4 null and slicing-defective mutant in Arabidopsis

PROVIDER: PRJNA344441 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4295730.fastq.gz	Fastqsanger.gz
	SRR4295740.fastq.gz	Fastqsanger.gz
	SRR4295721.fastq.gz	Fastqsanger.gz
	SRR4295731.fastq.gz	Fastqsanger.gz
	SRR4295741.fastq.gz	Fastqsanger.gz

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Small RNA-seq of ago4 null and slicing-defective mutant in Arabidopsis

Project description:To investigate the effect of AGO4 upon small RNA accumulation in Arabidopsis, we analyzed small RNA accumulation in ago4, ago4/ago6/ago9 triple mutant, stable transgenic lines expressing wild-type AGO4 and slicing-defective AGO4 in ago4 and ago4/ago6/ago9 background.

2017-05-27 | GSE87333 | GEO

RNA-directed DNA methylation involves co-transcriptional small RNA-guided slicing of Pol V transcripts in Arabidopsis.

Project description:Small RNAs regulate chromatin modifications such as DNA methylation and gene silencing across eukaryotic genomes. In plants, RNA-directed DNA methylation (RdDM) requires 24-nucleotide (nt) small RNAs (siRNAs) that bind ARGONAUTE4 (AGO4) and target genomic regions for silencing. It also requires non-coding RNAs transcribed by RNA POLYMERASE V (Pol V), that likely serve as scaffolds for binding of AGO4/siRNA complexes. Here we utilized a modified global nuclear run-on (GRO) protocol followed by deep sequencing to capture Pol V nascent transcripts genome-wide. We uncovered unique characteristics of Pol V RNAs, including a uracil (U) common at position 10. This uracil was complementary to the 5’ adenine found in many AGO4-bound 24-nt siRNAs and was eliminated in an siRNA-deficient mutant as well as in the ago4/6/9 triple mutant, suggesting that the +10U signature is due to siRNA-mediated co-transcriptional slicing of Pol V transcripts. Expressing wild-type AGO4 in ago4/6/9 was able to restore slicing of Pol V transcripts but a catalytically inactive AGO4 mutant did not correct the slicing defect. We also found that Pol V transcript slicing required the little understood elongation factor SPT5L. These results highlight the importance of Pol V transcript slicing in RNA-mediated transcriptional gene silencing, which is a conserved process in many eukaryotes.

2018-01-29 | GSE108078 | GEO

RNA-directed DNA methylation involves co-transcriptional small RNA-guided slicing of Pol V transcripts in Arabidopsis

Project description:Small RNAs regulate chromatin modifications such as DNA methylation and gene silencing across eukaryotic genomes. In plants, RNA-directed DNA methylation (RdDM) requires 24-nucleotide (nt) small RNAs (siRNAs) that bind ARGONAUTE4 (AGO4) and target genomic regions for silencing. It also requires non-coding RNAs transcribed by RNA POLYMERASE V (Pol V), although their function is largely unknown. We utilized a modified global nuclear run-on (GRO) protocol followed by deep sequencing to capture Pol V nascent transcripts genome-wide. We uncovered unique characteristics of Pol V RNAs, including a uracil (U) common at position 10. This uracil was complementary to the 5’ adenine found in many AGO4-bound 24-nt siRNAs and was eliminated in an siRNA-deficient mutant. This indicates co-transcriptional slicing of Pol V transcripts by AGO4-bound siRNAs. Pol V transcript slicing also required the elongation factor SPT5L. These results highlight a novel step in RNA-mediated transcriptional gene silencing, which is a conserved process in many eukaryotes.

2018-01-29 | GSE100010 | GEO

Arabidopsis thaliana

Project description:Functional analysis of Arabidopsis ARGONAUTE1 using a slicer-defective mutant: Small RNA immunoprecipitation

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Arabidopsis Argonaute4, Argonaute6 and Argonaute9 associated small RNAs

Project description:We sequenced the small RNA bound to AGO4, AGO6 and AGO9 and compared these sRNAs to other libraries isolated such as total sRNAs, ago4 mutant, drd3-1 mutant, an AGO4 D660A slicer mutant and AGO6 and AGO9 under the AGO4 promoter. Keywords: Epigenetics

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AGO4 slicer activity reveals the passenger strand function of plant 23 nt siRNAs and the post-slicing retention of target RNAs mediating RNA-directed DNA methylation [WGBS]

Project description:In plants, transcriptional silencing by RNA-directed DNA methylation (RdDM) is mediated by ARGONAUTE 4 (AGO4) and 24 nt short-interfering RNAs (siRNAs) that are generated in parallel with 23 nt RNAs of unknown function. We show that 23 nt RNAs serve as the passenger strands of 23/24 nt duplexes loaded into AGO4. The 24 nt siRNAs then guide AGO4 slicing of the passenger strands, generating 11 and 12 nt cleavage products. Unexpectedly, we find that the 12 nt products remain associated with the guide strand-AGO4 complexes. Long noncoding RNAs generated at RdDM loci are similarly sliced and retained by AGO4. These results suggest a model in which RNA POLYMERASE V transcripts at target loci are sliced repeatedly as transcription elongation proceeds, sequentially releasing AGO4-siRNA-scaffold RNA complexes that independently recruit the RdDM machinery. Consistent with this hypothesis, plant lines expressing wild-type versus slicing-defective AGO4 show quantitative variation in cytosine methylation and siRNA levels within RdDM loci.

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AGO4 slicer activity reveals the passenger strand function of plant 23 nt siRNAs and the post-slicing retention of target RNAs mediating RNA-directed DNA methylation [smallRNA-seq]

2023-02-17 | GSE201233 | GEO

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Project description:Transcriptome and small RNA-Seq analysis of PTGS-defective Arabidopsis mutants

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Expression data from 5-week-old Arabidopsis

Project description:AGO4 plays an important role in RNA-directed DNA methylation (RdDM). RdDM on specific genomic loci have the potential to silence the nearby protein coding gene. We used wild-type La-er and ago4-1 mutant Arabidopsis to identify AGO4-regulated genes.

2010-12-20 | GSE18928 | GEO

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