Tetrahymena thermophila CU428
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA312451 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3176650.fastq.gz | Fastqsanger.gz | |||
| SRR3176651_1.fastq.gz | Fastqsanger.gz | |||
| SRR3176651_2.fastq.gz | Fastqsanger.gz | |||
| SRR3176652.fastq.gz | Fastqsanger.gz | |||
| SRR3176653.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Somatic macronucleus (MAC) and germline micronucleus (MIC) of Tetrahymena thermophila are different in chromosome numbers, sizes, functions and cohesin complex locations. Loss of cohesin complex resulted in genome-wide disappearance of topologically associating domains (TADs) and chromatin loops in mammalian cells. However, the higher-level chromatin organization in Tetrahymena thermophila which contains both cohesin free MAC and cohesin located MIC are largely unknown. Here, using the Hi-C and HiChIP methods, we reveal that, these two nuclei possess distinct three-dimensional genome structures. In the MAC, each chromosome occupies its own territory and there are no chromatin compartmentalization or chromatin domains. The chromatin loops in MAC are mainly related to chromatin structures rather than transcriptional regulation. The MIC also without chromatin compartmentalization, but with chromatin domains and the domain boundaries are consistent with chromatin breakage sites (CBSs) which indicates that each MIC chromatin domain developed to one MAC chromosome during conjugation. Besides, we found the MIC exhibits unique intra-arm and inter-chromosome interactions at the crescent stage of conjugation, when the MIC undergoes meiotic recombination.
2020-10-01 | GSE125628 | GEO
Project description:In this study, we have employed MNase-Seq to reveal distinct nucleosome distribution patterns in morphologically and functionally differentiated MIC and MAC from asexually dividing Tetrahymena cells.
2016-09-14 | GSE77660 | GEO
Project description:The somatic macronucleus (MAC) and germline micronucleus (MIC) of Tetrahymena thermophila differ in chromosome numbers, sizes, functions, transcriptional activities, and cohesin complex location. However, the higher-order chromatin organization in T. thermophila which contains both cohesin free MAC and cohesin located MIC are largely unknown. Here, we examined the higher-order chromatin organization in the two distinct nuclei of T. thermophila using the Hi-C and HiChIP. Interestingly, we found that the crescent MIC possess specific chromosome interaction pattern. All the telomeres or centromeres on the five MIC chromosomes clustering together, respectively, which could help to identify the midpoints of centromeres in the MIC. We found the transcriptionally active MAC chromosomes lack A/B compartments, topologically associating domains (TADs) and chromatin loops. The transcriptionally inert MIC chromosomes also without A/B compartments and chromatin loops, but have TAD-like structures. The boundaries of the TAD-like structures in the MIC were highly consistent with the chromatin breakage sequence (CBS) sites, suggesting that each TAD-like structure of the MIC chromosomes develops into one MAC chromosome during MAC development during conjugation. Overall, we revealed the higher-order chromatin organization in the T. thermophila and found the chromatin structures might play important roles during the development of the MAC chromosomes.
2020-02-21 | GSE140429 | GEO
Project description:ChIP-Seq analysis of H3K4me2 and Pol II in Tetrahymena
| PRJNA311167 | ENA
Project description:Meiosis occurs in all sexually reproducing unicellular and multicellular eukaryotes. Bouquet formation is indispensible for homologous pairing or recombination during meiotic prophase I, but the regulatory mechanism of this process remain largely unknown. Cyclins regulate the precise meiosis progression by activating cyclin-dependent kinases. We therefore investigated the functional contribution of cyclin Cyc2p during bouquet (named crescent in Tetrahymena) formation in Tetrahymena thermophila. As a conjugation specific gene, CYC2 expression is significantly upregulated at 2-4 h after the initiation of conjugation and Cyc2p mainly localized in cytoplasm as well as weakly in the meiotic micronucleus (Mic). CYC2 knockout mutants failed to form elongated crescent structure and aborted meiotic development. Mic DNA double-strand breakage (DSB) decreased in ΔCYC2 cells as shown by γ-H2A.X staining, consistent with the finding that expression level of SPO11, DMC1, and RAD51 decreased in ΔCYC2 cells. However, ΔCYC2 cells failed to form crescent structure when artificial DSBs were induced, indicating that the inability to enter crescent phase was not completely due to the lack of DSBs. The localization of tubulin showed that impaired structure of nuclei and nuclear membrane may contribute to the blocked Mic elongation. This is further supported by the observation that expression levels of two microtubule associated kinesin genes, KIN11 and KIN141, were significantly downregulated in ΔCYC2 cells. Interestingly, scnRNA accumulation seemed intact in ΔCYC2 cells whereas the intensity of the heterochromatin marker H3K23me3 was abnormally increased. Together, these results showed that cyclin Cyc2p is required for micronuclear meiosis by controlling meiotic prophase chromosome breakage and the microtubule movement of nuclei in Tetrahymena.
2018-12-14 | GSE108064 | GEO
Project description:A conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream of transcription start sites (TSS). Recent studies indicate that trans-acting factors establish this stereotypical array. Here, we present the first genome-wide in vitro and in vivo nucleosome maps for the ciliate Tetrahymena thermophila. In contrast with previous studies in yeast, we find that the stereotypical nucleosome array is preserved in the in vitro reconstituted map, which is governed only by the DNA sequence preferences of nucleosomes. Remarkably, this average in vitro pattern arises from subsets of nucleosomes, rather than the whole array, being present in individual Tetrahymena genes. Variation in GC content contributes to the positioning of these sequence-directed nucleosomes, and affects codon usage and amino acid composition in genes. We propose that these ‘seed’ nucleosomes may aid the AT-rich Tetrahymena genome – which is intrinsically unfavorable for nucleosome formation – in establishing nucleosome arrays in vivo in concert with trans-acting factors, while minimizing changes to the coding sequences they are embedded within. All data are from the macronuclear genome. Datasets: 1) Log-phase cells, fixed chromatin, light MNase digest; 2) Log-phase cells, native chromatin, heavy MNase digest; 3) Starved cells, fixed chromatin, light MNase digest; 4) Starved cells, native chromatin, heavy MNase digest; 5) in vitro reconstituted chromatin, 50ul reaction, 4:10 histone:DNA ratio, light MNase digest; 6) in vitro reconstituted chromatin, 50ul reaction, 7:10 histone:DNA ratio, light MNase digest; 7) in vitro reconstituted chromatin, 150ul reaction, 4:10 histone:DNA ratio, light MNase digest; 8) in vitro reconstituted chromatin, 150ul reaction, 4:10 histone:DNA ratio, heavy MNase digest; Control dataset: 9): MNase-digested naked DNA
2015-07-30 | E-GEOD-64061 | biostudies-arrayexpress
Project description:Tetrahymena thermophila strain:CU427/CU428 Genome sequencing
| PRJNA338999 | ENA
Project description:Tetrahymena thermophila Transcriptome Sequencing
| PRJNA177770 | ENA
Project description:As a prototypic ciliated protozoan, Tetrahymena thermophila harbors two functionally and physically distinct nuclei within a shared cytoplasm. During the vegetative phase of the life cycle, the S phases of the diploid germline micronucleus and polyploid somatic macronucleus are temporally offset. Here we report the first RNA-Seq analysis across the cell cycle of a binucleated ciliated protozoan. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.
2023-01-11 | GSE209619 | GEO
Project description:Tetrahymena thermophila strain:B2086 x Cu428 Raw sequence reads
| PRJNA481118 | ENA