Non-catalytic function of PRC2 in the selective degradation of small RNAs during programmed genome elimination in Paramecium
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ABSTRACT:
PROVIDER: PRJEB59349 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR10817500.fastq.gz | Fastqsanger.gz | |||
| ERR10817501.fastq.gz | Fastqsanger.gz | |||
| ERR10817502.fastq.gz | Fastqsanger.gz | |||
| ERR10817503.fastq.gz | Fastqsanger.gz |
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Project description:Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics
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Project description:Ciliates undergo developmentally programmed genome elimination, in which small RNAs direct the removal of target DNA segments, including transposable elements. At each sexual generation, the development of the macronucleus (MAC) requires massive and reproducible elimination of a large proportion of the germline micronuclear (MIC) genome, leading to a highly streamlined somatic MAC genome. 25-nt long scnRNAs are produced from the entire germline MIC genome during meiosis, and this initial complex small RNA population is then transported to the maternal MAC, where selection of scnRNAs corresponding to germline (MIC)-specific sequences is thought to take place. Selected scnRNAs, loaded onto the PIWI protein Ptiwi09, guide the deposition of histone H3 post-translational modifications (H3K9me3 and H3K27me3) onto transposable elements in the developing macronucleus, ultimately triggering their specific elimination. How germline-specific MIC scnRNAs are selected remains to be determined. Here, we provide important mechanistic insights into the scnRNA selection pathway by identifying a Paramecium homolog of Gametocyte specific factor 1 (Gtsf1) as essential for the selective degradation of scnRNAs corresponding to retained somatic MAC sequences. Consistently, we also show that Gstf1 is exclusively localized in the maternal macronucleus, where scnRNA selection is presumed to occur, and associates with the scnRNA-binding protein Ptiwi09. Furthermore, Gtsf1 is necessary for DNA elimination and correct H3K9me3 and H3K27me3 localization in the new developing macronucleus, demonstrating that the scnRNA selection process is important for genome elimination. We propose that Gtsf1 is required for the coordinated degradation of Ptiwi09-scnRNA complexes that pair with nascent RNA transcribed from the maternal MAC genome, similarly to the mechanism suggested for microRNA target-directed degradation in metazoans.
2024-10-17 | PXD045266 | Pride
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:Organisms invest significant effort into maintaining genome stability. However, in diverse groups of eukaryotes, portions or entire chromosomes are lost in early development or during sex determination, a process known as programmed DNA elimination. Little is known about how different segments of the genome are reproducibly retained and discarded during programmed DNA elimination. We tested the hypothesis that selective retention is mediated by regulation of centromere-mediated association of chromosome segments with the mitotic spindle. We report that on the holocentric chromosomes of the nematode Ascaris, the core centromeric histone CENP-A is localized differently in cells undergoing DNA elimination from those undergoing germline mitosis. Prior to DNA elimination, CENP-A is significantly reduced in chromosome regions that will be lost. CENP-A reduction in eliminated genomic regions leads to the absence of kinetochores and microtubule attachment sites necessary for chromosome segregation, and thus the loss of these DNA regions during Ascaris programmed DNA elimination. Our results show that holocentric chromosome organization in Ascaris is regulated and that changes in CENP-A deposition specify which portions of chromosomes will be eliminated during programmed DNA elimination. A total of 62 samples are analyzed. These include: (1). CENP-A ChIP-seq on 12 developmental stages with input and replicates (12 x 2 x 2 samples); (2). CENP-C ChIP-seq on 3 developmental stages with input and replicates (total 8 samples); and (3). Histone marks ChIP-seq with 6 samples
2016-07-15 | E-GEOD-76914 | biostudies-arrayexpress
Project description:Signal amplification of the initial small RNA trigger is important to ensure the silencing of repetitive transposable elements (TEs). Curiously, secondary small RNA biogenesis occurs by various mechanisms that are coupled with distinct steps of TE silencing in different eukaryotes, such as nucleolytic cleavage of TE transcripts, recruitment of RNA-dependent RNA polymerase, and heterochromatin-directed transcription. How such a variety of small RNA amplification mechanisms has evolved has not been thoroughly elucidated to date. Ciliated protozoa perform small RNA-directed programmed DNA elimination of thousands of TE-related internal eliminated sequences (IESs) in the newly developed somatic nucleus. In the ciliate Paramecium, secondary small RNAs are produced after primary small RNAs induce the excision of IESs. To examine whether such post-excision production of secondary small RNAs is conserved, we investigate the causality between the excision of IESs and the biogenesis of secondary small RNAs in another ciliate, Tetrahymena. We show that secondary small RNAs accumulate at least a few hours before their derived IESs are excised and that DNA excision is dispensable for their biogenesis in this ciliate. Therefore, unlike the situation in Paramecium, small RNA amplification occurs prior to IES excision in Tetrahymena. This study reveals remarkable mechanistic diversity of secondary small RNA biogenesis mechanisms, even among ciliates showing similar DNA elimination processes, and thus raises the possibility that the evolution of TE-targeting small RNA amplification can be traced by investigating the DNA elimination mechanisms of ciliates.
2019-06-30 | GSE125297 | GEO
Project description:To study the role of structural maintenance of chromosome (SMC)4-1 and SMC4-2 during programmed genome rearrangement in Paramecium tetraurelia. Paramecium SMC4-1 and SMC4-2 was tagged with 3 FLAG and HA at its C-terminal separately. The recombinant plasmid was microinjected into macronuclear and used for co-immunoprecipitation and Mass spectrometry studies to identify interacting proteins of SMC4-1 and SMC4-2 that indicates the different functions between Paramecium SMC4s.
2023-12-05 | PXD041826 | Pride
Project description:Polycomb Repressive Complex 2 (PRC2) maintains transcriptionally silent genes in a repressed state via deposition of histone H3 K27 trimethyl (me3) marks. PRC2 has also been implicated in silencing transposable elements (TEs) yet how PRC2 is targeted to TEs remains unclear. To address this question, we performed tandem affinity purification combined with mass spectrometry and identified proteins that physically interact with the Paramecium Enhancer-of-zeste Ezl1 enzyme, which catalyzes H3K9me3 and H3K27me3 deposition at TEs. We show that the Paramecium PRC2 core complex comprises four subunits, each required in vivo for catalytic activity. We also identify PRC2 cofactors, including the RNA interference (RNAi) effector Ptiwi09, which are necessary to target H3K9me3 and H3K27me3 to TEs. We find that the physical interaction between PRC2 and the RNAi pathway is mediated by a RING finger protein and that small RNA recruitment of PRC2 to TEs is analogous to the small RNA recruitment of H3K9 methylation SU(VAR)3-9 enzymes.
2022-04-06 | PXD031335 | Pride
Project description:Domesticated PiggyBac transposases together carry out programmed DNA elimination in Paramecium
| PRJEB24171 | ENA
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.
2010-07-07 | GSE17998 | GEO
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.
2010-07-07 | GSE17997 | GEO