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| 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
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| 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.
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| Overall design |
FLAG::HRDE-1 immunoprecipitation from whole worm extract followed by small RNA purification, library preparation, and sequencing
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| Contributor(s) |
Phillips CM, Chen S |
| Citation(s) |
38302462 |
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| Submission date |
Jul 26, 2023 |
| Last update date |
Feb 14, 2024 |
| Contact name |
Carolyn Marie Phillips |
| E-mail(s) |
cphil@usc.edu
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| Organization name |
University of Southern California
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| Department |
Biological Sciences
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| Lab |
Phillips
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| Street address |
1050 Childs Way, RRI 201
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
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| Platforms (1) |
| GPL19757 |
Illumina NextSeq 500 (Caenorhabditis elegans) |
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| Samples (36)
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| GSM7662708 |
HRDE-1 (adult) - IP, replicate 1 |
| GSM7662709 |
HRDE-1 (adult) - IP, replicate 2 |
| GSM7662710 |
HRDE-1 (adult) - IP, replicate 3 |
| GSM7662711 |
HRDE-1, hrde-2 (adult) - input, replicate 1 |
| GSM7662712 |
HRDE-1, hrde-2 (adult) - input, replicate 2 |
| GSM7662713 |
HRDE-1, hrde-2 (adult) - input, replicate 3 |
| GSM7662714 |
HRDE-1, hrde-2 (adult) - IP, replicate 1 |
| GSM7662715 |
HRDE-1, hrde-2 (adult) - IP, replicate 2 |
| GSM7662716 |
HRDE-1, hrde-2 (adult) - IP, replicate 3 |
| GSM7662717 |
HRDE-1, simr-1 (adult) - input, replicate 1 |
| GSM7662718 |
HRDE-1, simr-1 (adult) - input, replicate 2 |
| GSM7662719 |
HRDE-1, simr-1 (adult) - input, replicate 3 |
| GSM7662720 |
HRDE-1, simr-1 (adult) - IP, replicate 1 |
| GSM7662721 |
HRDE-1, simr-1 (adult) - IP, replicate 2 |
| GSM7662722 |
HRDE-1, simr-1 (adult) - IP, replicate 3 |
| GSM7662723 |
HRDE-1, mut-2 (adult) - input, replicate 1 |
| GSM7662724 |
HRDE-1, mut-2 (adult) - input, replicate 2 |
| GSM7662725 |
HRDE-1, mut-2 (adult) - input, replicate 3 |
| GSM7662726 |
HRDE-1, mut-2 (adult) - IP, replicate 1 |
| GSM7662727 |
HRDE-1, mut-2 (adult) - IP, replicate 2 |
| GSM7662728 |
HRDE-1, mut-2 (adult) - IP, replicate 3 |
| GSM7662729 |
HRDE-1, mut-2; hrde-2 (adult) - input, replicate 1 |
| GSM7662730 |
HRDE-1, mut-2; hrde-2 (adult) - input, replicate 2 |
| GSM7662731 |
HRDE-1, mut-2; hrde-2 (adult) - input, replicate 3 |
| GSM7662732 |
HRDE-1, mut-2; hrde-2 (adult) - IP, replicate 1 |
| GSM7662733 |
HRDE-1, mut-2; hrde-2 (adult) - IP, replicate 2 |
| GSM7662734 |
HRDE-1, mut-2; hrde-2 (adult) - IP, replicate 3 |
| GSM7662735 |
HRDE-1, simr-1 mut-2 (adult) - input, replicate 1 |
| GSM7662736 |
HRDE-1, simr-1 mut-2 (adult) - input, replicate 2 |
| GSM7662737 |
HRDE-1, simr-1 mut-2 (adult) - input, replicate 3 |
| GSM7662738 |
HRDE-1, simr-1 mut-2 (adult) - IP, replicate 1 |
| GSM7662739 |
HRDE-1, simr-1 mut-2 (adult) - IP, replicate 2 |
| GSM7662740 |
HRDE-1, simr-1 mut-2 (adult) - IP, replicate 3 |
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| This SubSeries is part of SuperSeries: |
| GSE239291 |
Germ granule association drives small RNA specificity for a nuclear Argonaute protein |
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| Relations |
| BioProject |
PRJNA998763 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE239289_RAW.tar |
50.5 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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