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RIP-Chip analysis of the C. elegans FOG-1 and FOG-3 proteins

ABSTRACT: FOG-1/CPEB and FOG-3/Tob are the terminal regulators of the sex determination in C. elegans germ cells. CPEB and Tob proteins are both translational regulators. To investigate how FOG-1 and FOG-3 regulate germ cell sex determination we sought to identify the target mRNAs. We used transgenic epitope tagged animals (3xMyc::FOG-1 and FOG-3::3xFLAG). To identify the mRNA targets of FOG-1/CPEB and FOG-3/Tob on a genome wide scale we used RNA immunoprecipitation followed by microarray analysis. We found 81 putative mRNA targets of FOG-1 and 722 putative targets of FOG-3. 76 target mRNAs were common to both FOG-1 and FOG-3.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE73070 | GEO | 2015/12/14

SECONDARY ACCESSION(S): PRJNA295983

REPOSITORIES: GEO

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RIP-Chip analysis of the C. elegans FOG-1 and FOG-3 proteins

Project description:FOG-1/CPEB and FOG-3/Tob are the terminal regulators of the sex determination in C. elegans germ cells. CPEB and Tob proteins are both translational regulators. To investigate how FOG-1 and FOG-3 regulate germ cell sex determination we sought to identify the target mRNAs. We used transgenic epitope tagged animals (3xMyc::FOG-1 and FOG-3::3xFLAG). To identify the mRNA targets of FOG-1/CPEB and FOG-3/Tob on a genome wide scale we used RNA immunoprecipitation followed by microarray analysis. We found 81 putative mRNA targets of FOG-1 and 722 putative targets of FOG-3. 76 target mRNAs were common to both FOG-1 and FOG-3. FOG-1 RNA-coimmunoprecipitation (RIP) samples were prepared as follows. Parallel RIPs were performed with wild type animals as the control IP. Worm extracts were made from wildtype and 3xMyc::FOG-1 late L3/early L4 animals. Myc affinity gel was used to immunoprecipitate 3xMyc::FOG-1 from the extracts. RNA was extracted from the pellets and analyzed on Affymetrix microarrays. 7 biological replicates of both 3xMyc::FOG-1 and wildtype were used. FOG-3 RNA-coimmunoprecipitation (RIP) samples were prepared as follows. Parallel RIPs were performed with wild type animals as the control IP. Worm extracts were made from wildtype and FOG-3::3xFLAG late L3/early L4 animals. Myc affinity gel was used to immunoprecipitate FOG-3::3xFLAG from the extracts. RNA was extracted from the pellets and analyzed on Affymetrix microarrays. 7 biological replicates of both FOG-3::3xFLAG and wildtype were used.

2015-12-14 | E-GEOD-73070 | biostudies-arrayexpress

An RNA binding polymer specifies nematode sperm fate

Project description:Metazoan gamete development into sperm or oocytes requires specific programming cues. Many of these cues function through conserved proteins to regulate gene expression. In C. elegans, two proteins are the terminal regulators of the genetic regulatory network controlling sperm fate: FOG-1, a cytoplasmic polyadenylation element binding protein (CPEB), and FOG-3, a predicted Tob/BTG protein. Loss of either gene causes hermaphrodites or male germ cells to switch from making sperm to making oocytes. Characterized Tob/BTG proteins function as adaptor proteins, linking – in certain contexts – deadenylases to mRNA via CPEB RNA motifs. Through crosslinking and sequencing, we confirmed FOG-3 binds to RNA directly and observed a preference for mRNA 3’UTRs. Our results bring together prior genetics and molecular biology data to propose a new molecular function in germ cell specification with a Tob protein. We discuss the potential for FOG-3 to function as an mRNA packaging protein to inhibit target genes, as well as the potential for the existence of other hidden protein polymers in biology.

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Comparison of transcriptomes of N2 and fog-2(q71) mutant Caenorhabditis elegans

Project description:In this experiment, steady-state mRNA levels were determined for replicated samples of N2 (wild-type reference) and fog-2(q71) homozygous mutant C. elegans. All samples were adult XX animals, which for N2 are self-fertile hermaphrodites and for fog-2(q71) spermless hermaphrodites, i.e. true females. For the fog-2 mutant animals, only those that had mated with males, and were thus gravid, were picked for RNA isolation. This ensures that all comparisons are between similar, embryo-containing animals. The experiment was motivated by the role of FOG-2 in post-transcriptional control of gene expression in germ cells, inferred from its the germline-specific phenotype of its loss and from its physical associated with the GLD-1 RNA-binding protein. Specifically, a possible role for FOG-2 in influencing mRNA stability was addressed.

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The gene responses of the rice plant treated with both continuous simulated acid fog (pH3.0) and natural fog (pH5.6) treatments

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RNA-seq analysis of C. elegans CPEB homolog mutants.

Project description:Comparative transcriptomics study between C. elegans wild-type N2 and CPEB homolog mutants: fog-1, cpb-2, and cpb-3.

2017-08-03 | E-MTAB-4720 | biostudies-arrayexpress

Expression Data from E16.5 hearts from WT and FOG-2R3K5A siblings

2014-01-01 | GSE50426 | GEO

Spike-in SILAC MS of C. elegans CPEB homolog mutants.

Project description:Comparative proteomic study between C. elegans wild-type N2 and CPEB homolog mutants: fog-1, cpb-2, and cpb-3.

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The gene responses of the rice plant treated with both continuous simulated acid fog (pH3.0) and natural fog (pH5.6) treatments

Project description:Rice plants cultivated on mountain areas are frequently exposed to acid fog and natural fog events. In this report, we analyzed the expression profiles of the rice plant with acid fog (SiAF) or neutral fog (SiNF) treatment for 1 and 7 days. Microarray results suggested that ROS generation was induced by not only SiAF, but also SiNF treatment, and it occurred in apoplast, not in organelles. Genes for defense- and stress-responses was also induced by both SiAF and SiNF treatments. The induction occurred in plants treated with SiAF for both 1 day and 7 days, and it was also detected in plants treated with SiAF for 7 days. These results suggest that both SiAF and SiNF treatments are abiotic stresses accompanying ROS generation in apoplast. Comparison between continuous fog treated shoots and control shoots. Biological replicates: 3 simulated acid fog (pH 3.0) treated (SiAF) for 1 day; 3 simulated acid fog (pH 3.0) treated (SiAF) for 7 days; 3 simulated neutral fog (SiNF) treated for 1 day; 3 simulated neutral fog (SiNF) treated for 7 days; 3 controls for 1 day; 3 controls for 7 days. Independently grown and harvested. Cultivar: Hinohikari 1 sample derived from 5 plants grown under the same conditons. Total: 18 samples, 12 comparisons.

2012-06-30 | E-GEOD-31196 | biostudies-arrayexpress

The role of FOG-1 in GATA-1 transcriptional regulation of megakaryocyte differentiation

Project description:We explored the role of FOG-1 in GATA-1 transcriptional regulation of megakaryocyte differentiation through expression of wild-type GATA-1 and the FOG-binding mutant of GATA-1 (GATA-1^V205G) in G1ME cells.

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Expression Data from E16.5 hearts from WT and FOG-2R3K5A siblings

Project description:Heart development is modulated by FOG-2/NuRD interactions. FOG-2R3K5A is unable to recuit the NuRD complex and this results in cardiac defects such as ASD, VSD, and thin ventricular walls We used microarrays to detail the changes in gene expression in FOG-2R3K5A hearts to determine misexpression of genes that may be causing the observed phenotypes. Whole hearts from E16.5 Wild-type and FOG-2R3K5A siblings were processed for RNA extraction and hybridization on Affymetrix microarrays. We used three biological replicates of each genotype.

2014-01-01 | E-GEOD-50426 | biostudies-arrayexpress

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