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Germ granule association drives small RNA specificity for a nuclear Argonaute protein

ABSTRACT: Germ granule association drives small RNA specificity for a nuclear Argonaute protein

PROVIDER: PRJNA998759 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25426300_1.fastq.gz	Fastqsanger.gz
	SRR25426300_2.fastq.gz	Fastqsanger.gz
	SRR25426301_1.fastq.gz	Fastqsanger.gz
	SRR25426301_2.fastq.gz	Fastqsanger.gz
	SRR25428219.fastq.gz	Fastqsanger.gz

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Germ granule association drives small RNA specificity for a nuclear Argonaute protein [CUT&Tag]

Project description:Germ granule association drives small RNA specificity for a nuclear Argonaute protein [CUT&Tag]

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Germ granule association drives small RNA specificity for a nuclear Argonaute protein [mRNA-seq]

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Germ granule association drives small RNA specificity for a nuclear Argonaute protein [sRNA-seq]

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Germ granule association drives small RNA specificity for a nuclear Argonaute protein [CUT&Tag]

Project description:RNA interference (RNAi) is a conserved gene silencing process that exists in diverse organisms to protect genome integrity and regulate gene expression. In C. elegans, majority of RNAi components are located in phase-separated perinuclear germ granules, including P granule, Mutator foci, Z granule, and SIMR foci. However, the protein components and function of the newly discovered SIMR foci are unknown. Here we identified HRDE-2 as a SIMR foci component, which interacts with the germline nuclear RNAi Argonaute HRDE-1. We found that unloaded HRDE-1 localizes to SIMR foci and this localization depends on HRDE-2. In addition, HRDE-2 contributes to HRDE-1 small RNAs binding specificity and, in the absence of HRDE-2, HRDE-1 exclusively loads CSR-class 22G-RNAs rather than WAGO-class 22G-RNAs, promotes H3K9me3 deposition on CSR-targets, but does not silence these CSR-target genes. Thus, our study demonstrates that HRDE-2 is critical to ensure correct small RNAs are used to guide nuclear RNA silencing in the C. elegans germline.

2023-08-01 | GSE239285 | GEO

Germ granule association drives small RNA specificity for a nuclear Argonaute protein [sRNA-seq]

2023-08-01 | GSE239289 | GEO

Germ granule association drives small RNA specificity for a nuclear Argonaute protein [mRNA-seq]

2023-08-01 | GSE239286 | GEO

Germ granule association drives small RNA specificity for a nuclear Argonaute protein

Project description:RNA interference (RNAi) is a conserved gene silencing process that exists in diverse organisms to protect genome integrity and regulate gene expression. In C. elegans, the majority of RNAi pathway proteins localize to perinuclear, phase-separated germ granules, which are comprised of sub-domains referred to as P granules, Mutator foci, Z granules, and SIMR foci. However, the protein components and function of the newly discovered SIMR foci are unknown. Here we demonstrate that HRDE-2 localizes to SIMR foci and interacts with the germline nuclear RNAi Argonaute HRDE-1. Furthermore, HRDE-1 also localizes to SIMR foci, dependent on HRDE-2, but only in its small RNA unbound state. This germ granule localization is critical to promote the small RNA binding specificity of HRDE-1 and, in the absence of HRDE-2, HRDE-1 exclusively loads CSR-class 22G-RNAs rather than WAGO-class 22G-RNAs, resulting in H3K9me3 deposition on CSR-target genes. Thus, our study demonstrates that HRDE-2 is critical to ensure that the correct small RNAs are used to guide nuclear RNA silencing in the C. elegans germline.

2023-07-27 | MSV000092546 | MassIVE

Germ granule compartments and small RNA production

Project description:In this project, we identified an uncharted subcompartment of the C. elegans germ granule, which we termed the E granule. We show that the E granule is required for the synthesis of a specialized class of 22G-RNAs.

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Germ granule association drives small RNA specificity for a nuclear Argonaute protein

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-08-01 | GSE239291 | GEO

DEPS-1 promotes P granule assembly and RNA interference in C. elegans germ cells

Project description:P granules are germ-cell-specific cytoplasmic structures containing RNA and protein and required for proper germ cell development in C. elegans. A new P-granule-associated protein, DEPS-1, whose loss disrupts P granule structure and function was analysed in this study. Genome wide analysis of gene expression in deps-1 mutant germ lines identified additional targets of DEPS-1 regulation, many of which are also regulated by the RNAi factor RDE-3. Our studies suggest that DEPS-1 is a key component of the P granule assembly pathway and that its roles include promoting accumulation of some mRNAs, such as glh-1 and rde-4, and reducing accumulation of other mRNAs, perhaps by collaborating with RDE-3 to generate endogenous short interfering RNAs (endo-siRNAs). We isolated dissected gonads from deps-1 mutant adults and compared each to wild type dissected gonads. RNA was linearly amplified prior to labeling for all genotypes. The comparisons were done in quadruplicate on independently grown and isolated animals.

2010-05-26 | E-GEOD-9993 | biostudies-arrayexpress

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