Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression
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ABSTRACT:
PROVIDER: PRJNA480960 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9214970.fastq.gz | Fastqsanger.gz | |||
| SRR9214980.fastq.gz | Fastqsanger.gz | |||
| SRR9214971.fastq.gz | Fastqsanger.gz | |||
| SRR9214981.fastq.gz | Fastqsanger.gz | |||
| SRR9214972.fastq.gz | Fastqsanger.gz |
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Project description:The wide variety of specialized permissive and repressive mechanisms by which germ cells regulate developmental gene expression are not well understood genome-wide. Isolation of germ cells with high integrity and purity from living animals is necessary to address these open questions, but no straightforward methods are currently available. Here we present an experimental paradigm that permits the isolation of nuclei from C. elegans germ cells at quantities sufficient for genomic analyses. We demonstrate that these nuclei represent a very pure population and are suitable for both transcriptome analysis (RNA-seq) and chromatin immunoprecipitation (ChIP-seq) of histone modifications. The method does not require specialized transgenic strains or growth conditions and can be readily applied with minimal troubleshooting. This new capacity removes a major barrier in the field to dissect gene expression mechanisms in the germ line of C. elegans. Consequent discoveries using this technology will be relevant to conserved regulatory mechanisms across species.
2018-07-14 | GSE117061 | GEO
Project description:BackgroundThe wide variety of specialized permissive and repressive mechanisms by which germ cells regulate developmental gene expression are not well understood genome-wide. Isolation of germ cells with high integrity and purity from living animals is necessary to address these open questions, but no straightforward methods are currently available.ResultsHere we present an experimental paradigm that permits the isolation of nuclei from C. elegans germ cells at quantities sufficient for genomic analyses. We demonstrate that these nuclei represent a very pure population and are suitable for both transcriptome analysis (RNA-seq) and chromatin immunoprecipitation (ChIP-seq) of histone modifications. From these data, we find unexpected germline- and soma-specific patterns of gene regulation.ConclusionsThis new capacity removes a major barrier in the field to dissect gene expression mechanisms in the germ line of C. elegans. Consequent discoveries using this technology will be relevant to conserved regulatory mechanisms across species.
| S-EPMC6580472 | biostudies-literature
Project description:Chromatin organization in the C. elegans germ line is tightly regulated and critical for germ cell differentiation. While certain germline epigenetic regulatory mechanisms have been identified, how they influence chromatin structure and ultimately gene expression remains unclear, in part because most genomic studies have focused on data collected from whole worms. We therefore analyzed publicly available histone modification and chromatin accessibility data from isolated undifferentiated germ nuclei to define chromatin states. We then correlated these states with overall transcript abundance, spatio-temporal expression patterns, and the function of small RNA pathways. Because the essential role of the germ line is to transmit genetic information to the next generation and establish gene expression in the early embryo, we compared epigenetic and transcriptomic profiles from undifferentiated germ cells, oocytes, and embryos to define the epigenetic changes during this developmental transition. The active histone modification H3K4me3 exhibits particularly dynamic remodeling as germ cells differentiate into oocytes, with implications for establishing transcriptional activation of essential genes during early embryogenesis. Our results highlight the dynamism of the chromatin landscape in germ cells, and provide a resource for future investigation into epigenetic regulatory mechanisms.
2023-07-03 | GSE236076 | GEO
Project description:dsRNA-mediated gene silencing (RNAi) can be inherited for multiple generations in C. elegans. To understand this process we conducted a genetic screen for animals defective for transmitting RNAi silencing signals to future generations. This screen identified the gene heritable RNAi defective (hrde)-1. hrde-1 encodes an Argonaute (Ago) that associates with siRNAs in germ cells of the progeny of animals exposed to dsRNA. In nuclei of these germ cells, HRDE-1 engages the Nrde nuclear RNAi pathway to promote RNAi inheritance, and directs H3K9me3 chromatin marks at RNAi targeted genomic loci. Under normal growth conditions, HRDE-1 associates with endogenously expressed small RNAs, which direct nuclear gene silencing in germ cells. In RNAi inheritance mutant animals, silencing is lost over generational time. Concurrently, RNAi inheritance mutant animals exhibit progressively worsening germline defects that ultimately lead to sterility. These results establish that the Ago HRDE-1 directs gene-silencing events in germ cell nuclei, which are required for multi-generational RNAi inheritance and immortality of the germ cell lineage. We propose that C. elegans use the RNAi inheritance machinery to transmit epigenetic information, accrued by past generations, into future generations to ensure immortality of the germ cell lineage. H3K9me3 Chip-IP for C. elegans strains nrde-3, nrde-4, glp-4. Small RNA-seq for small RNAs co-immunoprecipitated with HRDE-1
2012-07-30 | E-GEOD-38041 | biostudies-arrayexpress
Project description:Nuclear pore complex (NPC) structure and maturity changed during early development before MBT in zebrafish embryos. Aiming to further confirm the difference of NPCs among different stages during MZT, we first isolated nuclei from 32-cell and 512-cell stage embryos as most zygotic genes have not been transcribed at these two stages yet. The lysates from identical number (about 12,500 nuclei per stage) isolated nuclei were then trypsin-digested and fractionated, followed by high-resolution LC-MS/MS analysis on the Q-Exactive HF-X mass spectrometers using a label-free assay. Whole blastomeres from 32-cell and 512-cell were also prepared with yolk removal to serve as total protein profile control, and the same amount lysates were analyzed by high-resolution LC-MS/MS with TMT labelled. Each sample for MS analysis had two repeats. Correlation analysis revealed that the abundance ratio from isolated Nuclei and whole deyolking balstomeres did not correlate well, but samples in Nuclei or Whole blastomeres were well correlated. This result indicates the convincible sample preparation as well as the variability in nuclei composition in early developmental period before MBT.
2023-08-25 | PXD017896 | Pride
Project description:Sex-determining chromosomes exhibit complex global regulation in germ cells, in part due to the absence of dosage compensatory mechanisms found in the soma. In the XX hermaphrodite germ line of C. elegans, the X chromosome houses few germline-expressed genes [1] and is poorly expressed, though not completely silent, through most of germ cell development [2]. A chromatin-modifying pathway consisting of the histone methyltransferase (HMT) MES-4 and the Polycomb Repressive Complex 2 (PRC2) orthologs MES-2/3/6 contributes to X silencing in C. elegans germ cells [3-5]. MES-4 promotes H3K36me3 accumulation on autosomes, which leads to concentration of H3K27me3 on the X by MES-2/3/6 [5]. Loss of MES activity results in inappropriate activation of X-linked genes and second-generation sterility [5, 6]. The two marks occupy mutually exclusive domains of the genome [5, 7], leading to a model in which the presence of one modification prevents the accumulation of the other at specific loci. However, further details about how this repulsion mechanism between H3K27me3 and H3K36me3 is established remain mysterious. Here we implicate the zinc-finger protein OEF-1 in counterbalancing the accumulation of H3K27me3 throughout the genome, particularly on the X chromosome. Strikingly OEF-1, like MES-4, is localized to sites of active gene expression in the germ line, and promotes H3K36me3 levels in mes-4 mutants. Our data thus identify OEF-1 as a novel modulator of the fundamental relationship between gene activation and gene silencing in the C. elegans germ line.
2020-03-24 | GSE147401 | GEO
Project description:In this project, we identified an uncharted subcompartment of the C. elegans germ granule, which we termed the E granule. We show that the E granule is required for the synthesis of a specialized class of 22G-RNAs.
2024-06-21 | PXD053319 |
Project description:Proliferating germ cells in C. elegans provide a useful model system for deciphering fundamental mechanisms underlying the balance between proliferation and differentiation. Using gene expression profiling of mutants with excess germ cell proliferation, we identified approximately 200 genes expressed in the proliferating germ cells of C. elegans. RNA isolated from young adult C. elegans hermaphrodites of the genotype unc-32(e189) (control) and from unc-32(e189)glp-1(oz112gf) (excess germ cell proliferation) was directly compared on DNA arrays representing >90% of C. elegans genes. Four biological replicates were performed, with balanced dye swaps.
2010-04-29 | E-GEOD-21531 | biostudies-arrayexpress
Project description:Proliferating germ cells in C. elegans provide a useful model system for deciphering fundamental mechanisms underlying the balance between proliferation and differentiation. Using gene expression profiling of mutants with excess germ cell proliferation, we identified approximately 200 genes expressed in the proliferating germ cells of C. elegans.
2010-04-29 | GSE21531 | GEO
Project description:Germ granules are biomolecular condensates that promote germ cell totipotency in most, if not all, animals. In C. elegans, MEG-3 and MEG-4 are two intrinsically disordered proteins that are redundantly required for the phase separations that drive germ granule assembly in germline blastomeres. Here, we show that animals lacking MEG-3/4 exhibit defects in dsRNA-mediated gene silencing (RNAi) that are due, at least in part, to defects in systemic RNAi. Interestingly, these RNAi defects are transgenerationally disconnected from meg-3/4 genotype: RNAi defects do not arise until 5-9 generations after animals become mutant for meg-3/4, and RNAi defects persist for 9-11 generations after meg-3/4 genotype is restored to wild type. Similar non-Mendelian patterns of inheritance are associated with other mutations that disrupt germ granule formation, indicating that germ granule disruption is the likely cause of genotype/phenotype disconnects. Loss of germ granules is associated with the production of aberrant populations of endogenous siRNAs, which, remarkably, are propagated for ≅10 generations in wild-type descendants of animals that lacked germ granules. sid-1, which encodes a factor required for systemic RNAi in C. elegans, is inappropriately and heritably silenced by aberrantly expressed sid-1 endogenous siRNAs, suggesting that transgenerational silencing of sid-1 likely underlies the heritable defect in RNAi. We conclude that one function of germ granules is to organize RNA-based epigenetic inheritance pathways and that failure to assemble germ granules has consequences that persist across many generations.
2019-08-08 | GSE134683 | GEO