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The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans

ABSTRACT: The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans

PROVIDER: PRJNA633158 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12316400.fastq.gz	Fastqsanger.gz
	SRR12316401.fastq.gz	Fastqsanger.gz
	SRR12316402.fastq.gz	Fastqsanger.gz
	SRR12316403.fastq.gz	Fastqsanger.gz
	SRR12316404.fastq.gz	Fastqsanger.gz

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The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans

Project description:Eukaryotic cells regulate 5’ triphosphorylated (ppp) RNAs to promote cellular functions and to prevent recognition by viral RNA sensors. For example, the triphosphatase domain of RNA capping enzymes removes the γ phosphate of ppp-RNAs in RNA capping reactions. Members of a related RNA polyphosphotase family including human PIR1 remove both the β and γ phosphates from ppp-RNAs. Here we demonstrate that C. elegans PIR-1, previously identified as a Dicer-interacting protein, dephosphorylates single and double-stranded ppp-RNAs, and is required for the maturation of 26G-RNAs, which regulate thousands of genes during spermatogenesis and embryogenesis. We find that 26G-RNAs are generated in a unique semi-phasing manner in which primary 26G-RNAs are required for generating secondary 26G-RNAs and PIR-1 is required for removing a diphosphate group from each triphosphorylated precursor, which only generates one 26G-RNA. Our findings also implicate PIR-1 in regulating ppp-RNAs in Dicer-independent pathways, supporting PIR-1 as a master phosphatase regulating ppp-RNAs.

2021-05-14 | GSE150690 | GEO

The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans.

Project description:Eukaryotic cells regulate 5'-triphosphorylated RNAs (ppp-RNAs) to promote cellular functions and prevent recognition by antiviral RNA sensors. For example, RNA capping enzymes possess triphosphatase domains that remove the γ phosphates of ppp-RNAs during RNA capping. Members of the closely related PIR-1 (phosphatase that interacts with RNA and ribonucleoprotein particle 1) family of RNA polyphosphatases remove both the β and γ phosphates from ppp-RNAs. Here, we show that C. elegans PIR-1 dephosphorylates ppp-RNAs made by cellular RNA-dependent RNA polymerases (RdRPs) and is required for the maturation of 26G-RNAs, Dicer-dependent small RNAs that regulate thousands of genes during spermatogenesis and embryogenesis. PIR-1 also regulates the CSR-1 22G-RNA pathway and has critical functions in both somatic and germline development. Our findings suggest that PIR-1 modulates both Dicer-dependent and Dicer-independent Argonaute pathways and provide insight into how cells and viruses use a conserved RNA phosphatase to regulate and respond to ppp-RNA species.

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Phosphoglycolate phosphatase homologs act as glycerol-3-phosphate phosphatase to control stress and healthspan in C. elegans

Project description:Metabolic stress due to nutrient excess and lipid accumulation is at the root of many age-associated disorders and the identification of therapeutic targets that mimic the beneficial effects of calorie restriction has clinical importance. Here, using C. elegans as a model organism, we study the roles of a recently discovered enzyme at the heart of metabolism in mammalian cells, glycerol-3-phosphate phosphatase (G3PP) (gene name Pgp) that hydrolyzes glucose-derived glycerol-3-phosphate to glycerol. We identify three Pgp homologues in C. elegans (pgph) and demonstrate in vivo that their protein products have G3PP activity, essential for glycerol synthesis. We demonstrate that PGPH/G3PP regulates the adaptation to various stresses, in particular hyperosmolarity and glucotoxicity. Enhanced G3PP activity reduces fat accumulation, promotes healthy aging and acts as a calorie restriction mimetic at normal food intake without altering fertility. Thus, PGP/G3PP can be considered as a target for age-related metabolic disorders.

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RNA interference and retinoblastoma related genes are required for repression of endogenous siRNA targets in C. elegans

Project description:Expession data from L1-L2 stage nematodes (C. elegans), wild type and four mutants (alg-1, zfp-1, rde-4, lin-35). In C. elegans, a vast number of endogenous short RNAs corresponding to thousands of genes have been discovered recently. This finding suggests that these short interfering RNAs may contribute to regulation of many developmental and other signaling pathways in addition to silencing viruses and transposons. Based on this microarray analysis of gene expression in RNA interference (RNAi)-related mutants rde-4, zfp-1 and alg-1 and the Retinoblastoma (Rb) mutant lin-35, we found that a component of Dicer complex RDE-4 and a chromatin-related zinc finger protein ZFP-1, not implicated previously in endogenous RNAi, regulate overlapping sets of genes. Notably, genes a) upregulated in the rde-4 and zfp-1 mutants and b) upregulated in the lin-35(Rb) mutant, but not the downregulated genes are highly represented in the set of genes with corresponding endogenous short interfering RNAs (endo-siRNAs). Keywords: wildtype-mutant comparison, RNAi, Rb, endo-siRNA

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Analyses of endogenous rna substrates of xrn and exosome and ptgs pathways; Integrating RNA Quality Control and RNA Silencing Pathways

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mut-16 and other mutator-class genes modulate 22G and 26G siRNA pathways in Caenorhabditis elegans

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2011-02-01 | E-GEOD-26165 | biostudies-arrayexpress

The RNA polymerase II CTD phosphatase SSUP-72 regulates alternative polyadenylation in C. elegans neurons.

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2015-06-01 | GSE67649 | GEO

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