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Regulation of germline gene expression in C. elegans germline stem cells.

ABSTRACT: ChIP-Seq study to understand regulation of germline stem cell gene expression by immunoprecipitation of stem-cell factor Notch and associated transcriptional cofactor LAG-1 in C. elegans.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE70426 | GEO | 2019/07/01

REPOSITORIES: GEO

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Next Generation Sequencing for Transcriptomes Analysis in GLP-1 Notch receptor ON and OFF genetic background

Project description:Purpose: Ultilize the Next Generation Sequencing to determine the genes that are activated or repressed by GLP-1 Notch receptor in C. elegans germline. The list of genes generated from RNA-seq were intersected with the LAG-1 germline ChIP-seq data to identify direct transcriptional targets of the GLP-1/LAG-1 transcriptional complex in C. elegans germline stem cells. Methods: RNA isolated from hand dissected C. elegans germline tumor (one day old adult animals) are used for RNA-seq library. Results: 94 genes were identified as activated by GLP-1 Notch receptor from 5 biological replicates with the following criteria: gene counts per million greater than 2.0; fold of change greater than 2.0; false discovery rate (FDR) <0.05. Conclusions: lst-1 and sygl-1, two previously reported genes, were identified as direct transcriptional target for GLP-1/LAG-1 in C. elegans germline stem cells.

2020-02-17 | GSE144229 | GEO

Next Generation Sequencing for Transcriptomes Analysis for LAG-1 time course by auxin treatment.

Project description:Purpose: Ultilize Next Generation Sequencing to identify genes that are activated or repressed by LAG-1 (following auxin treatment to specifically deplete LAG-1 in C. elegans germline). The list of genes generated from RNA-seq identify primary and secondary targets of LAG-1 in C. elegans germline stem cells. Methods: RNA isolated from hand dissected C. elegans germline tumor (one day old adult animals) were used for RNA-seq library. Results: two genes (lst-1 and sygl-1) were identified as primary target for LAG-1 (2 hours auxin treatment); five additional genes are identified as secondary targets of LAG-1 based on their RNA accumulation depend on primary targets lst-1 and sygl-1 activity (4 hours auxin treatment). 94 genes are identified to be activated by LAG-1 (48 hours auxin treatment) from 4 biological replicates with the following criteria: gene counts per million greater than 2.0; fold of change greater than 2.0; false discovery rate (FDR) <0.05. Conclusions: lst-1 and sygl-1, two previously reported genes, are identified as primary transcriptional target for LAG-1 in C. elegans germline stem cells.

2020-02-17 | GSE144227 | GEO

Genome-wide profiling of C. elegans gonadal RNA

Project description:To better understand the role of Notch signaling in germline biology, we analyzed GLP-1/Notch- and PRC2-dependent changes in gene expression in C. elegans.

2016-09-10 | GSE49395 | GEO

DOS-3 mediates cell-non-autonomous DAF-16/FOXO activity in antagonizing age-related loss of C. elegans germline stem

Project description:Age-related depletion of stem cells causes tissue degeneration and failure to tissue regeneration, driving aging at the organismal level. Previously we reported a cell-non-autonomous DAF-16/FOXO activity in antagonizing the age-related loss of germline stem/progenitor cells (GSPCs) in C. elegans, indicating that regulation of stem cell aging occurs at the organ system level. Here we discover the molecular effector that links the cell-non-autonomous DAF-16/FOXO activity to GSPC maintenance over time by performing a tissue-specific DAF-16/FOXO transcriptome analysis. Our data show that dos-3, which encodes a non-canonical Notch ligand, is a direct transcriptional target of DAF-16/FOXO and mediates the effect of the cell-non-autonomous DAF-16/FOXO activity on GSPC maintenance through activating Notch signaling in the germ line. Importantly, expression of a human homologous protein can functionally substitute for DOS-3 in this scenario. As Notch signaling controls the specification of many tissue stem cells, similar mechanisms may exist in other aging stem cell systems.

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Global profile of germline gene expression in C. elegans

Project description:We used DNA microarrays to profile gene expression patterns in the C. elegans germline and identified 1416 germline-enriched transcripts that define three groups. The sperm-enriched group contains an unusually large number of protein kinases and phosphatases. The oocyte-enriched group includes potentially new components of embryonic signaling pathways. The germline-intrinsic group, defined as genes expressed similarly in germlines making only sperm or only oocytes, contains a family of piwi-related genes that may be important for stem cell proliferation. Finally, examination of the chromosomal location of germline transcripts revealed that sperm-enriched and germline-intrinsic genes are nearly absent from the X chromosome, but oocyte-enriched genes are not. This research has been described more fully in Reinke V et al.(2000) Mol Cell 6:605-16 Keywords: other

2001-07-24 | GSE5 | GEO

C. elegans germline-ablated (Z2-, Z3-) animals versus intact animals, N2 strain

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C. elegans DLC-1 is a component of diverse ribonucleoprotein complexes

Project description:Ribonucleoprotein complexes, which contain mRNAs and their regulator proteins, carry out post-transcriptional control of gene expression. The function of many RNA-binding proteins depends on their association with cofactors. Here we use a genomic approach to identify transcripts associated with DLC-1, a protein previously identified as a cofactor of two unrelated RNA-binding proteins that act in the C. elegans germline. Among the 2732 potential DLC-1 targets, most are germline mRNAs. Removal of DLC-1 affects expression of its targets, meg-1 and meg-3. We propose that DLC-1 acts as a cofactor for multiple ribonucleoprotein complexes, thus making diverse contributions to RNA regulation in the germline.

2018-10-01 | GSE115281 | GEO

C. elegans germline-ablated (Z2-, Z3-) animals versus intact animals, N2 strain

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Caenorhabditis elegans

Project description:Regulation of germline gene expression in C. elegans germline stem cells.

| PRJNA288637 | ENA

C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts

Project description:Piwi Argonautes and Piwi-interacting RNAs (piRNAs) mediate genome defense by targeting transposons. However, many piRNA species lack obvious sequence complementarity to transposons or other loci. For example, only one C. elegans transposon is a known piRNA target. Here we show that, in mutants lacking the Piwi Argonaute PRG-1 and associated piRNAs (21U-RNAs), many silent loci in the germline exhibit increased levels of mRNA expression and depletion of an amplified RNAdependent RNA polymerase (RdRP)-derived species of small RNA termed 22G-RNAs. Sequences depleted of 22G-RNAs are enriched nearby potential target sites that base pair imperfectly but extensively to 21U-RNAs. We show that PRG-1 is required to initiate, but not to maintain, silencing of transgenes engineered to contain complementarity to endogenous 21U-RNAs. Our findings support a model in which C. elegans piRNAs utilize their enormous repertoire of targeting capacity to scan the germline transcriptome for foreign sequences, while endogenous germline-expressed genes are actively protected from piRNA-induced silencing. Examine small RNA population changes in prg-1 and rescued strains

2012-09-01 | E-GEOD-38723 | biostudies-arrayexpress

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