PID-1 is a novel factor that operates during 21U RNA biogenesis in Caenorhabditis elegans
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ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE55309 | GEO | 2014/03/17
SECONDARY ACCESSION(S): PRJNA239266
REPOSITORIES: GEO
Similar Datasets
Project description:Animal germ cells employ small RNA-based mechanisms to recognize and silence DNA that invades their genome. One of these pathways is named the Piwi:piRNA pathway. Biogenesis of piRNAs is poorly understood. In C. elegans, the piRNA (21U-RNA)-binding Argonaute protein PRG-1 is the only known player acting downstream of pre-cursor transcription. From a screen aimed at the isolation of M-bM-^@M-^XpiRNA-induced silencing defectiveM-bM-^@M-^Y mutations we identified, amongst known Piwi-pathway components like MUT-7, RDE-3 and HRDE-1, PID-1 as a novel player. PID-1 is essential for 21U RNA biogenesis and affects an early step in the processing or transport of 21U precursor transcripts. 12 small RNA samples were analyzed as singletons.
2014-03-17 | E-GEOD-55309 | biostudies-arrayexpress
Project description:Piwi Argonautes and Piwi-interacting RNAs (piRNAs) mediate genome defense by targeting transposons. However, many piRNA species lack obvious sequence complementarity to transposons or other loci. For example, only one C. elegans transposon is a known piRNA target. Here we show that, in mutants lacking the Piwi Argonaute PRG-1 and associated piRNAs (21U-RNAs), many silent loci in the germline exhibit increased levels of mRNA expression and depletion of an amplified RNAdependent RNA polymerase (RdRP)-derived species of small RNA termed 22G-RNAs. Sequences depleted of 22G-RNAs are enriched nearby potential target sites that base pair imperfectly but extensively to 21U-RNAs. We show that PRG-1 is required to initiate, but not to maintain, silencing of transgenes engineered to contain complementarity to endogenous 21U-RNAs. Our findings support a model in which C. elegans piRNAs utilize their enormous repertoire of targeting capacity to scan the germline transcriptome for foreign sequences, while endogenous germline-expressed genes are actively protected from piRNA-induced silencing. Examine small RNA population changes in prg-1 and rescued strains
2012-09-01 | E-GEOD-38723 | biostudies-arrayexpress
Project description:Piwi Argonautes and Piwi-interacting RNAs (piRNAs) mediate genome defense by targeting transposons. However, many piRNA species lack obvious sequence complementarity to transposons or other loci. For example, only one C. elegans transposon is a known piRNA target. Here we show that, in mutants lacking the Piwi Argonaute PRG-1 and associated piRNAs (21U-RNAs), many silent loci in the germline exhibit increased levels of mRNA expression and depletion of an amplified RNAdependent RNA polymerase (RdRP)-derived species of small RNA termed 22G-RNAs. Sequences depleted of 22G-RNAs are enriched nearby potential target sites that base pair imperfectly but extensively to 21U-RNAs. We show that PRG-1 is required to initiate, but not to maintain, silencing of transgenes engineered to contain complementarity to endogenous 21U-RNAs. Our findings support a model in which C. elegans piRNAs utilize their enormous repertoire of targeting capacity to scan the germline transcriptome for foreign sequences, while endogenous germline-expressed genes are actively protected from piRNA-induced silencing.
2012-09-01 | GSE38723 | GEO
Project description:The Piwi-piRNA pathway represents a germline specific transposon-defense system. C. elegans Piwi, prg-1, is a non-essential gene and triggers a secondary RNAi response that depends on so-called mutator genes, endo-siRNAs (22G-RNAs) and at least one 22G-RNA-binding Argonaute protein, HRDE-1. Interestingly, through a poorly understood mechanism, silencing of PRG-1 targets can become PRG-1 independent. This state, also known as RNAe, is heritable and depends on mutator genes and HRDE-1. We studied how the transgenerational memory of RNAe and the piRNA pathway interact. We find that maternally provided PRG-1 is required for the de-novo establishment of 22G-RNA populations, especially those targeting transposons. Strikingly, attempts to re-establish 22G-RNAs in absence of both PRG-1 and RNAe memory result in severe germline proliferation defects. This is accompanied by a disturbed balance between gene-activating and -repressing 22G-RNA pathways. We propose a model in which CSR-1 prevents the loading of HRDE-1 and that both PRG-1 and HRDE-1 help to keep mutator activity focused on the proper targets.
2015-08-13 | GSE68988 | GEO
Project description:In Caenorhabditis elegans, the piRNA (21U RNA) pathway is required to establish proper gene regulation and an immortal germline. To achieve this, PRG-1-bound 21U RNAs trigger silencing mechanisms mediated by RNA-dependent RNA polymerase (RdRP)-synthetized 22G RNAs. This silencing can become PRG-1-independent, and heritable over many generations. This state is named RNAe. It is unknown how and when RNAe is established, and how it is maintained. We show that maternally provided 21U RNAs can be sufficient to trigger RNAe in embryos. Additionally, we identify the IDR-containing protein PID-2, as a factor required to establish and maintain RNAe. PID-2 interacts with two novel, partially redundant, eTudor domain proteins, PID-4 and PID-5. Additionally, PID-5 has a domain related to the X-prolyl aminopeptidase protein APP-1, and binds APP-1, implicating N-terminal proteolysis in RNAe. All three proteins are required for germline immortality, localize to perinuclear foci and affect Z granules, and are required for balancing of 22G RNA populations. Overall, our study identifies three new proteins with crucial functions in the C. elegans small RNA silencing network.
2020-09-21 | PXD018402 | Pride
Project description:Piwi proteins are important for germ cell development and function in almost all animals studied thus far. These proteins are guided to specific targets, such as transposable elements, by small guide RNAs, often referred to as piRNAs, or 21U RNAs in C. elegans. In this organism, even though genetic screens have uncovered a number of potential 21U RNA biogenesis factors, little is known about how these factors interact or what they do. Based on the previously identified 21U biogenesis factor PID-1, we here define a novel protein complex, PETISCO, that is required for 21U RNA biogenesis. PETISCO contains both potential 5’-cap and 5’-phosphate RNA binding activities, suggesting involvement in 5’ end processing. We define the interaction architecture of PETISCO and reveal a second function required for embryonic development. This essential function of PETISCO is not mediated by PID-1, but by TOST-1. Vice versa, TOST-1 is not involved in 21U RNA biogenesis. Both PID-1 and TOST-1 are small, intrinsically disordered proteins that interact directly with the PETISCO protein ERH-2 (enhancer of rudimentary homolog 2) using a conserved sequence motif. Finally, our data suggest an important role for TOST-1:PETISCO in SL1 homeostasis in the early embryo. Our work describes the first molecular platform for 21U RNA production in C. elegans, and reveals that 21U RNA biogenesis is built upon a much more widely used snRNA-related pathway.
2024-04-08 | PXD011500 | Pride
Project description:Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs. Caenorhabditis elegans encodes two Piwi family proteins called PRG-1 and PRG-2, and PRG-1 interacts with the C. elegans piRNAs (21U-RNAs). Previous studies found that the prg-1 mutation causes a marked reduction in the expression of 21U-RNAs, temperature-sensitive defects in fertility and other phenotypic defects.To systematically demonstrate the function of PRG-1 on regulating small RNAs and their targets. We use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs in six stages(embryo,L1,L2,L3,L4,young audlt) and mRNAs in four stages (L1,L2,L3,L4) after prg-1 mutation. prg-1 mutation can not only lead to a decrease in the expression of 21U-RNAs, but also cause 35~40% of miRNAs to be significantly down-regulated; approximately 3% (6.00% in L4) of protein-coding genes are differentially expressed after mutating prg-1, and 60~70% of these substantially changed protein-coding genes are up-regulated.
2014-06-09 | GSE56272 | GEO
Project description:Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs. Caenorhabditis elegans encodes two Piwi family proteins called PRG-1 and PRG-2, and PRG-1 interacts with the C. elegans piRNAs (21U-RNAs). Previous studies found that the prg-1 mutation causes a marked reduction in the expression of 21U-RNAs, temperature-sensitive defects in fertility and other phenotypic defects.To systematically demonstrate the function of PRG-1 on regulating small RNAs and their targets. We use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs in six stages(embryo,L1,L2,L3,L4,young audlt) and mRNAs in four stages (L1,L2,L3,L4) after prg-1 mutation. prg-1 mutation can not only lead to a decrease in the expression of 21U-RNAs, but also cause 35~40% of miRNAs to be significantly down-regulated; approximately 3% (6.00% in L4) of protein-coding genes are differentially expressed after mutating prg-1, and 60~70% of these substantially changed protein-coding genes are up-regulated.
2014-06-09 | GSE56271 | GEO
Project description:Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs. Caenorhabditis elegans encodes two Piwi family proteins called PRG-1 and PRG-2, and PRG-1 interacts with the C. elegans piRNAs (21U-RNAs). Previous studies found that the prg-1 mutation causes a marked reduction in the expression of 21U-RNAs, temperature-sensitive defects in fertility and other phenotypic defects.To systematically demonstrate the function of PRG-1 on regulating small RNAs and their targets. We use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs in six stages(embryo,L1,L2,L3,L4,young audlt) and mRNAs in four stages (L1,L2,L3,L4) after prg-1 mutation. prg-1 mutation can not only lead to a decrease in the expression of 21U-RNAs, but also cause 35~40% of miRNAs to be significantly down-regulated; approximately 3% (6.00% in L4) of protein-coding genes are differentially expressed after mutating prg-1, and 60~70% of these substantially changed protein-coding genes are up-regulated. Examination of small RNA expression in six different developmental stages (embryo, L1, L2, L3, L4, young adult) and mRNA expression in four stages (L1,L2,L3,L4) of C. elegans prg-1 mutant (wm161) .
2014-06-09 | E-GEOD-56272 | biostudies-arrayexpress
Project description:Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs. Caenorhabditis elegans encodes two Piwi family proteins called PRG-1 and PRG-2, and PRG-1 interacts with the C. elegans piRNAs (21U-RNAs). Previous studies found that the prg-1 mutation causes a marked reduction in the expression of 21U-RNAs, temperature-sensitive defects in fertility and other phenotypic defects.To systematically demonstrate the function of PRG-1 on regulating small RNAs and their targets. We use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs in six stages(embryo,L1,L2,L3,L4,young audlt) and mRNAs in four stages (L1,L2,L3,L4) after prg-1 mutation. prg-1 mutation can not only lead to a decrease in the expression of 21U-RNAs, but also cause 35~40% of miRNAs to be significantly down-regulated; approximately 3% (6.00% in L4) of protein-coding genes are differentially expressed after mutating prg-1, and 60~70% of these substantially changed protein-coding genes are up-regulated. Examination of small RNA expression in six different developmental stages (embryo, L1, L2, L3, L4, young adult) and mRNA expression in four stages (L1,L2,L3,L4) of C. elegans prg-1 mutant (wm161) .
2014-06-09 | E-GEOD-56271 | biostudies-arrayexpress