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Zebrafish preserve preserve germline epigenetic memory globally but demethylate and amplify sex-linked rDNA during feminisation

ABSTRACT: Zebrafish preserve preserve germline epigenetic memory globally but demethylate and amplify sex-linked rDNA during feminisation

PROVIDER: PRJNA506038 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8207080.fastq.gz	Fastqsanger.gz
	SRR8207090.fastq.gz	Fastqsanger.gz
	SRR8207100.fastq.gz	Fastqsanger.gz
	SRR8207110.fastq.gz	Fastqsanger.gz
	SRR8207120.fastq.gz	Fastqsanger.gz

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Zebrafish preserve preserve germline epigenetic memory globally but demethylate and amplify sex-linked rDNA during feminisation

Project description:The germline is unique because it is the only cellular lineage capable of transferring genetic information from one generation to the next. Intergenerational transmission of epigenetic memory is also possible; however, in mammals this is largely prevented by extensive epigenetic erasure during germline definition from somatic precursors. We report that the ‘preformed’ germline of zebrafish, defined by inheritance of cellular components from the egg and not cellular reprogramming, shows consistently high levels of DNA methylation throughout development. This demonstrates epigenetic erasure is not a barrier to transgenerational epigenetic inheritance in zebrafish and likely other vertebrates with preformed germlines. Our analysis also uncovered female-specific germline amplification and demethylation of an 11.5-kb repeat region encoding 45S ribosomal RNA (fem-rDNA). The peak of fem-rDNA expansion coincided with the initial expansion of stage IB oocytes, the poly-nucleolar cell type responsible for zebrafish feminisation. Given that fem-rDNA overlaps with the only zebrafish locus identified thus far as sex-linked, we hypothesize fem-rDNA expansion is intrinsic to sex determination in this species.

2018-11-20 | GSE122695 | GEO

Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription

Project description:Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription

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Zebrafish preserve global germline DNA methylation while sex-linked rDNA is amplified and demethylated during feminisation.

Project description:The germline is the only cellular lineage capable of transferring genetic information from one generation to the next. Intergenerational transmission of epigenetic memory through the germline, in the form of DNA methylation, has been proposed; however, in mammals this is largely prevented by extensive epigenetic erasure during germline definition. Here we report that, unlike mammals, the continuously-defined 'preformed' germline of zebrafish does not undergo genome-wide erasure of DNA methylation during development. Our analysis also uncovers oocyte-specific germline amplification and demethylation of an 11.5-kb repeat region encoding 45S ribosomal RNA (fem-rDNA). The peak of fem-rDNA amplification coincides with the initial expansion of stage IB oocytes, the poly-nucleolar cell type responsible for zebrafish feminisation. Given that fem-rDNA overlaps with the only zebrafish locus identified thus far as sex-linked, we hypothesise fem-rDNA expansion could be intrinsic to sex determination in this species.

| S-EPMC6635516 | biostudies-literature

Nuclear release of eIF1 globally increases stringency of start codon selection to preserve mitotic arrest physiology

Project description:Regulated start codon selection has the potential to reshape the proteome through the differential production of uORFs, canonical proteins, and alternative translational isoforms. However, conditions under which start codon selection is altered remain poorly defined. Here, using transcriptome-wide translation initiation site profiling, we reveal a global increase in the stringency of start codon selection during mammalian mitosis. Low-efficiency initiation sites are preferentially repressed in mitosis, resulting in pervasive changes in the translation of thousands of start sites and their corresponding protein products. This increased stringency of start codon selection during mitosis results from increased associations between the 40S ribosome and the key regulator of start codon selection, eIF1. We find that increased eIF1-40S ribosome interactions during mitosis are mediated by the release of a nuclear pool of eIF1 upon nuclear envelope breakdown. Selectively depleting the nuclear pool of eIF1 eliminates the changes to translational stringency during mitosis, resulting in the altered synthesis of thousands of protein isoforms. In addition, preventing mitotic translational rewiring results in substantially increased cell death and decreased mitotic slippage in cells that experience a mitotic delay induced by anti-mitotic chemotherapeutics. Thus, cells globally control translation initiation stringency with critical roles during the mammalian cell cycle to preserve mitotic cell physiology.

2024-10-07 | PXD054183 | Pride

Nuclear release of eIF1 globally increases stringency of start codon selection to preserve mitotic arrest physiology

2025-05-07 | PXD054179 | Pride

Jump-seq: Capture and amplify 5hmC Sites Whole Genome-Wide

Project description:We developed an efficient and precise method, which we name as Jump-seq, to capture and amplify 5hmC signal whole genome-wide, bridge the gap between base resolution (TAB-seq) and economic cost (hmC-seal).

2019-03-07 | GSE127906 | GEO

Vreteno, a gonad-specific protein, is essential for germline development and primary piRNA biogenesis in Drosophila

Project description:In Drosophila, Piwi proteins associate with Piwi-interacting RNAs (piRNAs) and protect the germline genome by silencing mobile genetic elements. This defense system acts in germline and gonadal somatic tissue to preserve germline development. Genetic control for these silencing pathways varies greatly between tissues of the gonad. Here, we identified Vreteno (Vret), a novel gonad-specific protein essential for germline development. Vret is required for piRNA-based transposon regulation in both germline and somatic gonadal tissues. We show that Vret, which contains Tudor domains, associates physically with Piwi and Aubergine (Aub), stabilizing these proteins via a gonad-specific mechanism, absent in other fly tissues. In the absence of vret, Piwi-bound piRNAs are lost without changes in piRNA precursor transcript production, supporting a role for Vret in primary piRNA biogenesis. In the germline, piRNAs can engage in an Aub/Argonaute 3 (AGO3)-dependent amplification in the absence of Vret, suggesting that Vret function can distinguish between primary piRNAs loaded into Piwi/Aub complexes and piRNAs engaged in the amplification cycle. We propose that Vret acts at an early step in primary piRNA processing where it plays an essential role in transposon regulation. These studies show that vreteno (vret) has a role in germline development and primary piRNA regulation in Drosophila. Transposable element expression profiles from Drosophila ovaries mutant for vreteno, piwi and aubergine were compared using genome-wide mRNA expression profiling by Affymetrix GeneChip arrays (Drosophila 2.0). Key targets were validated by qPCR experiments.

2011-09-28 | E-GEOD-30360 | biostudies-arrayexpress

Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription.

Project description:Extrachromosomal, circular DNA (ecDNA) is emerging as a prevalent yet less characterized oncogenic alteration in cancer genomes. We leverage ChIA-PET and ChIA-Drop chromatin interaction assays to characterize genome-wide ecDNA-mediated chromatin contacts that impact transcriptional programs in cancers. ecDNAs in glioblastoma patient-derived neurosphere and prostate cancer cell cultures are marked by widespread intra-ecDNA and genome-wide chromosomal interactions. ecDNA-chromatin contact foci are characterized by broad and high-level H3K27ac signals converging predominantly on chromosomal genes of increased expression levels. Prostate cancer cells harboring synthetic ecDNA circles composed of characterized enhancers result in the genome-wide activation of chromosomal gene transcription. Deciphering the chromosomal targets of ecDNAs at single-molecule resolution reveals an association with actively expressed oncogenes spatially clustered within ecDNA-directed interaction networks. Our results suggest that ecDNA can function as mobile transcriptional enhancers to promote tumor progression and manifest a potential synthetic aneuploidy mechanism of transcription control in cancer.

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Y-linked rDNA deletions in Drosophila melanogaster

Project description:Please see publication. These experiments were performed to ascertain the contribution of Y-linked rDNA copy number variation in the modulation of gene expression. Males (XY) and female (XXY) genotypes were probed. Dye swaps and direct comparisons within each sex

2011-07-31 | E-GEOD-27695 | biostudies-arrayexpress

TfR1 globally regulates transcription and alternative splicing

Project description:TfR1 globally regulates transcription and alternative splicing

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