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12 results for “Paramecium tetraurelia”
Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics
<p>With its nuclear dualism, the ciliate <em>Paramecium</em> constitutes an original model to study how host genomes cope with transposable elements (TEs). <em>P. tetraurelia</em> harbors two germline micronuclei (MIC) and a polyploid somatic macronucleus (MAC) that develops from the MIC at each sexual cycle. Throughout evolution, the MIC genome has been continuously colonized by TEs and related sequences that are removed from the somatic genome during MAC development. Whereas TE elimination is generally imprecise, excision of ~45000 TE-derived Internal Eliminated Sequences (IESs) is precise, allowing for functional gene assembly. Programmed DNA elimination is concomitant with genome amplification. It is guided by non-coding RNAs and repressive chromatin marks. A subset of IESs are excised independently of this epigenetic control, raising the question of how they are targeted for elimination. To gain insight into the determinants of IES excision, we determined the developmental timing of DNA elimination genome-wide by combining fluorescence-assisted nuclear sorting with next-generation sequencing. Essentially all IESs are excised within one endoduplication round only (32C to 64C), while TEs are eliminated at a later stage. We show that time, rather than replication, controls the progression of DNA elimination. Further analyses defined four IES classes according to excision timing and revealed that the earliest excised IESs tend to be independent of epigenetic factors, display strong sequence signals at their ends and originate from the most ancient integration events. We conclude that old IESs have been optimized during evolution for early and accurate excision, by acquiring stronger sequence determinants and escaping epigenetic control.</p>
A development-specific POLX essential for programmed genome rearrangement in Paramecium tetraurelia
<p><span>During the sexual cycle, programmed genome rearrangement (PGR) in <em>Paramecium tetraurelia</em> involves the non-homologous end joining (NHEJ) DNA repair pathway to eliminate specific germinal Internal Eliminated Sequences (IESs) from the newly developing somatic nucleus. In addition to the core NHEJ factors Ku70/80 and Xrcc4/Lig4, additional enzymes are required to process the 4-base 5’-protruding ends generated following DNA cleavage at IES boundaries, prior to their ligation. Here, we report that PolX (a,b,c,d), four <em>P. tetraurelia</em> distant orthologs of the human Pol</span><span>l</span><span> DNA polymerase, are involved in repair of IES excision junctions. During rearrangements, PolX-depleted cells accumulate genome-wide errors, such as unrepaired double-strand breaks, 1-nucleotide deletions and IES retention. Although all PolX paralogs can process DNA ends, two of them (PolXa&b) are induced during PGR and have acquired tight nuclear anchoring properties through their N-terminal region, which contains a predicted BRCT domain. Finally, we show that PolXa accumulates in nuclear foci together with other NHEJ proteins and the Dicer-like enzyme Dcl5, which is involved in the biogenesis of IES-specific small RNAs. We propose</span><span><span> </span></span><span>that these “DNA repair foci” correspond to the sites where IES concatemers, a by-product of IES excision, are ligated together to produce the precursors of iesRNAs.</span></p>
Paramecium tetraurelia trichocyst exocytosis recovery
GEO Series GSE17930. Paramecium tetraurelia. 12 samples. Type: Expression profiling by genome tiling array.
Paramecium tetraurelia autogamy series 2 (ND7-silenced and control cells)
GEO Series GSE18002. Paramecium tetraurelia. 11 samples. Type: Expression profiling by genome tiling array.
Paramecium tetraurelia autogamy series 3
GEO Series GSE17998. Paramecium tetraurelia. 6 samples. Type: Expression profiling by genome tiling array.
Paramecium tetraurelia autogamy series 1
GEO Series GSE17996. Paramecium tetraurelia. 12 samples. Type: Expression profiling by genome tiling array.
Paramecium tetraurelia autogamy series 4
GEO Series GSE17997. Paramecium tetraurelia. 4 samples. Type: Expression profiling by genome tiling array.
Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia
GEO Series GSE32256. Paramecium tetraurelia. 58 samples. Type: Expression profiling by array; Expression profiling by genome tiling array.
Paramecium tetraurelia reciliation (log phase)
GEO Series GSE12620. Paramecium tetraurelia. 8 samples. Type: Expression profiling by array.
Transcriptome analysis, Paramecium tetraurelia ICL (as a control) vs. Rdr3 silencing
GEO Series GSE59390. Paramecium tetraurelia. 6 samples. Type: Expression profiling by array.
Screening of the Paramecium tetraurelia megabase chromosome for autogamy-specific genes
GEO Series GSE12988. Paramecium tetraurelia. 12 samples. Type: Expression profiling by array.
Paramecium tetraurelia reciliation (stationary phase)
GEO Series GSE14631. Paramecium tetraurelia. 5 samples. Type: Expression profiling by array.
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.