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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome analysis upon TFIIS4 silencing during autogamy time course

ABSTRACT: 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.

ORGANISM(S): Paramecium tetraurelia

SUBMITTER: Olivier ARNAIZ

PROVIDER: E-GEOD-64682 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome analysis upon TFIIS4 silencing during autogamy time course

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

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Project description:In the ciliate Paramecium tetraurelia, autogamy is a self-fertilization process, during which the zygotic nucleus results from the fusion of two identical gametic nuclei. This phenomenon occurs in response to starvation. It starts with meiosis of the germline nuclei (micronuclei or MIC) and fragmentation of the parental somatic nucleus (macronucleus or MAC). This is followed by mitotic division of one haploid nucleus issued from meiosis to yield two identical gametic nuclei, then karyogamy takes place, followed by mitosis of zygotic nucleus and differentiation of new MICs and MACs from the resulting copies of the zygotic nucleus. Within the developing new MACs, developmentally programmed DNA amplification and extensive genome rearrangements (precise excision of short non coding Internal Eliminated Sequences and chromosome fragmentation associated with the imprecise elimination of repetitive DNA) give rise to the highly polyploid somatic genome. To gain further insight into the complex regulation of these successive steps, we used whole genome microarrays to study the different gene networks that become activated throughout autogamy. Total RNA was extracted before the begining of autogamy (reference sample) and at 3 different time points during the process of autogamy.

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Project description:In the ciliate Paramecium tetraurelia, autogamy is a self-fertilization process, during which the zygotic nucleus results from the fusion of two identical gametic nuclei. This phenomenon occurs in response to starvation. It starts with meiosis of the germline nuclei (micronuclei or MIC) and fragmentation of the parental somatic nucleus (macronucleus or MAC). This is followed by mitotic division of one haploid nucleus issued from meiosis to yield two identical gametic nuclei, then karyogamy takes place, followed by mitosis of zygotic nucleus and differentiation of new MICs and MACs from the resulting copies of the zygotic nucleus. Within the developing new MACs, developmentally programmed DNA amplification and extensive genome rearrangements (precise excision of short non coding Internal Eliminated Sequences and chromosome fragmentation associated with the imprecise elimination of repetitive DNA) give rise to the highly polyploid somatic genome. To gain further insight into the complex regulation of these successive steps, we used whole genome microarrays to study the different gene networks that become activated throughout autogamy. Total RNA was extracted before the begining of autogamy (reference sample) and at 5 different time points during the process of autogamy. There are two biological replicates for each point.

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2010-07-07 | E-GEOD-17998 | biostudies-arrayexpress

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