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

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

PROVIDER: PRJNA868292 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21002352_1.fastq.gz	Fastqsanger.gz
	SRR21002352_2.fastq.gz	Fastqsanger.gz
	SRR21002353_1.fastq.gz	Fastqsanger.gz
	SRR21002353_2.fastq.gz	Fastqsanger.gz
	SRR21002354_1.fastq.gz	Fastqsanger.gz

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Multilevel interrogation of H3.3 dynamics reveals a primordial role in transcription regulation in Tetrahymena.

Project description:Multilevel interrogation of H3.3 dynamics reveals a primordial role in transcription regulation in Tetrahymena.

| PRJNA868288 | ENA

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

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

| PRJNA868291 | 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

Multilevel interrogation of H3.3 reveals a primordial role in transcription regulation.

Project description:Eukaryotic cells can rapidly adjust their transcriptional profile in response to molecular needs. Such dynamic regulation is, in part, achieved through epigenetic modifications and selective incorporation of histone variants into chromatin. H3.3 is the ancestral H3 variant with key roles in regulating chromatin states and transcription. Although H3.3 has been well studied in metazoans, information regarding the assembly of H3.3 onto chromatin and its possible role in transcription regulation remain poorly documented outside of Opisthokonts. We used the nuclear dimorphic ciliate protozoan, Tetrahymena thermophila, to investigate the dynamics of H3 variant function in evolutionarily divergent eukaryotes. Functional proteomics and immunofluorescence analyses of H3.1 and H3.3 revealed a highly conserved role for Nrp1 and Asf1 histone chaperones in nuclear influx of histones. Cac2, a putative subunit of H3.1 deposition complex CAF1, is not required for growth, whereas the expression of the putative ortholog of the H3.3-specific chaperone Hir1 is essential in Tetrahymena. Our results indicate that Cac2 and Hir1 have distinct localization patterns during different stages of the Tetrahymena life cycle and suggest that Cac2 might be dispensable for chromatin assembly. ChIP-seq experiments in growing Tetrahymena show H3.3 enrichment over the promoters, gene 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.

| S-EPMC10080907 | biostudies-literature

Multilevel interrogation of H3.3 dynamics reveals a primordial role in transcription regulation in Tetrahymena.

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-04-03 | GSE210903 | GEO

Nonsense-mediated mRNA decay in Tetrahymena is EJC independent and requires a protozoa-specific nuclease

Project description:Nonsense-mediated mRNA decay (NMD) is essential for removing premature termination codon (PTC)-containing transcripts from cells. Studying the NMD pathway in model organisms can help to elucidate the NMD mechanism of humans and improves our understanding of how this biologically important process has evolved. Protozoa are among the earliest branching eukaryotes. Their NMD mechanism is poorly understood and may be primordial. We demonstrate that highly conserved Upf proteins (Upf1a, Upf2, and Upf3) are involved in the NMD pathway of the ciliate, Tetrahymena thermophila. We further show that a novel protozoa-specific nuclease, Smg6L, is responsible for destroying many NMD-targeted transcripts. The transcriptome-wide identification and characterization of NMD-targeted transcripts in vegetative Tetrahymena cells showed that many have exon–exon junctions downstream of the termination codon. However, Tetrahymena homologs of exon junction complex (EJC) core components do not form a complex and are dispensable for NMD, suggesting that NMD is EJC independent in this early branching eukaryote.

2017-07-17 | GSE90899 | GEO

Tetrahymena thermophila

Project description:Tetrahymena thermophila

| PRJNA11958 | ENA

Tetrahymena

Project description:Nucleotide sequences of Tetrahymena species

| PRJEB23142 | ENA

Profiling of H3.3

Project description:Histone variants can effect nucleosome stability or affect histone of DNA modifications. H3.3 is a major H3 histone variant that is incorporated into chromatin outside of S-phase in various eukaryotes. In animals, H3.3 is associated with active transcription and possibly maintenance of transcriptional memory. Plant H3.3, which evolved independently of animal H3.3, is much less well understood. We performed ChIP-chip using chromatin from rosette leaves of 35S:H3.3-YFP plants.

2014-03-10 | E-MTAB-1685 | biostudies-arrayexpress

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