Tetrahymena thermophila
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ABSTRACT:
PROVIDER: PRJNA261680 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Analysis of Early-scnRNAs of Tetrahymena
| PRJNA317177 | ENA
Project description:Analyses of Early- and Late-scnRNAs of Tetrahymena
| PRJNA282767 | ENA
Project description:Analyses of Early- and Late-scnRNAs of Tetrahymena
| PRJNA325439 | ENA
Project description:The ciliated protozoan Tetrahymena undergoes extensive programmed DNA elimination when the germline micronucleus produces the new macronucleus during sexual reproduction. DNA elimination is epigenetically controlled by DNA sequences of the parental macronuclear genome, and this epigenetic regulation is mediated by small RNAs (scnRNAs) of approximately 28-30 nucleotides that are produced and function by an RNAi-related mechanism. Here, we examine scnRNA production and turnover by deep sequencing. scnRNAs are produced exclusively from the micronucleus and non-homogeneously from a variety of chromosomal locations. scnRNAs are preferentially derived from the eliminated sequences, and this preference is mainly determined at the level of transcription. Despite this bias, a significant fraction of scnRNAs is also derived from the macronuclear-destined sequences, and these scnRNAs are degraded during the course of sexual reproduction. These results indicate that the pattern of DNA elimination in the new macronucleus is shaped by the biased transcription in the micronucleus and by the selective degradation of scnRNAs in the parental macronucleus. GRO-Seq and Examination of siRNAs in wild-type,nullisomic 4, EMA1 KO, and TWI1 KO Tetrahymena cells
2012-06-21 | E-GEOD-38768 | biostudies-arrayexpress
Project description:Distinct classes of small RNAs are often selectively sorted to different Argonaute proteins. Various properties of small RNAs, such as length, terminal nucleotide, thermodynamic asymmetry and duplex mismatches, can impact sorting in different RNA silencing pathways in diverse eukaryotes. The developmentally regulated ~26-32 nt siRNAs, which are involved in programmed DNA elimination in Tetrahymena, show a strong bias for uracil at the 5' end. In this study, we analyzed loaded and unloaded populations of ~26-32 nt siRNAs by deep RNA sequencing. We show that the production process is the main determinant of size, whereas the 5' uracil bias is attributed not only to the process of loading siRNAs into the Argonaute protein Twi1p but also significantly to the initial processing of the siRNAs. We also show that both the loaded and the unloaded ~26-32 nt siRNAs have a strong bias for adenine as the 3rd base from the 3' terminus, suggesting that most of these siRNAs are direct Dicer products and little post-processing amplification of this class of siRNAs occurs. Further, we demonstrate that the siRNA-loading process in vivo can be deduced from the fraction of siRNAs with uracil as the first base. These findings provide biochemical bases for the attributes of ~26-32 nt siRNAs, which should help improve our understanding of their production and turnover in vivo. Examination of siRNA populations in wild-type and TWI1 KO Tetrahymena cells
2012-10-01 | E-GEOD-37696 | biostudies-arrayexpress
Project description:Analyses of scnRNAs in the mutatnts defective in an RNAi-heterochromatin positive feedback loop in Tetrahymena [scnRNA]
| PRJNA343220 | ENA
Project description:The ciliated protozoan Tetrahymena undergoes extensive programmed DNA elimination when the germline micronucleus produces the new macronucleus during sexual reproduction. DNA elimination is epigenetically controlled by DNA sequences of the parental macronuclear genome, and this epigenetic regulation is mediated by small RNAs (scnRNAs) of approximately 28-30 nucleotides that are produced and function by an RNAi-related mechanism. Here, we examine scnRNA production and turnover by deep sequencing. scnRNAs are produced exclusively from the micronucleus and non-homogeneously from a variety of chromosomal locations. scnRNAs are preferentially derived from the eliminated sequences, and this preference is mainly determined at the level of transcription. Despite this bias, a significant fraction of scnRNAs is also derived from the macronuclear-destined sequences, and these scnRNAs are degraded during the course of sexual reproduction. These results indicate that the pattern of DNA elimination in the new macronucleus is shaped by the biased transcription in the micronucleus and by the selective degradation of scnRNAs in the parental macronucleus.
2012-06-21 | GSE38768 | GEO
Project description:12 genome-wide microarrays to investigate the Tetrahymena thermophila gene expression changes in TRX1 and EZL2 gene knockout and hydroxyurea (HU) treatment conditions. For the TRR1 knockout (KO) condition, wild type (WT427) cells and TRX1 KO cells were cultured using 1XSPP, 30 degrees, 100 rpm shaking, until 350,000 cells/ml. For the EZL21 knockout (KO) condition, wild type (WT427) cells and EZL2 KO cells were cultured using 1XSPP, 30 degrees, 100 rpm shaking, until 350,000 cells/ml. For the HU treatment condition, HU was used to treat the WT427 cells for 48 hours, setting wild type (WT427) as the control; cells were cultured using 1XSPP, 30 degrees, 100 rpm shaking. Each sample has two biological replicates.
2013-09-04 | E-GEOD-44990 | biostudies-arrayexpress