Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide analysis of replication initiation in Tetrahymena

ABSTRACT: We mapped Tetrahymena macronuclear replication origins on a genome-wide scale using Okazaki fragments sequencing (OK-seq). OK-seq permits a high-resolution, quantitative analysis of replication fork initiation on a genome-wide scale that is dependent on the depth of coverage within a population of molecules. Replication initiation sites of the TXR1 (Histone H3 K27 monomethyltranferase) deletion strain were also studied compare to wild type using OK-seq.

ORGANISM(S): Tetrahymena thermophila

PROVIDER: GSE210487 | GEO | 2025/07/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide analysis of replication initiation in a TXR1 (Histone H3 K27 monomethyltranferase) overexpression strain in Tetrahymena

Project description:We mapped Tetrahymena macronuclear replication origins in TXR1 overexpression strain on a genome-wide scale using Okazaki fragments sequencing (OK-seq). Replication initiation sites of TXR1 overexpression strain followig cadmium induction of MMT1 promoter driven-TXR1 were studied compare to the uninduced TXR1 overexpression strain without cadmium using OK-seq.

2025-07-31 | GSE210493 | GEO

Tetrahymena thermophila SB210

Project description:Tetrahymena thermophila SB210 macronuclear genome sequencing

| PRJNA12564 | ENA

Biased transcription and selective degradation of small RNAs shape the pattern of DNA elimination in Tetrahymena

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

OKseqHMM: a genome-wide replication fork directionality analysis toolkit

Project description:During each cell division, tens of thousands of DNA replication origins are coordinately activated to ensure the complete duplication of the entire human genome. However, the progression of replication forks can be challenged by numerous factors. One such factor is transcription-replication conflict (TRC), which can either be co-directional or head-on and the latter has been revealed as more dangerous for genome integrity. In order to study the direction of replication fork movement and TRC, we developed a bioinformatics tool, called OKseqHMM, to direct measure the replication fork directionality (RFD) as well as replication initiation and termination, along human genome obtained by sequencing of Okazaki fragments (OK-Seq) and related techniques. We have gathered and analyzed OK-seq data from a large number of organisms including yeast, mouse and human, to generate high-quality RFD profiles and determine initiation zones and termination zones by using Hidden Markov Model (HMM) algorithm (all tools and data are available at https://github.com/CL-CHEN-Lab/OK-Seq). In addition, we have extended our analysis to data obtained by related techniques, such as eSPAN and TrAEL-seq, which also contain RFD information. Our works, therefore, provide an important tool and resource for the community to further study TRC and genome instability, in a wide range of cell line models and growth conditions, which is of prime importance for human health.

2022-12-31 | GSE193547 | GEO

Genome-wide analysis of replication initiation in Tetrahymena

Project description:Genome-wide analysis of replication initiation in Tetrahymena

| PRJNA865777 | ENA

Transcriptome analysis of the binucleate ciliate Tetrahymena thermophila cells after mating and re-feeding.

Project description:During macronuclear development the five germline chromosomes undergo massive rearrangement, and the entire epigenome is remodeled from an obligate heterochromatic to obligate euchromatic state. The ~180 unique macronuclear chromosomes undergo two development waves of endo-reduplication to achieve a final copy number of ~45C, while the 21 kb rDNA minichromosome is amplified to ~9000C. The first period (endoreplication phase I) involves two rounds of DNA replication and generates an 8 C macronucleus (6–18 h after mating). Upon re-feeding, a second re-replication period (endoreplication phase II) is initiated generating a macronuclear DNA content of 32–64 C. This study focused on RNA expression profile of cell in endoreplication phase II.

2025-07-29 | GSE210103 | GEO

Genome-wide analysis of replication initiation in a TXR1 (Histone H3 K27 monomethyltranferase) overexpression strain in Tetrahymena

Project description:Genome-wide analysis of replication initiation in a TXR1 (Histone H3 K27 monomethyltranferase) overexpression strain in Tetrahymena

| PRJNA865780 | ENA

Multilevel interrogation of H3.3 dynamics reveals a primordial role in transcription regulation in Tetrahymena [RNA-seq]

Project description:Through epigenetic modifications and selective incorporation of histone variants into chromatin, eukaryotic cells can adjust their transcriptional profile in response to molecular needs. We used the nuclear dimorphic ciliate protozoan, Tetrahymena thermophila, as a model system to investigate the dynamics of H3 variant function. H3.3 is the ancestral H3 variant with key roles in regulating chromatin states and transcription. Functional proteomics and immunofluorescence analyses of H3.1 and H3.3 revealed a conserved role for Nrp1 and Asf1 histone chaperones in nuclear influx of histones. Cac2 and Hir1 have distinct localization patterns during different stages of the Tetrahymena life cycle and suggests that both Cac2 and Hir1 might be dispensable for the replication-dependent and -independent deposition of H3.1 and H3.3, respectively. ChIP-seq experiments in growing Tetrahymena show H3.3 enrichment over promoters, genes bodies, and transcription termination sites of highly transcribed genes. H3.3 knockout followed by RNA-seq reveals large-scale transcriptional alterations in functionally important genes. Our results provide an evolutionary perspective on H3.3’s conserved role in maintaining the transcriptional landscape of cells and on the emergence of specialized chromatin assembly pathways.

2023-04-03 | GSE210902 | GEO

Multilevel interrogation of H3.3 dynamics reveals a primordial role in transcription regulation in Tetrahymena [ChIP-seq]

2023-04-03 | GSE210901 | GEO

Biased transcription and selective degradation of small RNAs shape the pattern of DNA elimination in Tetrahymena

2012-06-21 | GSE38768 | GEO