Argonaute CSR-1A promotes H3K9me3 maintenance to protect somatic development in offspring
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ABSTRACT:
PROVIDER: PRJNA1090892 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28424644_1.fastq.gz | Fastqsanger.gz | |||
| SRR28424644_2.fastq.gz | Fastqsanger.gz | |||
| SRR28424645_1.fastq.gz | Fastqsanger.gz | |||
| SRR28424645_2.fastq.gz | Fastqsanger.gz | |||
| SRR28424646_1.fastq.gz | Fastqsanger.gz |
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Project description:Paternal stress can be encoded into altered epigenetic information to influence their offspring. How environment-induced perturbation in sperm epigenome is reprogrammed to protect offspring is less well understood. In the nematode Caenorhabditis elegans, parental Argonaute and small RNA pathway defend offspring against viruses, starvation, and pathogenic bacteria. Here we report that, when challenged by universal heat-shock stress, paternal Argonaute CSR-1A potentiates recovery of spermic H3K9me3 to secure the late somatic developmental competence of offspring. CSR-1A employs its repetitive RG motif to engage with SET-25/32, putative histone 3 lysine 9 (H3K9) methyltransferases, and helps germ cell to rescue suppressive chromatin marks H3K9me3 following stress, protecting the late development of somatic cells in the progeny. Finally, among the genes regulated by CSR-1A, we identified dim-1, at which decreased H3K9me3 persists in the progeny, and RNAi of dim-1 mitigates the somatic defects associated with csr-1a loss under stress. Thus, CSR-1A coordinates the epigenetic machinery to shield the latter stages of a progeny's development from the influences of the paternal environment. We speculate that, driven by both natural environmental stressors and the unique characteristics of spermatogenic chromatin, the emergence of multiple RG motif-featured and spermatogenesis-specific CSR-1A and small RNA serves as an adaptive strategy to safeguard against variability in the orchestration of inherited developmental programs from the paternal lineage.
2025-02-07 | GSE262244 | GEO
Project description:Paternal stress can be encoded into altered epigenetic information to influence their offspring. How environment-induced perturbation in sperm epigenome is reprogrammed to protect offspring is less well understood. In the nematode Caenorhabditis elegans, parental Argonaute and small RNA pathway defend offspring against viruses, starvation, and pathogenic bacteria. Here we report that, when challenged by universal heat-shock stress, paternal Argonaute CSR-1A potentiates recovery of spermic H3K9me3 to secure the late somatic developmental competence of offspring. CSR-1A employs its repetitive RG motif to engage with SET-25/32, putative histone 3 lysine 9 (H3K9) methyltransferases, and helps germ cell to rescue suppressive chromatin marks H3K9me3 following stress, protecting the late development of somatic cells in the progeny. Finally, among the genes regulated by CSR-1A, we identified dim-1, at which decreased H3K9me3 persists in the progeny, and RNAi of dim-1 mitigates the somatic defects associated with csr-1a loss under stress. Thus, CSR-1A coordinates the epigenetic machinery to shield the latter stages of a progeny's development from the influences of the paternal environment. We speculate that, driven by both natural environmental stressors and the unique characteristics of spermatogenic chromatin, the emergence of multiple RG motif-featured and spermatogenesis-specific CSR-1A and small RNA serves as an adaptive strategy to safeguard against variability in the orchestration of inherited developmental programs from the paternal lineage.
2025-02-07 | GSE262243 | GEO
Project description:Argonaute CSR-1A promotes H3K9me3 maintenance to protect somatic development in offspring
| PRJNA1090893 | ENA
Project description:CSR-1 is an essential Argonaute protein that binds to a subclass of 22G-RNAs targeting most germline-expressed genes. Here we show that the two isoforms of CSR-1 have distinct expression patterns; CSR-1B is ubiquitously expressed throughout the germline and during all stages of development while CSR-1A expression is restricted to germ cells undergoing spermatogenesis. Furthermore, CSR-1A associates preferentially with 22G-RNAs mapping to spermatogenesis-specific genes whereas CSR-1B-bound small RNAs map predominantly to oogenesis-specific genes. Interestingly, the exon unique to CSR-1A contains multiple dimethylarginine modifications, which are necessary for the preferential binding of CSR-1A to spermatogenesis-specific 22G-RNAs. Thus, we have discovered a regulatory mechanism for C. elegans Argonaute proteins that allows for specificity of small RNA binding between similar Argonaute proteins with overlapping temporal and spatial localization.
2021-06-17 | PXD021227 | Pride
Project description:CSR-1 is an essential Argonaute protein that binds to a subclass of 22G-RNAs targeting most germline-expressed genes. Here we show that the two isoforms of CSR-1 have distinct expression patterns; CSR-1B is ubiquitously expressed throughout the germline and during all stages of development while CSR-1A expression is restricted to germ cells undergoing spermatogenesis. Furthermore, CSR-1A associates preferentially with 22G-RNAs mapping to spermatogenesis-specific genes whereas CSR-1B-bound small RNAs map predominantly to oogenesis-specific genes. Interestingly, the exon unique to CSR-1A contains multiple dimethylarginine modifications, which are necessary for the preferential binding of CSR-1A to spermatogenesis-specific 22G-RNAs. Thus, we have discovered a regulatory mechanism for C. elegans Argonaute proteins that allows for specificity of small RNA binding between similar Argonaute proteins with overlapping temporal and spatial localization.
2021-06-04 | GSE151828 | GEO
Project description:The C. elegans genome encodes nineteen functional Argonaute proteins that utilize 22G-RNAs, 26G-RNAs, miRNAs, or piRNAs to regulate their target transcripts. Only one of these proteins is essential under normal laboratory conditions: CSR-1. While CSR-1 has been studied in various developmental and functional contexts, nearly all studies investigating CSR-1 have overlooked the fact that the csr-1 locus encodes two isoforms. These isoforms differ by an additional 163 amino acids present in the N-terminus of CSR-1a. Using CRISPR-Cas9 genome editing to introduce GFP::3xFLAG epitopes into the long (CSR-1a) and short (CSR-1b) isoforms of CSR-1, we identified differential expression patterns for the two isoforms. CSR-1a is expressed specifically during spermatogenesis and in select somatic tissues, including the intestine. In contrast, CSR-1b, is expressed constitutively in the germline. Essential functions of csr-1 described in the literature coincide with CSR-1b. In contrast,CSR-1a plays tissue specific functions during spermatogenesis, where it integrates into a spermatogenesis sRNA regulatory network including ALG-3, ALG-4, and WAGO-10 that is necessary for male fertility. CSR-1a is also required in the intestine for the silencing of repetitive transgenes. Sequencing of small RNAs associated with each CSR-1 isoform reveals that CSR-1a engages with 22G- and 26G-RNAs, while CSR-1b interacts with only 22G-RNAs to regulate distinct groups of germline genes and regulate both sperm and oocyte-mediated fertility.
2020-07-19 | GSE154678 | GEO
Project description:In the Caenorhabditis elegans germline, thousands of mRNAs are concomitantly expressed with antisense 22G-RNAs, which are loaded into the Argonaute CSR-1. Despite their essential functions for animal fertility and embryonic development, how CSR-1 22G-RNAs are produced remains unknown. Here, we show that CSR-1 slicer activity is primarily involved in triggering the synthesis of small RNAs on the coding sequences of germline mRNAs and post-transcriptionally regulates a fraction of targets. CSR-1-cleaved mRNAs prime the RNA-dependent RNA polymerase, EGO-1, to synthesize 22G-RNAs in phase with ribosome translation in the cytoplasm, in contrast to other 22G-RNAs mostly synthesized in germ granules. Moreover, codon optimality and efficient translation antagonize CSR-1 slicing and 22G-RNAs biogenesis. We propose that codon usage differences encoded into mRNA sequences might be a conserved strategy in eukaryotes to regulate small RNA biogenesis and Argonaute targeting
2021-04-23 | PXD020293 | Pride
Project description:Organisms can develop adaptive sequence-specific immunity by reexpressing pathogen-specific small RNAs that guide gene silencing. For example, the C. elegans PIWI-Argonaute/piwi-interacting RNA (piRNA) pathway recruits RNA-dependent RNA polymerase (RdRP) to foreign sequences to amplify a transgenerational small-RNA-induced epigenetic silencing signal (termed RNAe). Here, we provide evidence that, in addition to an adaptive memory of silenced sequences, C. elegans can also develop an opposing adaptive memory of expressed/self-mRNAs. We refer to this mechanism, which can prevent or reverse RNAe, as RNA-induced epigenetic gene activation (RNAa). We show that CSR-1, which engages RdRP-amplified small RNAs complementary to germline-expressed mRNAs, is required for RNAa. We show that a transgene with RNAa activity also exhibits accumulation of cognate CSR-1 small RNAs. Our findings suggest that C. elegans adaptively acquires and maintains a transgenerational CSR-1 memory that recognizes and protects self-mRNAs, allowing piRNAs to recognize foreign sequences innately, without the need for prior exposure.
2013-12-23 | GSE49532 | GEO
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
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 | GSE239289 | GEO