Caenorhabditis elegans
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ABSTRACT:
PROVIDER: PRJNA326738 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:PUF RNA-binding proteins control stem cells in diverse species, including mammalian, arthropod, and nematode, in addition to other biological functions. The C. elegans PUF protein FBF serves as a paradigm for metazoan PUFs. FBF is essential for the maintenance of germline stem cells but also regulates the hermpahrodite sperm/oocyte cell fate switch and is critical for the process of spermatogenesis. We have attempted to “disentangle” the different roles of FBF by comparing its targets in spermatogenic and oogenic germlines. To this end, we used FBF iCLIP to learn its binding profile in an adult hermaphrodite germline that is sexually transformed and makes only sperm due to a temperature-sensitive sex-determination mutant. As a control, we analyzed FBF iCLIP data from oogenic germlines at the same temperature. Using a modified peak calling algorithm, we identified FBF binding sites in oogenic animals at 20°C, oogenic animals at 25°C, and spermatogenic animals at 25°C. Oogenic FBF targets were similar at 20°C and 25°C. By contrast, FBF mRNA targets in spermatogenetic animals had a distinct profile, revealing sperm-specific targets that are likely critical for the FBF role in spermatogenesis. Most importantly, we found FBF bound to mRNAs regardless of germline gender. In particular, a group of 22 mRNAs clustered as bound with high frequency in a gender- and temperature-independent manner. These 22 mRNAsencode RNA-binding proteins and stem cell regulators and may be crucial for the FBF role in in stem cell maintenance.
2018-03-30 | GSE83695 | GEO
Project description:A new dataset of spermatogenic vs oogenic transcriptomes in the nematode C. elegans
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Project description:The nematode Caenorhabditis elegans is an important model for studies of germ cell biology, including specification as sperm or oocyte, the meiotic cell cycle and gamete differentiation. Fundamental to those studies is a genome-level knowledge of the germline transcriptome. Here we use RNA-Seq to identify genes expressed in isolated XX gonads, which are roughly 95% germline and 5% somatic gonadal tissue. We generate data from mutants making either sperm [fem-3(q96)] or oocytes (fog-2), both grown at 22M-BM-0C. Our dataset identifies a total of 10,754 mRNAs in the polyadenylated transcriptome of XX gonads, with 1,723 enriched in spermatogenic gonads, 2,869 enriched in oogenic gonads and the remaining 6,274 not enriched in either. These spermatogenic, oogenic and gender-neutral gene datasets compare well with those of earlier studies, but double the number of genes identified. We also query our RNA-Seq data for differential exon usage and find 351 mRNAs with sex-specific isoforms. We suggest that this new dataset will prove useful for studies focusing on C. elegans germ cell biology. Comparison of spermatogenic vs oogenic transcriptomes
2014-07-29 | E-GEOD-57109 | biostudies-arrayexpress
Project description:To explore the roles of piRNAs and WAGO-class 22G-RNAs in regulating gene expression and transposon silencing in Caenorhabditis elegans, we used RNA-seq to assess changes in small RNA and mRNA levels in prg-1 and mut-16 mutants, which disable the piRNA and WAGO-class 22G-RNA pathways respectively. We identified numerous roles for piRNAs and WAGO-class 22G-RNAs in regulating germline genes, including transposons, histones, and spermatogenic and oogenic transcripts.
2019-12-03 | GSE141243 | GEO
Project description:Differential gene expression between feminized C. elegans male and female germlines
| PRJNA361492 | ENA
Project description:The nematode Caenorhabditis elegans is an important model for studies of germ cell biology, including specification as sperm or oocyte, the meiotic cell cycle and gamete differentiation. Fundamental to those studies is a genome-level knowledge of the germline transcriptome. Here we use RNA-Seq to identify genes expressed in isolated XX gonads, which are roughly 95% germline and 5% somatic gonadal tissue. We generate data from mutants making either sperm [fem-3(q96)] or oocytes (fog-2), both grown at 22°C. Our dataset identifies a total of 10,754 mRNAs in the polyadenylated transcriptome of XX gonads, with 1,723 enriched in spermatogenic gonads, 2,869 enriched in oogenic gonads and the remaining 6,274 not enriched in either. These spermatogenic, oogenic and gender-neutral gene datasets compare well with those of earlier studies, but double the number of genes identified. We also query our RNA-Seq data for differential exon usage and find 351 mRNAs with sex-specific isoforms. We suggest that this new dataset will prove useful for studies focusing on C. elegans germ cell biology.
2014-07-29 | GSE57109 | GEO
Project description:Histone H3 Lys 4 methylation (H3K4me) is deposited by the conserved SET1/MLL methyltransferases acting in multiprotein complexes including Ash2 and Wdr5. While individual subunits contribute to complex activity, how they influence gene expression in a specific tissue remains largely unknown. In caenorhabditis elegans, SET-2/SET1, WDR-5.1 and ASH-2 are differentially required for germline H3K4 methylation. Using expression profiling on germlines from animals lacking set-2, ash-2 or wdr-5.1, we show that these subunits play unique and redundant functions to promote expression of germline genes and repress somatic genes. We further show that in set-2 and wdr-5.1 deficient germlines, somatic gene misexpression is associated with conversion of germ cells into somatic cells, and that nuclear RNAi acts in parallel with SET-2 and WDR-5.1 to maintain germline identity. These findings uncover a unique role for SET-2 and WDR-5.1 in preserving germline pluripotency, and underline the complexity of the cellular network regulating this process. Gene misregulation in SET1/set-2, wdr-5.1 and ash-2 defective germlines
2014-09-04 | E-GEOD-61094 | biostudies-arrayexpress
Project description:C. elegans ALG-1 iCLIP raw sequencing reads
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Project description:Transcriptomic profiling of germlines and intestines of C. elegans deficient in the COMPASS H3K4me3 methyltransferase complex
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Project description:The nematode Caenorhabditis elegans has evolutionarily conserved EV signaling pathways. In this study, we apply a recently published method for high specificity purification of EVs from C. elegans to carry out target-independent proteomic and RNA analysis of EVs from C. elegans. Our experiments uncovered diverse coding and non-coding RNA transcripts as well as protein cargo types commonly found in human EVs.
2020-08-05 | GSE146973 | GEO