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RNA profiling of skeletal muscle in RP58 knockout mice

ABSTRACT: To predict RP58-regulated genes involved in skeletal myogenesis, RNA profiling experiments were performed, comparing RNA derived from skeletal muscle tissue of a RP58+/+ mouse to that from a RP58 knockout (KO) mouse at E18.5. Importantly, well-known dominant-negative inhibitors of muscle differentiation, the Id family of genes (Id1/Id2/Id3), were upregulated in the RP58 KO muscle. On the contrary, a number of muscle differentiation-related genes, such as Ckm, troponin and Myosin, were downregulated in the same sample. These results indicate that the repressor protein RP58 is important for muscle terminal differentiation, possibly suppressing the gene expression of muscle differentiation genes such as the Ids. Keywords: Knockout tissue

ORGANISM(S): Mus musculus

PROVIDER: GSE16595 | GEO | 2009/07/31

SECONDARY ACCESSION(S): PRJNA116161

REPOSITORIES: GEO

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RNA profiling of skeletal muscle in RP58 knockout mice

Project description:To predict RP58-regulated genes involved in skeletal myogenesis, RNA profiling experiments were performed, comparing RNA derived from skeletal muscle tissue of a RP58+/+ mouse to that from a RP58 knockout (KO) mouse at E18.5. Importantly, well-known dominant-negative inhibitors of muscle differentiation, the Id family of genes (Id1/Id2/Id3), were upregulated in the RP58 KO muscle. On the contrary, a number of muscle differentiation-related genes, such as Ckm, troponin and Myosin, were downregulated in the same sample. These results indicate that the repressor protein RP58 is important for muscle terminal differentiation, possibly suppressing the gene expression of muscle differentiation genes such as the Ids. Keywords: Knockout tissue Skeletal muscles of WT and RP58 KO mice (E18.5 diaphragm) were dissected under a microscope and RNA was extracted using ISOGEN (Nippongene). After EtOH precipitation, RNA was dissolved into DEPC-DW and its concentration was determined. Microarray analysis - cRNA was synthesized. 10 ug of cRNA were hybridized to Affymetrix mouse 430A 2.0 arrays. Signal intensities were calculated using the RMA method. MAPPFinder (www.genmapp.org) was used to integrate expression data with known pathways.

2009-07-31 | E-GEOD-16595 | biostudies-arrayexpress

RP58 controls neuron and astrocyte differentiation by downregulating the expression of Id1-4 genes in the developing cortex

Project description:Appropriate number of neurons and glial cells is generated from neural stem cells (NSCs) by the regulation of cell cycle exit and subsequent differentiation. Although the regulatory mechanism remains obscure, Id (inhibitor of differentiation) proteins are known to contribute critically to NSC proliferation by controlling cell cycle. Here we report that a transcriptional factor, RP58, negatively regulates all 4 Id genes (Id1-Id4) in developing cerebral cortex. Consistently, Rp58 knockout (KO) mice demonstrated enhanced astrogenesis accompanied with an excess of NSCs. These phenotypes were mimicked by the overexpression of all Id genes in wild-type cortical progenitors. Furthermore, Rp58 KO phenotypes were rescued by the knockdown of all Id genes in mutant cortical progenitors but not by the knockdown of each single Id gene. Finally, we determined p57 as an effector gene of RP58-Id-mediated cell fate control. These findings establish RP58 as a novel key regulator that controls the self-renewal and differentiation of NSCs and restriction of astrogenesis by repressing all Id genes during corticogenesis. Sample RNAs were obtained from E16.5 Rp58 KO mouse cerebral cortex or control cortex. Two independent total RNA samples from each mouse strain were mixed and purified using the RNeasy Mini Kit (Qiagen). Oligonucleotide microarray analysis was performed using Panorama Micro Array gene expression chips, each containing approx 22000 probe sets (Sigma-Aldrich) according to the manufacturer's instructions.

2014-12-08 | E-GEOD-34327 | biostudies-arrayexpress

RP58 controls neuron and astrocyte differentiation by downregulating the expression of Id1-4 genes in the developing cortex

2014-12-08 | GSE34327 | GEO

Mus musculus

Project description:RNA profiling of skeletal muscle in RP58 knockout mice

| PRJNA116161 | ENA

Gene expression profiles in the hippocampus of the Rp58 hetero-KO and the control wild-type mice in adulthood and old age.

Project description:The early onset of microglia activation in the Rp58 hetero-KO mice raised the possibility that chronic inflammation in the brain was induced by mutation even in the early life stage. To test this possibility, we examined gene expression profiles in the hippocampus of the Rp58 hetero-KO and the control wild-type mice in adulthood and old age months. Among the genes whose expression level was down-regulated in the aged wild-type mice, 341 genes were down-regulated in the adulthood Rp58 hetero-KO mice when both were compared with the adulthood wild-type mice. Conversely, the expression levels of 103 genes were up-regulated both in the adulthood Rp58 hetero-KO and the aged wild-type mice. In the pathway enrichment analysis, these 103 up-regulated genes included Cxcl10, Oas2, Oas1a, and Oasl2, which are associated with a pathway of immune response interferon gamma action on extracellular matrix and cell differentiation.

2022-07-16 | GSE207955 | GEO

Cpt2 knockout in muscle stem cells

Project description:Analysis of skeletal muscle satellite cells with specific knockout (KO) of Carnitine Palmitoyltransferase 2 (Cpt2) gene in mouse (named Cpt2PKO). Cpt2 knockout disrupts fatty acid oxidation in satellite cells and causes energy insufficiency and alteration of protein acetylation, which eventually impedes their expansion and differentiation, leading to impairments in muscle regeneration.

2024-07-31 | GSE158912 | GEO

Impact of Cugbp1 knockout on skeletal muscle and brain trancsriptome in neonatal mice

Project description:To elucidate the role of Cugbp1 knockout on the structure and function of skeletal muscle and brain, we have performed a microarray of mRNA obtained from skeletal muscle and brain samples obtained from neonatal WT and Cugbp1 KO mice. Between-genotype differences were assessed using a Student's T-test, with a p-value cutoff of 0.05 and fold change cutoff of 1.5. 929 genes were identified as differentially regulated; ontological enrichments within this geneset indicated Cugbp1 may regulate differentiation, extracellulat matrix and other muscle functions during myogenesis.

2018-08-08 | GSE85396 | GEO

shRNA of mouse C2C12 culture: myogenesis timecourse and shRp58 treatment

Project description:To predict Rp58-regulated gene involved in myogenesis, RNA profiling experiments were performed, comparing RNA derived from C2C12 with or without expressing shRNA for Rp58. As a result, 271 genes were upregulated in C2C12 stably expressing shRNA-Rp58 cells compared with control C2C12 cells. As Rp58 is repressor in C2C12, we hypothesized that Rp58 regulates gene cluster which expression is downregulated in accordance with Rp58 expression and myogenesis progression. In this regard, we also characterized dynamic gene expression patterns during myogenesis by microarray at 4 different stage (GM, day 0, 2, 4) of C2C12 myogenesis assays and found that 399 genes expression is characterized as downregulation pattern during myogenesis. Importantly, this down regulation gene set and upregulated genes by shRNA for Rp58 were highly overlapped. Experiment Overall Design: C2C12 murine skeletal muscle cells were purchased from American Type Experiment Overall Design: culture Collection (ATCC). These cells were mainteined in GM (DMEM Experiment Overall Design: supplemented with 10% FBS). Cells were grown in GM and after reaching Experiment Overall Design: counfluence, the medium was switched to DM (DMEM supplemented with 2% hourse serum) and further incubated. The medium was changed every 2 days. Culture was performed by using within five passages cells. For the experiment of shRNA for Rp58, transfection was performed by using Lipofectamin 2000 (Invitrogen). Stable transfectants were obtained by selection of the transfected C2C12 cells for two weeks. Experiment Overall Design: Microarray analysis - RNA was isolated as described from C2C12, and cRNA was synthesized. 10 ug of cRNA were hybridized to Affymetrix mouse 430 2.0 arrays. Intensity values were quantified using RMA algorithm. Experiment Overall Design: MAPPFinder (www.genmapp.org) was used to integrate expression data with known pathways.

2009-08-09 | E-GEOD-12993 | biostudies-arrayexpress

Microarray analysis of satellite cells in Dnmt3a knockout mice

Project description:DNA methylation occurs as 5-methylcytosines mainly at cytosine-guanine dinucleotides, so-called CpG sites, and such methylation is a well-studied epigenetic mechanism for transcriptional regulation. Generally, DNA methylation of the gene promoter is correlated with transcriptional repression. Genomic DNA methylation patterns are established by the actions of the de novo methyltransferases Dnmt3a and Dnmt3b, and are maintained by the methyltransferase Dnmt1. Expression of Dnmt3a mRNA is relatively high in skeletal muscle, suggesting a major role in transcriptional regulation. Also, denervation of skeletal muscle decreased expression of Dnmt3a mRNA, suggesting involvement of Dnmt3a in pathophysiology during atrophy. Decreased regeneration capacity in atrophied skeletal muscle hampers muscle mass recovery after injury and the impaired muscle function, lowers the quality of life. We found that in skeletal muscle of atrophy models, Dnmt3a was decreased. Muscle regeneration was delayed in the skeletal muscle-specific Dnmt3a knockout (Dnmt3a-KO) mice, in which Dnmt3a was deleted in skeletal muscle as well as in satellite cells, important for muscle regeneration. In this study, we used Dnmt3a-KO mice, and attempt to clarify the mechanism of reduced muscle regeneration during atrophy. The microarray data shows that expression of a Gdf/Bmp family protein Gdf5, which suppressed differentiation of satellite cells, is activated in Dnmt3a-KO mice compared with wild-type mice.

2019-04-01 | GSE97340 | GEO

miR-487b, miR-3963 and miR-6412 delayed myogenic differentiation in C2C12 mouse myoblast-derived cells.

Project description:We newly identified skeletal muscle differentiation-associated miRNAs by comparing miRNA expression profile between C2C12 cell and Wnt4-overexpressing C2C12 cell. miR-487b, miR-3963 and miR-6412 are significantly down-regulated in differentiating C2C12 cells, and transfection of their mimics resulted in reduced expression of myogenic differentiation markers including Troponin T, myosin heavy chain fast and slow type.

2015-11-24 | GSE63454 | GEO

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