Planarians recruit piRNAs for mRNA turnover in adult stem cells
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ABSTRACT:
PROVIDER: PRJNA503908 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:PIWI proteins utilize small RNAs called piRNAs to silence transposable elements, thereby protecting germline integrity. In planarian flatworms, PIWI proteins are essential for regeneration, which requires adult stem cells termed neoblasts. Here, we characterize planarian piRNAs and examine the roles of PIWI proteins in neoblast biology. We find that the planarian PIWI proteins SMEDWI-2 and SMEDWI-3 cooperate to degrade active transposons via the ping-pong cycle. Unexpectedly, we discover that SMEDWI-3 plays an additional role in planarian mRNA surveillance. While SMEDWI-3 degrades numerous neoblast mRNAs in a homotypic ping-pong cycle, it is also guided to another subset of neoblast mRNAs by antisense piRNAs and binds these without degrading them. Mechanistically, the distinct activities of SMEDWI-3 are primarily dictated by the degree of complementarity between target mRNAs and antisense piRNAs. Planarian PIWI proteins thus act as both nucleases and RNA-binding proteins, enabling planarians to repurpose piRNAs for critical roles in neoblast mRNA turnover.
2019-09-04 | GSE122199 | GEO
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Project description:MyoD is a conserved myogenic factor which controls formation of longitundinal muscle fibers in planarians. nkx1-1 is a conserved transcription factor which controls formation of circular muscle fibers in planarians.
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Project description:Nkx2.2 is an intestine-enriched transcription factor required for regeneration in planarians. The goal of this study was to identify differentially expressed transcripts in uninjured nkx2.2(RNAi) planarians.
2022-05-24 | GSE174228 | GEO
Project description:Small RNAs were deep sequenced from the liver and spleen of adult mice in an effort to identify somatic piRNAs. Following sequencing of all small RNAs, known non-coding RNAs were computationally removed from the dataset. The remaining RNAs were then mapped to the genome and analyzed for sequence characteristics (5' base, length) typical of known piRNAs. To determine if any of the identified small RNAs were MIWI2 dependent, we deep sequenced small RNAs from liver and spleen of MIWI2 KO mice and analyzed them as above.
2015-06-10 | GSE47093 | GEO
Project description:piRNAs are required to maintain germline integrity and fertility but their mechanism of action is poorly understood. Here we demonstrate that C. elegans piRNAs silence transcripts in trans through imperfectly complementary sites. We find that target silencing is independent of Piwi endonuclease activity or “slicing”. Instead, we show that piRNAs initiate a localized secondary endogenous small interfering RNA (endo-siRNA) response. Endogenous protein-coding gene, pseudogene and transposon transcripts exhibit Piwi-dependent endo-siRNAs at sites complementary to piRNAs and are derepressed in Piwi mutants. Genomic loci of piRNA biogenesis are depleted of protein-coding genes but not pseudogenes or transposons. Our data suggest that nematode piRNA clusters are evolving to generate piRNAs against active mobile elements. Thus, piRNAs provide heritable, sequence-specific triggers for RNAi in C. elegans.
2012-06-18 | GSE37432 | GEO
Project description:Time-course RNA-Seq of X-ray irradiated planarians Dugesia japonica.
2023-10-02 | GSE223928 | GEO
Project description:The planarian Dugesia japonica has amazing ability to regenerate a head from the anterior ends of the amputated stump with maintenance of the original anterior-posterior polarity. Although planarians present an attractive system for molecular investigation of regeneration and research has focused on clarifying the molecular mechanism of regeneration initiation in planarians, but proteomic studies are still in the early stages. Here, a global proteomics analysis of regenerating head fragments in planarians at 0h, 2h and 6h after amputation was performed using isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics coupled with LC-MS/MS strategy. Then the significantly changed proteins were identified. The correlation betwwen protein expression profiles and signaling pathways/biological processes was analyzed by bioinformatics and systems biology.
2015-07-07 | PXD002100 | Pride
Project description:piRNAs are required to maintain germline integrity and fertility but their mechanism of action is poorly understood. Here we demonstrate that C. elegans piRNAs silence transcripts in trans through imperfectly complementary sites. We find that target silencing is independent of Piwi endonuclease activity or “slicing”. Instead, we show that piRNAs initiate a localized secondary endogenous small interfering RNA (endo-siRNA) response. Endogenous protein-coding gene, pseudogene and transposon transcripts exhibit Piwi-dependent endo-siRNAs at sites complementary to piRNAs and are derepressed in Piwi mutants. Genomic loci of piRNA biogenesis are depleted of protein-coding genes but not pseudogenes or transposons. Our data suggest that nematode piRNA clusters are evolving to generate piRNAs against active mobile elements. Thus, piRNAs provide heritable, sequence-specific triggers for RNAi in C. elegans. Affymetrix mRNA expression data from wild-type and two independent prg-1;prg-2 double mutant C. elegans strains (mRNA)
2012-06-17 | E-GEOD-37432 | biostudies-arrayexpress
Project description:Small RNAs were deep sequenced from the liver and spleen of adult mice in an effort to identify somatic piRNAs. Following sequencing of all small RNAs, known non-coding RNAs were computationally removed from the dataset. The remaining RNAs were then mapped to the genome and analyzed for sequence characteristics (5' base, length) typical of known piRNAs. To determine if any of the identified small RNAs were MIWI2 dependent, we deep sequenced small RNAs from liver and spleen of MIWI2 KO mice and analyzed them as above. We deep sequenced small RNAs from the liver and spleen of one WT mouse and one MIWI2 knock-out mouse. We then trimmed sequencing adapters and removed known ncRNAs (rRNA, tRNA, snoRNA, snRNA, miRNA) from the dataset before aligning reads to the mm9 assembly of the mouse genome.
2015-06-10 | E-GEOD-47093 | biostudies-arrayexpress