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Profile of testicular polysomal gene expression regulated by Gonadotropin Regulated Testicular RNA helicase in adult mice

ABSTRACT: The down-regulation of known genes concerned with spermatogenesis at polysomal sites in GRTH KO and their association with GRTH in WT coupled with early findings of minor or unchanged total mRNAs and abolition of their protein expression in KO, underscore the relevance of GRTH in translation. Studies showed the association of GRTH bound polysome genes with the ubiquitin-proteasome-heat shock protein signaling network pathway and NFκB/TP53/TGFB1 signaling networks were derived from the differentially expressed gene analysis. Microarray differential gene expression analysis was performed using polysome-bound RNA isolated from testes of wild type (WT) and GRTH KO mice.

ORGANISM(S): Mus musculus

SUBMITTER: Chon-Hwa Tsai-Morris

PROVIDER: E-GEOD-33860 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Profile of testicular polysomal gene expression regulated by Gonadotropin Regulated Testicular RNA helicase in adult mice

Project description:The down-regulation of known genes concerned with spermatogenesis at polysomal sites in GRTH KO and their association with GRTH in WT coupled with early findings of minor or unchanged total mRNAs and abolition of their protein expression in KO, underscore the relevance of GRTH in translation. Studies showed the association of GRTH bound polysome genes with the ubiquitin-proteasome-heat shock protein signaling network pathway and NFκB/TP53/TGFB1 signaling networks were derived from the differentially expressed gene analysis.

2012-11-21 | GSE33860 | GEO

Role of gonadotropin regulated testicular RNA helicase (GRTH/Ddx25) on polysomal associated mRNAs in mouse testis.

Project description:Gonadotropin Regulated Testicular RNA Helicase (GRTH/Ddx25) is a testis-specific multifunctional RNA helicase and an essential post-transcriptional regulator of spermatogenesis. GRTH transports relevant mRNAs from nucleus to cytoplasmic sites of meiotic and haploid germ cells and associates with actively translating polyribosomes. It is also a negative regulator of steroidogenesis in Leydig cells. To obtain a genome-wide perspective of GRTH regulated genes, in particularly those associated with polyribosomes, microarray differential gene expression analysis was performed using polysome-bound RNA isolated from testes of wild type (WT) and GRTH KO mice. 792 genes among the entire mouse genome were found to be polysomal GRTH-linked in WT. Among these 186 were down-regulated and 7 up-regulated genes in GRTH null mice. A similar analysis was performed using total RNA extracted from purified germ cell populations to address GRTH action in individual target cells. The down-regulation of known genes concerned with spermatogenesis at polysomal sites in GRTH KO and their association with GRTH in WT coupled with early findings of minor or unchanged total mRNAs and abolition of their protein expression in KO underscore the relevance of GRTH in translation. Ingenuity pathway analysis predicted association of GRTH bound polysome genes with the ubiquitin-proteasome-heat shock protein signaling network pathway and NFκB/TP53/TGFB1 signaling networks were derived from the differentially expressed gene analysis. This study has revealed known and unexplored factors in the genome and regulatory pathways underlying GRTH action in male reproduction.

| S-EPMC3316541 | biostudies-literature

Trancriptome-wide association of Not1and Polysomal occupancy in wt and not5 background

Project description:The following data contains sequencing files for RNA IP and Polysome profiling experiments in wt and not5delta strains with background of Not1-TAP tagged strain (MAT_ leu2_20 ura3_ met15_ lys2_ his3delta1 not1::NOT1-Tap-tag-URA3). The RNA IP experiments have been performed as described previously (Gupta et al 2014) and the Polysome profiling experiments have been performed as described in (Albanese 2010). The libraries have been sequenced using polyadenylation isoform specific profiling protocol. The Not1 RIP experiments demonstrate genome-wide association of RNA with the central essential scaffold of the Ccr4-Not complex. The same RIP experiment in the not5delta background demonstrates the specificity of not5 in determining Not1 binding specificity to pulled down RNA. The polysome profiling experiments demonstrate the role of not5 in determining the translatability of ribosomal RNA.

2015-12-19 | E-MTAB-3195 | biostudies-arrayexpress

Transcription profiling of mouse erythroblasts during erythroid differentiation

Project description:The I/11 and R10 erythroid progenitor cell line was cultivated in serum free medium (StemPro34) supplemented with Epo (0,5U/ml), SCF (100ng/ml) and dexamethasone (10-6M). To identify genes specifically regulated by Epo/SCF-induced polysome recruitment, cells were factor deprived for 4h and subsequently treated for 2h with 5U/ml Epo and 200ng/ml SCF or left untreated. Subsequently we isolated both total and polysome bound mRNA from each condition, which was hybridised to oligonucleotide arrays (Affymetrix). Analysis of data with Rosetta Resolver allowed to identify and compare Epo/SCF induced gene expression in total and polysome bound RNA. To assess gene expression during erythroid differentiation, cells were induced to differentiate in presence of 5U/ml Epo and 0.5mg/ml Fe-loaded transferrin. Polysome bound mRNA was isolated from cells proliferating in presence of Epo, SCF and dexamethasone (renewal conditions), and from cells induced to differentiate for 48h or 60h.

2008-07-11 | E-MEXP-1689 | biostudies-arrayexpress

Changes in polysome association of mRNA throughout growth and development in Arabidopsis thaliana (Polysome association)

Project description:Translational control is a key regulatory step in the expression of genes as proteins. In plant cells, translational efficiency of mRNAs differs on different mRNA species, and the efficiency dynamically changes in various conditions. To gain a global view of translational control throughout growth and development, we performed genome-wide analysis of polysome association of mRNA over growth and leaf development in Arabidopsis thaliana by applying the mRNAs in polysome to DNA microarray. This analysis revealed that the degree of polysome association of mRNA had different levels depending on mRNA species, and the polysome association changed greatly throughout growth and development for each. In the growth stage, transcripts showed varying changes in polysome association from strongly depressed to unchanged degree, with the majority of transcripts showing dissociation from ribosomes. On the other hand, during leaf development, the polysome association of transcripts showed a normal distribution from repressed to activated mRNAs when comparing between expanding and expanded leaves. In addition, functional category analysis of the microarray data suggested that translational control has a physiological significance in plant growth and development process, especially in category of signaling and protein synthesis. Besides this, we compared changes in polysome association of mRNAs between various conditions and characterized translational controls in each. This result suggested that mRNAs translation might be controlled by complicated mechanisms for response to each condition. Our results highlight the importance of dynamic changes in mRNA translation in plant development and growth. Experiment using two-flactionated mRNA in 4 developmental stages, Polysomal mRNA vs. total mRNA. Biological replicates: 2. Compared 2DAG and 21DAG, or Young leaves and Mature leaves.

2015-09-01 | E-GEOD-69069 | biostudies-arrayexpress

Polysome-bound mRNA during oocyte maturation

Project description:Oocyte maturation, fertilization, and early embryonic development occur in the absence of gene transcription. Therefore, it is critical to understand at a global level the post-transcriptional events that are driving these transitions. Here, we have used a systems approach by combining polysome mRNA profiling and bioinformatics to identify RNA binding motifs in mRNAs that either enter or exit the polysome pool during mouse oocyte maturation. Association of mRNA with the polysomes correlates with active translation. Forty-eight hours (h) after PMSG injection, mice were stimulated with hCG for 0, 4, or 14 h, and GV-, MI- and MII-stage oocytes were collected. Polysome-bound mRNAs were purified, reverse-transcribed and linearly amplified with the WT-Ovation FFPE RNA Amplification System V2 (NuGEN). 5µg cDNA were fragmented and hybridized with Affymetrix Mouse Genome 430.2 array chips. Experiments were done using 3 independent sample sets.

2012-01-14 | E-GEOD-35106 | biostudies-arrayexpress

Expression & polysome association in pluripotent human embryonic stem cells

Project description:The goal was to measure the expression and polysome association of genes with polysomes in human embryonic stem cells H9 human embryonic stem cells were kept in pluripotent conditions. Total RNA and polysome extracts were isolated.

2012-09-01 | E-GEOD-31768 | biostudies-arrayexpress

Gonadotropin-regulated testicular helicase (DDX25), an essential regulator of spermatogenesis, prevents testicular germ cell apoptosis.

Project description:Gonadotropin-regulated testicular helicase (GRTH)/DDX25 is an essential post-transcriptional regulator of spermatogenesis. In GRTH null mice severe apoptosis was observed in spermatocytes entering the metaphase of meiosis. Pro- and anti-apoptotic factors were found to be under GRTH regulation in comparative studies of spermatocytes from wild type and GRTH(-/-) knock-out (KO) mice. KO mice displayed decreased levels of Bcl-2 and Bcl-xL (anti-apoptotic factors), an increase in Bid, Bak, and Bad (pro-apoptotic), reduced phospho-Bad, and release of cytochrome c. Also, an increase on Smac, a competitor of inhibitor apoptotic proteins that release caspases, was observed. These changes caused an increase in cleavage of caspases 9 and 3, activation of caspase 3 and increases in cleavage products of PARP. The half-life of caspase 3 transcripts was markedly increased in KO, indicating that GRTH had a negative role on its mRNA stability. IkappaBalpha, which sequesters NF-kappaB from its transcriptional activation of pro-apoptotic genes, was highly elevated in KO, and its phospho-form, which promotes its dissociation, was reduced. The increase of HDAC1 and abolition of p300 expression in KO indicated a nuclear action of GRTH on the NF-kappaB-mediated transcription of anti-apoptotic genes. It also regulates the associated death domain pathway and caspase 8-mediated events. GRTH-mediated apoptotic regulation was further indicated by its selective binding to pro- and anti-apoptotic mRNAs. These studies have demonstrated that GRTH, as a component of mRNP particles, acts as a negative regulator of the tumor necrosis factor receptor 1 and caspase pathways and promotes NF-kappaB function to control apoptosis in spermatocytes of adult mice.

| S-EPMC2427358 | biostudies-literature

Polysome-seq in zebrafish early embryonic development

Project description:We followed the polysomal association of maternal and early zygotic transcriptome over the first few hours of embryonic development, prior to and after MBT. We isolated polysome-associated (bound) and non-polysome-associated (unbound) mRNAs using sucrose gradient centrifugation followed by size fractionation. Using next generation sequencing (RNA-seq), we profiled the transcriptome in polysome-bound and unbound fractions. Our analysis revealed distinct dynamics of polysome association of cytoplasmically polyadenylated maternal mRNAs.

2017-10-14 | GSE88776 | GEO

PSN1 Polysome and INK128

Project description:Polysome-bound mRNA was analyzed to determine the effects of INK128 and radiation on mRNA translation 4 samples were analyzed with 3 biological replicates

2014-02-03 | E-GEOD-48098 | biostudies-arrayexpress

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