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Characterization of active piRNAs and piRNA machinery in WRR-1 cells deficient for the Hippo pathway (deficient for the warts tumor suppressor) and expressing activated RasV12

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Delphine Fagegaltier

PROVIDER: E-GEOD-83877 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Oncogenic transformation of Drosophila somatic cells induces a functional piRNA pathway.

Fagegaltier Delphine D Falciatori Ilaria I Czech Benjamin B Castel Stephane S Perrimon Norbert N Simcox Amanda A Hannon Gregory J GJ

Genes & development 20160701 14

Germline genes often become re-expressed in soma-derived human cancers as "cancer/testis antigens" (CTAs), and piRNA (PIWI-interacting RNA) pathway proteins are found among CTAs. However, whether and how the piRNA pathway contributes to oncogenesis in human neoplasms remain poorly understood. We found that oncogenic Ras combined with loss of the Hippo tumor suppressor pathway reactivates a primary piRNA pathway in Drosophila somatic cells coincident with oncogenic transformation. In these cells, ...[more]

PMID: 27474441

Similar Datasets

Characterization of active piRNAs and piRNA machinery in WRR-1 cells deficient for the Hippo pathway (deficient for the warts tumor suppressor) and expressing activated RasV12 (RNA-seq)

Project description:We have found that oncogenic Ras combined with loss of the Hippo tumour-suppressor pathway reactivates a primary piRNA pathway in Drosophila somatic cells, coincident with oncogenic transformation. In these cells, Piwi becomes loaded with piRNAs derived from generative loci, which are normally restricted to either the germline or the somatic follicle cells. Negating the pathway leads to increases in the expression of a wide variety of transposons and also to altered expression of some protein coding genes. This correlates with a reduction in the proliferation of the transformed cells in culture, suggesting that at least in this context, the piRNA pathway may play a functional role in cancer. Small RNAs cloned from whole cells, Piwi-bound small RNAs and long RNA-Seq were performed in wts-RNAi;RasV12 cells to identify piRNAs and gene expression changes compared to RasV12 cells, somatic OSS cells, and germline UAS-wts-RNAi;UAS-RasV12 control ovaries. After knock-down of components of the piRNA machinery in WRR-1 cells ([piwi, zuchini, armitage, aubergine, argonaute3) and GFP and/or dsRED control knock-downs, small RNAs were cloned and gene expression (RNA-Seq) profiles were established.

2016-08-01 | E-GEOD-83843 | biostudies-arrayexpress

Characterization of active piRNAs and an piRNA machinery in WRR-1 cells deficient for the Hippo pathway (deficient for the warts tumor suppressor) and expressing activated RasV12 (small RNA)

Project description:We have found that oncogenic Ras combined with loss of the Hippo tumour-suppressor pathway reactivates a primary piRNA pathway in Drosophila somatic cells, coincident with oncogenic transformation. In these cells, Piwi becomes loaded with piRNAs derived from generative loci, which are normally restricted to either the germline or the somatic follicle cells. Negating the pathway leads to increases in the expression of a wide variety of transposons and also to altered expression of some protein coding genes. This correlates with a reduction in the proliferation of the transformed cells in culture, suggesting that at least in this context, the piRNA pathway may play a functional role in cancer. Small RNAs cloned from whole cells, piwi-bound small RNAs and long RNA-Seq were performed in wts-RNAi;RasV12 cells to identify piRNAs and gene expression and compared to RasV12 cells, somatic OSS cells, and germline UAS-wts-RNAi;UAS-RasV12 control ovaries. After knock-down of several components of the piRNA machinery in WRR-1 cells (piwi, zuchini, armitage, aubergine, argonaute3) and GFP and/or dsRED control knock-downs, small RNAs were cloned and gene expression profiles (RNA-Seq) were established.

2016-08-01 | E-GEOD-83871 | biostudies-arrayexpress

The hub protein Loqs connects the miRNA and endo-siRNA pathways in mosquitos

Project description:Aedes aegypti mosquitoes vector several arboviruses of global health significance, including dengue viruses and chikungunya virus. RNA interference (RNAi) plays an important role in antiviral immunity, gene regulation and protection from transposable elements. Double-stranded RNA binding proteins (dsRBPs) are important for efficient RNAi; in Drosophila functional specialization of the miRNA, endo-siRNA and exo-siRNA pathway is aided by the dsRBPs Loqs-PB, Loqs-PD and R2D2, respectively. However, this functional specialization has not been investigated in other dipterans. Characterization of the gene structure, expression pattern and interactions with other RNAi/miRNA components revealed that mosquito Loqs/R3D1 isoform -PA, but not -PB interacted readily with both AeAGO1 and AeAGO2. This interaction was mapped to a 32 a.a. region predicted to be structurally similar to the unique 22 a.a. tail of Drosophila Loqs-PD. No -PD isoforms could be detected in Ae. aegypti; analysis of other dipteran genomes demonstrated that this isoform is not conserved outside of Drosophila. Overexpression experiments indicated that Loqs/R3D1-PA participates in endo-siRNA, but not exo-siRNA based silencing. We conclude that the functional specialization of Loqs-PD in Drosophila is a recently derived trait, and that in other dipterans, including the medically important mosquitoes, Loqs/R3D1-A participates in both the miRNA and endo-siRNA based pathways. 12 samples, 3 replicates of each type of sample. The GFP sample is the reference sample

2015-04-08 | E-GEOD-65070 | biostudies-arrayexpress

RNAi knock down of four Argonaute paralogs (AGO1, AGO2, PIWI and Aubergine) and the microRNA-processing enzyme Drosha in Drosophila

Project description:RNA silencing pathways are conserved gene regulation mechanisms that lead to degradation, translational repression or transcriptional silencing of target-transcripts selected based on complementarity with small RNA molecules. The fraction of the genome regulated by these pathways has not been established. Argonaute proteins play fundamental roles in RNA silencing. To identify their physiological targets at the genomic level, we examined expression profiles in Drosophila cells depleted of 4 Argonaute paralogs (i.e. AGO1, AGO2, PIWI or Aubergine). We also profiled cells depleted of the microRNA (miRNA)-processing enzyme Drosha.

2006-11-20 | E-MEXP-295 | biostudies-arrayexpress

PRL-1 selectively dephosphorylates TIMELESS

Project description:The timing of behavior under natural light-dark conditions is a function of circadian clocks and photic input pathways. Yet a mechanistic understanding of how these pathways collaborate in animals is lacking. Here we demonstrate in Drosophila that the Phosphatase of Regenerating Liver-1 (PRL-1) sets period length and behavioral phase gated by photic signals. PRL-1 knockdown in PDF clock neurons dramatically lengthens circadian period. PRL-1 mutants exhibit allele-specific interactions with the light- and clock-regulated gene timeless (tim). Moreover, we show that PRL-1 promotes TIM accumulation and dephosphorylation. Interestingly, the PRL-1 mutant period lengthening is suppressed in constant light and PRL-1 mutants display a delayed phase under short, but not long, photoperiod conditions. Thus, our studies reveal that PRL-1 dependent dephosphorylation of TIM is a core mechanism of the clock that sets period length and phase in darkness, enabling the behavioral adjustment to changing day-night cycles.

2020-11-11 | PXD020986 | Pride

Transcriptome and transposable element dynamics during PIWI regulation in Drosophila ovarian cell cultures

Project description:This study examines the regulatory capacity of the Piwi protein in the Drosophila OSS cell. Piwi CLIP-Seq, mRNA-Seq and nascent RNAseq datasets were integrated to determine how Piwi proteins where using piRNAs and binding interactions to regulate the expression of transcripts. We also sequenced the genomes of various OSS cell lines. We first performed several replicates of a Piw CLIP-Seq experiment to isolate RNA fragments as CLIP-tags to discover which transcripts are preferentially bound by the Piwi protein. Then we performed several types of mRNA expression profiling experiments using several forms of mRNA-Seq library construction formats. Finally, we sequenced the genomes from various OSS cell lines. The genomic sequencing component of the study is represented by BioProject PRJNA240323. The genomic sequencing raw data have been deposited at SRA (SRP039565).

2014-09-15 | E-GEOD-45112 | biostudies-arrayexpress

Transcriptional networks controlling the cell cycle (RNA-seq)

Project description:Transcription profiling by RNA-seq of Drosophila S2 cells after knock down of strongest cell cycle regulators to map their genome-wide transcriptional targets (155 assays). RNA samples used for this experiment are a subset of the 200 samples used in Affymetrix microarray experiment E-MTAB-453. E-MTAB-1648, E-MTAB-1364 and E-MTAB-453 are all data from: Bonke M, et al. (2013) Transcriptional networks controlling the cell cycle. G3 (Bethesda) 3, 75-90, PMID: 23316440.

2012-11-26 | E-MTAB-1364 | biostudies-arrayexpress

Transcriptional networks controlling the cell cycle

Project description:In this work, we use RNAi and subsequent RNA isolation and Affymetrix Expression array analysis to map the genome-wide transcriptional targets of 107 of the strongest cell cycle regulators. Drosophila S2 cells were used with RNAi target gene knockdown compared to control (GFP dsRNA). RMA normalized data re-annotated using a custom CDF is available on the FTP site for this experiment. E-MTAB-1648, E-MTAB-1364 and E-MTAB-453 are all data from: Bonke M, et al. (2013) Transcriptional networks controlling the cell cycle. G3 (Bethesda) 3, 75-90, PMID: 23316440.

2012-06-30 | E-MTAB-453 | biostudies-arrayexpress

RNA elements in precursors instruct directional and processive primary piRNA biogenesis

Project description:PIWI-interacting RNAs (piRNAs) are animal gonad-specific small RNAs that control the activity of transposable elements. Long single stranded RNAs from a variety of sources are substrates for the nebulous primary processing pathway that converts these into thousands of 24-30 nucleotide (nt) piRNAs. How these transcripts are selected as precursors is not known. Here we show that targeting a transcript with PIWI slicer activity of cysosolic Ago3 is sufficient to trigger ~30-nt waves of non-overlapping primary piRNAs in the fly ovarian germline. The generated primary piRNAs are almost exclusively loaded into the nuclear PIWI protein, Piwi. In the fly ovarian somatic environment we find that an RNA fragment from the 5? end of a piRNA cluster is able to direct a heterologous sequence into primary processing. This piRNA trigger sequence (PTS) element drives generation of overlapping piRNAs from the transcript. Both mechanisms proceed with general 5?-3? directionality. We propose that the former pathway serves to link cytoplasmic silencing of a target to nuclear transcriptional repression, while the latter extracts silencing information from a wide variety of genomic sources including piRNA clusters, select protein coding and transposon transcripts. Total or immunoprecipitated small RNAs were purified from transfected BmN4 cells, Drosophila ovarian somatic cells (OSC) and from fly ovaries and high-throughput sequencing libraries were prepared. The mouse testicular RNAs were purified after ribozero treatment.

2015-07-09 | E-GEOD-69102 | biostudies-arrayexpress

Short duplex RNAs induce potent immunostimulation via Hoogsteen G-G base pairing-mediated dimerization

Project description:Here we describe a new class of immunostimulatory short duplex RNAs that potently induce production of type I interferon (IFN-I), and particularly IFN-β, in a wide range ofhuman cell types via end-to-end dimerization, direct binding to RIG-I, and activation of the RIG-I/IRF3 pathway. These RNAs require a minimum of 20 base pairs, lack any sequence or structural characteristics of known immunostimulatory RNAs, and instead require a unique conserved sequence motif (sense strand: 5’-C, antisense strand: 3’-GGG) that mediates the self-assembly of end-to-end RNA dimers by Hoogsteen G-G base-pairing. The presence of terminal hydroxyl or monophosphate groups, blunt or overhanging ends, or terminal RNA or DNA bases also did not affect their ability to induce IFN-I production. Immune stimulation mediated by these duplex RNAs results in broad spectrum inhibition of infections by many respiratory viruses with pandemic potential, including SARS-CoV-2, SARS-CoV, MERS-CoV, and influenza A, as well as the common cold virus HCoV-NL63 in cell lines and in human Lung Chips that mimic organlevel lung pathophysiology. These novel immunostimulatory motifs potentially could be harnessed to create broad-spectrum antiviral therapeutics, but they should be avoided when designing siRNAs to minimize immunological side effects.

2022-09-01 | PXD027838 | Pride

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