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Hairpin RNA induces secondary small interfering RNA synthesis and silencing in trans in fission yeast

ABSTRACT: We provide evidence of the generation of Rdp1-mediated secondary siRNAs in vivo in fission yeast. Secondly, we show that the presence of Ago1-associated siRNAs does not guarantee robust silencing.

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE20330 | GEO | 2010/02/15

SECONDARY ACCESSION(S): PRJNA125397

REPOSITORIES: GEO

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Hairpin RNA induces secondary small interfering RNA synthesis and silencing in trans in fission yeast

Project description:We provide evidence of the generation of Rdp1-mediated secondary siRNAs in vivo in fission yeast. Secondly, we show that the presence of Ago1-associated siRNAs does not guarantee robust silencing. We obtained sequences from gel purified small RNAs of wt and rdp1delta fission yeast cells and FLAG-ago1 associated small RNAs.

2010-02-15 | E-GEOD-20330 | biostudies-arrayexpress

Hairpin RNA induces secondary small interfering RNA synthesis and silencing in trans in fission yeast.

Project description: Not available

| S-EPMC2828748 | biostudies-literature

Effects of RNAi protein overexpression in mutant cells on H3K9 dimethylation in fission yeast cells

Project description:We test the effects of overexpressing RNAi proteins Dcr1, Rdp1, or Ago1 in wildtype, dcr1∆, ago1∆, or rdp1∆ cells. We find that overexpression does not generally affect H3K9me2 at euchromatic loci, but there are varying effects in H3K9me2 on centromeric heterochromatin.

2013-12-26 | GSE52444 | GEO

Effects of RNAi protein overexpression in mutant cells on H3K9 dimethylation in fission yeast cells

Project description:We test the effects of overexpressing RNAi proteins Dcr1, Rdp1, or Ago1 in wildtype, dcr1M-bM-^HM-^F, ago1M-bM-^HM-^F, or rdp1M-bM-^HM-^F cells. We find that overexpression does not generally affect H3K9me2 at euchromatic loci, but there are varying effects in H3K9me2 on centromeric heterochromatin. Examination of genome-wide enrichment in H3K9 dimethylation in fission yeast haploid cells

2013-12-26 | E-GEOD-52444 | biostudies-arrayexpress

FIERY1 promotes microRNA accumulation by suppressing rRNA-derived small interfering RNAs in Arabidopsis [RNA-seq]

Project description:Plant microRNAs (miRNAs) associate with ARGONAUTE1 (AGO1) to direct post-transcriptional gene silencing and regulate numerous biological processes. Although AGO1 predominantly binds miRNAs in vivo, AGO1 also associates with endogenous small interfering RNAs (siRNAs). It is unclear whether the miRNA/siRNA balance affects miRNA activities. Here we report that FIERY1 (FRY1), which is involved in 5’-3’ RNA degradation, regulates miRNA abundance and function by suppressing the biogenesis of ribosomal RNA-derived siRNAs (risiRNAs). In mutants of FRY1 and the nuclear 5’-3’ exonuclease genes XRN2 and XRN3, we found that a large number of 21-nt risiRNAs were generated through an endogenous siRNA biogenesis pathway. The production of risiRNAs correlated with pre-rRNA processing defects in these mutants. We also show that these risiRNAs were loaded into AGO1, causing reduced loading of miRNAs. This study reveals a previously unknown link between rRNA processing and miRNA accumulation.

2019-10-08 | GSE133411 | GEO

FIERY1 promotes microRNA accumulation by suppressing rRNA-derived small interfering RNAs in Arabidopsis [miRNA-seq]

2019-10-08 | GSE126482 | GEO

Schizosaccharomyces pombe

Project description:Generation of Rdp1-independent primary siRNAs

| PRJNA229166 | ENA

Generation of Rdp1-independent primary siRNAs

Project description:We tested whether we could increase the population of Rdp1-independent primary siRNAs in fission yeast by overexpressing the Dcr1 ribonuclease. We found that in addition to generation of centromeric siRNAs, which was expected, Dcr1 overexpression also resulted in generation of genome-wide primary siRNAs, mapping to many open reading frames.

2013-12-26 | GSE52532 | GEO

Molecular and Functional Characterization of the role of RNA silencing components in Cryptococcus neoformans [RNAi_Serotype D]

Project description:The RNA interference (RNAi) mediated by homology-dependent degradation of the target mRNA with small RNA molecules plays a key role in controlling transcription and translation processes in a number of eukaryotic organisms. The RNAi machinery is also evolutionarily conserved in a wide variety of fungal species, including pathogenic fungi. To elucidate the physiological functions of the RNAi pathway in Cryptococcus neoformans that causes fungal meningitis, here we performed genetic analyses for genes encoding Argonaute (AGO1 and AGO2), RdRP (RDP1), and Dicers (DCR1 and DCR2) in both serotype A and D C. neoformans. The present study shows that Ago1, Rdp1, and Dcr2 are the major components of the RNAi process occurring in C. neoformans. However, the RNAi machinery is not involved in regulation of production of two virulence factors (capsule and melanin), sexual differentiation, and diverse stress response. To further gain insights into the global regulatory circuit governed by the RNAi pathway, comparative transcriptome analysis using the serotype A and D RNAi mutants was performed. Notably, an increase in transcript abundance of active transposons, such as T2 and T3, was observed in the rdp1Δ mutant. Therefore, this study can improve our understanding of the role of the RNAi genes in human fungal pathogens including C. neoformans. RNAi_D: 6 slides are used in this analysis, 3 biological replicate experiments are performed, total RNAs are extracted from 4 strains (NE519 MAT alpha, NE520 MAT a backcrossed Wild type strain, NE517 rdp1 mutant MAT alpha, NE518 rdp1 mutant MAT a). We use Cy5 as rdp1 mutant dye and Cy3 as a WT dye

2010-05-01 | E-GEOD-21177 | biostudies-arrayexpress

A non-Dicer RNase III and four other novel factors required for RNAi-mediated transposon suppression in the human pathogenic yeast C. neoformans

Project description:The human pathogenic yeast Cryptococcus neoformans silences transposable elements using endo-siRNAs and an Argonaute, Ago1. Endo-siRNAs production requires the RNA-dependent RNA polymerase, Rdp1, and two partially redundant Dicer enzymes, Dcr1 and Dcr2, but is independent of histone H3 lysine 9 methylation. We describe here an insertional mutagenesis screen for factors required to suppress the mobilization of the C. neoformans HARBINGER family DNA transposon HAR1. Validation experiments uncovered five novel genes (RDE1-5) required for HAR1 suppression and global production of suppressive endo-siRNAs. The RDE genes impact global siRNA levels and transposon mobilization but not global transcript levels, suggesting the endo-siRNAs do not act by impacting target transcript synthesis or turnover. RDE3 encodes a non-Dicer RNase III related to S. cerevisiae Rnt1, RDE4 encodes a predicted terminal nucleotidyltransferase, while RDE5 has no strongly predicted encoded domains. Affinity purification-mass spectrometry studies reveal that Rde3 and Rde5 are physically associated. RDE1 encodes a G-patch protein homologous to the S. cerevisiae Sqs1/Pfa1, a nucleolar protein that directly activates the essential helicase Prp43 during rRNA biogenesis. Rde1 copurifies Rde2, another novel protein obtained in the screen, as well as Ago1, a homolog of Prp43, and numerous predicted nucleolar proteins. We also describe the isolation of conditional alleles of PRP43, which are defective in RNAi. This work reveals unanticipated requirements for a non-Dicer RNase III and presumptive nucleolar factors for endo-siRNA biogenesis and transposon mobilization suppression in C. neoformans.

2020-07-13 | GSE128009 | GEO

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