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Arabidopsis thaliana

ABSTRACT: Exogenous Transposable Elements Circumvent Homology Permitting the Dissection of Expression Dependent Silencing

PROVIDER: PRJNA342506 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4228560.fastq.gz	Fastqsanger.gz
	SRR4228561.fastq.gz	Fastqsanger.gz
	SRR4228562.fastq.gz	Fastqsanger.gz
	SRR4228558.fastq.gz	Fastqsanger.gz
	SRR4228559.fastq.gz	Fastqsanger.gz

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Exogenous Transposable Elements Circumvent Homology Permitting the Dissection of Expression Dependent Silencing

Project description:The propagation of epigenetic marks has received a great deal of attention, yet the initiation of epigenetic silencing on a new transgene, virus, or transposable element remains incompletely characterized. The overlapping function of multiple silencing mechanisms has obscured this area of investigation. Here, we have revealed two broad mechanisms that are both able to initiate silencing independently: homology-based silencing and expression-dependent silencing. By transforming exogenous transposable elements into Arabidopsis, we circumvented homology-based silencing allowing us to isolate and investigate the molecular mechanism of expression-dependent silencing. We found that several small RNA-generating mechanisms all trigger de novo expression-dependent RNA-directed DNA methylation (RdDM) through RNA Polymerase V. In addition, the silencing of transposable elements fragments stalls at the RdDM phase, while full-length elements quickly progress through RdDM to maintenance methylation and heterochromatin formation. We found that there is a narrow window of time for the transition to a fully silenced state. Transformation into a mutant genotype followed by introgression into wild-type does not result in the same level of silencing as direct transformation into wild-type. This demonstrates that the genotype of transposable element insertion or transgene transformation is key for establishing the transgenerational extent of epigenetic silencing.

2017-08-25 | GSE86787 | GEO

Arabidopsis thaliana

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Arabidopsis thaliana

Project description:Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

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Genome-wide EML1 binding sites in Arabidopsis thaliana seedlings

Project description:To identify genomic targets involved in the EML-dependent control of seed development, we performed ChIP-chip using whole genome Arabidopsis tiling arrays from p35S::EML1-GFP seedlings using GFP antibodies. The analysis showed that EML1 displayed preferential binding to transposable elements (TEs), while showing no preference for protein coding genes.

2021-04-23 | GSE98977 | GEO

The activity of the Caenorhabditis elegans Aquarius helicase EMB-4 enables the nuclear RNAi machinery to engage nascent RNA

Project description:Germline small RNA pathways initiate silencing of repetitive elements in animals and an interplay of nuclear small RNAs and chromatin modifications maintain this silencing, protecting the germline from spreading of transposable elements. In C. elegans germline, nuclear argonaute protein HRDE-1 initiates the transcriptional silencing pathway that is crucial for long term and heritable silencing of genes and repetitive regions. Here, we show that HRDE-1 interacts with components of the splicing machinery and the exon-junction complex. One such factor is the conserved RNA helicase EMB-4/AQR that binds introns and recruits the exon-junction proteins to newly spliced RNA. Our data shows that EMB-4/AQR is required for the transcriptional silencing pathway initiated by HRDE-1 and it functions by removing the intronic barriers to silencing thorugh its helicase function.

2017-06-30 | PXD004416 | Pride

An RNAi-dependent Polycomb Repression Pathway Is Required for Co-transcriptional Silencing of Transposable Elements

Project description:An RNAi-dependent Polycomb Repression Pathway Is Required for Co-transcriptional Silencing of Transposable Elements

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Bisulfite-Seq and RNA-seq in rootstock of Arabidopsis thaliana grafts

Project description:RNA silencing is a mechanism for regulating gene expression at the transcriptional and post-transcriptional levels. Its functions include regulating endogenous gene expression and protecting the cell against viruses and invading transposable elements (TEs). A key component of the mechanism is small RNAs (sRNAs) of 21-24 nucleotides (nt) in length, which direct the silencing machinery in a sequence specific manner to target nucleic acids. sRNAs of 24 nt are involved in methylation of cytosine residues of target loci in three sequence contexts (CG, CHG and CHH), referred to as RNA-directed DNA methylation (RdDM). We previously demonstrated that 24 nt sRNAs are mobile from shoot to root in Arabidopsis thaliana. In this study we demonstrated that methylation of thousands of loci in root tissues is dependent upon mobile sRNAs from the shoot. Furthermore, we found that mobile sRNA-dependent DNA methylation occurs predominantly in non-CG contexts. These findings were made using base-resolution next generation sequencing approaches and genome wide analyses. Specific classes of short TEs are the predominant targets of mobile sRNA-dependent DNA methylation; classes typically found in gene-rich euchromatic regions. Mobile sRNA-regulated genes were also identified. Mechanistically, we demonstrate that mobile sRNA-dependent non-CG methylation is largely independent of the CMT2/3 RdDM pathway but dependent upon the DRM1/DRM2 RdDM pathway. This is in contrast to non-mobile sRNA-dependent DNA methylation, which predominantly depends upon the CMT2/3 RdDM pathway. These data are complementary to the small RNA sequencing data from Arabidopsis root grafts described in Molnar et al (Science, 2010 May 14;328(5980):872-5).

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