Ontology highlight
ABSTRACT:
PROVIDER: PRJNA789403 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17246000.fastq.gz | Fastqsanger.gz | |||
| SRR17246001.fastq.gz | Fastqsanger.gz | |||
| SRR17246002.fastq.gz | Fastqsanger.gz | |||
| SRR17246003.fastq.gz | Fastqsanger.gz | |||
| SRR17246004.fastq.gz | Fastqsanger.gz |
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Project description:The unicellular eukaryote Paramecium tetraurelia contains functionally distinct nuclei: germline micronuclei (MICs) and a somatic macronucleus (MAC). During sexual reproduction, the MIC genome is reorganized into a new MAC genome and the old MAC is lost. Almost 45,000 unique Internal Eliminated Sequences (IESs) located throughout the genome require precise excision to guarantee a functional new MAC genome. Here, we characterize a pair of paralogous PHD finger proteins involved in DNA elimination. DevPF1, the early-expressed paralog, is present in only some of the gametic and post-zygotic nuclei during meiosis. Both DevPF1 and DevPF2 localize in the new developing MACs, where IESs excision occurs. In DevPF2 knockdown (KD), long IESs are preferentially retained and late-expressed small RNAs decrease; no length preference for retained IESs was observed in DevPF1-KD and development-specific small RNAs were abolished. The expression of at least two genes from the new MAC seems to be influenced by DevPF1- and DevPF2-KD. Thus, both PHD fingers are crucial for new MAC genome development, with distinct functionalities, potentially via regulation of non-coding and coding transcription in the MICs and new MACs.
2024-08-30 | PXD046704 | Pride
Project description:Differential transcriptome of Paramecium tetraurelia strain 51 undergoing RNAi by feeding against ICL7a (as a control) and RDR3 for nine days.
2014-07-15 | GSE59390 | GEO
Project description:At each sexual cycle, during development of the somatic macronucleus (MAC) from the germline micronucleus (MIC), the genome of the ciliate Paramecium tetraurelia is massively rearranged through the reproducible elimination of germline-specific sequences. It has been reported previously that targeting of these sequences is mediated by non-protein-coding RNAs including different classes of small RNAs and longer non-coding transcripts. Using RNA interference, we showed that TFIIS4 gene encoding development-specific TFIIS elongation factor is essential for the formation of a functional somatic genome. We demonstrated that genome rearrangements taking place during MAC development were inhibited in TFIIS4-depleted cells, which led to high lethality in the sexual progeny. The role of TFIIS4 elongation factor in coding transcription at the genome-wide level was studied by performing a microarray hybridization experiment using RNA samples extracted during vegetative growth and at five time points during the progression of the sexual cycle (autogamy).
2015-06-12 | GSE64682 | GEO
Project description:The Spt4-Spt5 complex is conserved and essential RNA polymerase elongation factor. To investigate the role of the Spt4-Spt5 complex in non-coding transcription during development, we used the unicellular model Paramecium tetraurelia. In this organism harboring both germline (micronucleus - MIC) and somatic nuclei (macronucleus - MAC), massive transcription of the entire germline genome takes place during meiosis. This phenomenon starts a series of events mediated by different classes of non-coding RNAs that control developmentally programmed DNA elimination. We focused our study on Spt4, a small zinc-finger protein encoded in P. tetraurelia by two genes expressed constitutively and two genes expressed during meiosis. SPT4 genes are not essential in vegetative growth, but they are indispensable for sexual reproduction, even though genes from both expression families show functional redundancy. As we were mostly interested in transcription of the germline genome in the MIC during meiosis, we decided to probe the composition of the Spt5-Spt4 complex characteristic to this nucleus. Experiments in which Spt4mB-3xFLAG was used as bait demonstrated its interaction with either Spt5m or Spt5v, which is consistent with the Spt4mB-GFP localization pattern. Interestingly, mass spectrometry revealed that Spt5m-3xFLAG (which is present only in the MIC at the analyzed stage) interacts either with the meiotic Spt4mB or with Spt4vA. Silencing of the SPT4 genes resulted in the absence of double-stranded ncRNAs and reduced levels of scnRNAs – 25 nt-long sRNAs produced from these double-stranded precursors in the germline nucleus. Moreover, we observed that the presence of a germline-specific Spt4-Spt5m complex is necessary for transfer of the scnRNA-binding PIWI protein between the germline and somatic nucleus. Our study establishes that Spt4, together with Spt5m, is essential for expression of the germline genome and necessary for developmental genome rearrangements.
2022-04-27 | PXD027748 | Pride
Project description:At each sexual cycle, during development of the somatic macronucleus (MAC) from the germline micronucleus (MIC), the genome of the ciliate Paramecium tetraurelia is massively rearranged through the reproducible elimination of germline-specific sequences. It has been reported previously that targeting of these sequences is mediated by non-protein-coding RNAs including different classes of small RNAs and longer non-coding transcripts. Using RNA interference, we showed that TFIIS4 gene encoding development-specific TFIIS elongation factor is essential for the formation of a functional somatic genome. We demonstrated that genome rearrangements taking place during MAC development were inhibited in TFIIS4-depleted cells, which led to high lethality in the sexual progeny. The role of TFIIS4 elongation factor in coding transcription at the genome-wide level was studied by performing a microarray hybridization experiment using RNA samples extracted during vegetative growth and at five time points during the progression of the sexual cycle (autogamy). Total RNA samples were extracted during vegetative growth and at five different time points of autogamy from mass cultures fed with bacteria producing dsRNA to induce TFIIS4 or ICL7a silencing. TFIIS4 gene encodes TFIIS elongation factor and is strongly induced during autogamy, a self-fertilization process. RNAi against TFIIS4 leads to strong lethality in post-autogamous progeny. ICL7a is a non-essential gene; the loss of function of this gene by with dsRNA feeding results in mutant phenotypes: absence of intraciliary lattice and defect in calcium-induced cell contractility.
2015-06-12 | E-GEOD-64682 | biostudies-arrayexpress
Project description:To study the role of chromatin remodeler during programmed genome reorganization in Paramecium tetraurelia. Paramecium ISWI1 was tagged with 3 FLAG and HA at its C-terminal. The recombinant plasmid was transformed into Paramecium and used for co-immunoprecipitation and Mass spectrometry studies to identify novel interacting partners of Paramecium ISWI1 protein that modulates the elimination of transposable elements.
2023-03-11 | PXD027206 | Pride
Project description:P. tetraurelia, like all ciliates, is a unicellular eukaryote processing two different kinds of nuclei, germline micronuclei (mic) and somatic macronucleus (mac). The diploid micronuclei undergo meiosis during sexual events to transmit the germline genome to the next generation. The highly polyploid mac (~800 n) is responsible for transcription during the life cycle but is lost after fertilisation; the new mic and mac develop from mitotic copies of the zygotic nucleus. During development of the new mac, the germline genome is amplified from 2n to ~800n and is extensively rearranged by two distinct kinds of DNA elimination. The micronuclear 50 to 60 Chromosomes are fragmented into ~200 shorter molecules caped by de novo telomere addition as a result of the imprecise elimination transposons and minisatellites. Moreover, approximately 60,000 short, single-copy elements called internal eliminated sequences (IESs) are precisely removed from coding and non-coding sequences. It was shown that the rearrangements in the developing mac appear to reproduce the rearrangements observed in the old mac, implying the existence of homology dependent cross talk between germline and somatic genomes during sexual event. To understand the molecular mechanisms and the genetic control involved in genome rearrangements, we studied the evolution of the transcriptome during Paramecium tetraurelia sexual reproduction.
2010-07-07 | GSE18002 | GEO
Project description:Interventions: Case series:Nil
Primary outcome(s): intestinal microecological disorders;blood non-coding RNAs and immune status
Study Design: Randomized parallel controlled trial
| 2681498 | ecrin-mdr-crc