Identification of MBL-1 target transcript through RIP-seq.
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE249408 | GEO | 2023/12/12
REPOSITORIES: GEO
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Project description:MBL-1 is an RNA-binding protein important for the differentiation and development of many animal tissues. An evolutionarily conserved alternative splicing mechanism generates MBL-1 isoforms that are either expressed in the nucleus or show a more cytoplasmic distribution. We used small RNA-seq to investigate the individual contribution of evolutionarily conserved mbl-1 isoform expression of C. elegans miRNA expression. The analysis was done on L4 stage animals
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Project description:MBL-1 is an RNA-binding protein important for the differentiation and development of many animal tissues. An evolutionarily conserved alternative splicing mechanism generates MBL-1 isoforms that are either expressed in the nucleus or show a more cytoplasmic distribution. We used RNA-seq to investigate the individual contribution of evolutionarily conserved mbl-1 isoform expression of C. elegans gene expression and to identify pathways associated with isoform expression. The analysis was done on L4 stage animals
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Project description:Homozygous masterblind (mbl-/-) zebrafish exhibit reduced or absent eyes and telecephalon, and the expansion of the diencephalic fates to the front of the brain. A missense mutation in the GSK3-binding domain of zebrafish axin1, a scaffolding protein in the Wnt signaling pathway, results in the mbl phenotype. In an effort to identify and study the genes affected by Wnt signaling, we used a 14,000-oligonucleotide-gene microarray to determine differentially expressed genes in mbl/axin1 (-/-) and wild type control zebrafish embryos and larvae. Keywords: zebrafish, Danio rerio, wild-type mbl, axin1, development
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Project description:While many general RNA-binding proteins have been described in eukaryotes, the small RNA chaperone Hfq and the translational regulator CsrA remain the only known global RNA-associated cofactors involved in the bacterial post-transcriptional gene expression control. Here, using an RNA-seq-based analysis of the biochemically partitioned ensemble of cellular RNAs, we uncovered a large group of transcripts that interact with the RNA-binding protein ProQ in Salmonella enterica. We show that ProQ is a conserved abundant protein with a wide range of targets, including a new class of ProQ-associated small RNAs, and predicted functions in many cellular pathways. ProQ preferentially associates with highly structured RNAs, filling the so-far vacant niche of a global double-stranded RNA-binding protein and expanding the range of the post-transcriptional regulation in bacteria." This dataset includes representative RIP experiments carried out to characterize the in vivo interactome of the bacterial global RNA-binding protein ProQ. They include a series of RIPs performed on a Salmonella Typhimurium SL1344 ProQ-3xFLAG strain grown to the exponential (OD600=0.5), transition (OD600=2.0) or stationary (6 hours after cells reached OD600=2.0) phases; a RIP perfomed on an Escherichia coli W3110 ProQ-3xFLAG strain grown to the transition phase; a control series of RIPs performed on Salmonella Typhimurium SL1344 ProQ-3xFLAG and PhoP-3xFLAG strains grown to the transition phase. The first series shows how the ProQ RNA interactome evolves over growth in Salmonella, the second reveals ProQ targets in Escherichia, the third illustrates the lack of RNA-binding activity in a negative control, DNA-binding transcription regulator PhoP.
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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.
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2018-03-15 | GSE90639 | GEO
Project description:modENCODE_submission_2454 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: NC1790 (engineered, target gene dpy-7 tagged by 3xFlag::PAB-1); Tissue: hypodermis (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: unc-119(ed1); wdEx626[unc-119+; dpy-7::3xFLAG::PAB-1]; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1790 (engineered, target gene dpy-7 tagged by 3xFlag::PAB-1); temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue hypodermis (L3-L4)
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