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Series GSE239289 Query DataSets for GSE239289
Status Public on Aug 01, 2023
Title Germ granule association drives small RNA specificity for a nuclear Argonaute protein [sRNA-seq]
Organism Caenorhabditis elegans
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary 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.
 
Overall design FLAG::HRDE-1 immunoprecipitation from whole worm extract followed by small RNA purification, library preparation, and sequencing
 
Contributor(s) Phillips CM, Chen S
Citation(s) 38302462
Submission date Jul 26, 2023
Last update date Feb 14, 2024
Contact name Carolyn Marie Phillips
E-mail(s) cphil@usc.edu
Organization name University of Southern California
Department Biological Sciences
Lab Phillips
Street address 1050 Childs Way, RRI 201
City Los Angeles
State/province CA
ZIP/Postal code 90089
Country USA
 
Platforms (1)
GPL19757 Illumina NextSeq 500 (Caenorhabditis elegans)
Samples (36)
GSM7662705 HRDE-1 (adult) - input, replicate 1
GSM7662706 HRDE-1 (adult) - input, replicate 2
GSM7662707 HRDE-1 (adult) - input, replicate 3
This SubSeries is part of SuperSeries:
GSE239291 Germ granule association drives small RNA specificity for a nuclear Argonaute protein
Relations
BioProject PRJNA998763

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE239289_RAW.tar 50.5 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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