Genome-wide mRNA targets of CPEB1 in muscle stem cells
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ABSTRACT:
PROVIDER: PRJNA626471 | ENA |
REPOSITORIES: ENA
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Project description:We performed CPEB1 RIP-seq on freshly isolated muscle stem cells. We found that CPEB1 associated genes are enriched in translational regulation pathways.
2021-11-02 | GSE148912 | GEO
Project description:We performed CPEB4 RIP-seq on freshly isolated muscle stem cells. We found that CPEB4 associated genes are enriched in metabolic relevant pathways such as some mitochondrial protein coding genes
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Project description:Muscle Stem Cells or satellite cells (SCs) are required for muscle regeneration. In resting muscles, SCs are kept in quiescence. After injury, SCs undergo rapid activation, proliferation and differentiation to repair damaged muscles. The transcriptome alteration during SC activation is well characterized. While transcriptome is not exactly represent proteome because of post-transcriptional regulations such as miRNA induced gene silencing. However, little is known about SC proteome. We obtained quisecent SCs (QSCs) and freshly isolated SCs (fiSCs, early activated SCs) and activated SCs (ASCs) for high resolution mass spectrometry Bruker timsTOF Pro. Thus, we uncovered the QSC proteome. By comparison of QSC proteome to fiuSCs proteome or ASCs proteome, we identified the pathways that are differentially expressed between them. Forthermore, we characterized a translational regulator CPEB1 reprogrammed translation landscape for SC activation.
2021-11-05 | PXD018865 | Pride
Project description:This experiment was conducted to identify novel MLL4 targets in skeletal muscle Enhancers play central role in controlling gene expression in time and space. Primed enhancers are marked by histone H3 lysine 4 (H3K4) mono/di-methylation (H3K4me1/2). Mixed-lineage leukemia 4 (MLL4/KMT2D) is an evolutionarily conserved H3K4me1/2 methyltransferase that is required for enhancer activation. Here, we identified the genome-wide MLL4 occupancy in mouse skeletal muscle by ChIP-seq coupled with RNA-seq analysis. Gene ontology analysis revealed that MLL4 controls muscle fiber-type switching. We thus have revealed novel MLL4 targets involved in muscle metabolism.
2020-10-01 | GSE138994 | GEO
Project description:Skeletal muscle degenerates progressively, loses mass (sarcopenia) along in years, and leads to reduced physical ability, often causing secondary diseases such as diabetes and obesity. It is known that regulation of gene expression by microRNAs is a key event in muscle development and disease. To understand genome-wide changes in microRNAs and mRNAs during muscle aging, we sequenced microRNAs as well as mRNAs from mouse gastrocnemius muscles at two different ages (6 versus 24-month-old). Thirty-four microRNAs (15 up-regulated and 19 down-regulated) were differentially expressed with age among which were microRNAs such as miR-206 or -434 which were differentially expressed in aged muscle in previous studies. Interestingly, seven microRNAs in a microRNA cluster at imprinted Dlk1-Dio3 locus on chromosome 12 were coordinately down-regulated. In addition, sixteen novel microRNAs were identified. Integrative analysis of microRNA and mRNA expression revealed that microRNAs contribute to muscle aging possibly through the positive regulation of transcription, metabolic process, and kinase activity. Many of the age-related microRNAs were implicated in human muscular diseases. We suggest that genome-wide microRNA profiling helps to expand our knowledge of microRNA function in the muscle aging process. mRNA profiles of gastrocnemius muscle tissues (n=10) were generated by deep sequencing using Illumina Hiseq-2000
2014-08-08 | E-GEOD-55163 | biostudies-arrayexpress
Project description:Skeletal muscle degenerates progressively, loses mass (sarcopenia) along in years, and leads to reduced physical ability, often causing secondary diseases such as diabetes and obesity. It is known that regulation of gene expression by microRNAs is a key event in muscle development and disease. To understand genome-wide changes in microRNAs and mRNAs during muscle aging, we sequenced microRNAs as well as mRNAs from mouse gastrocnemius muscles at two different ages (6 versus 24-month-old). Thirty-four microRNAs (15 up-regulated and 19 down-regulated) were differentially expressed with age among which were microRNAs such as miR-206 or -434 which were differentially expressed in aged muscle in previous studies. Interestingly, seven microRNAs in a microRNA cluster at imprinted Dlk1-Dio3 locus on chromosome 12 were coordinately down-regulated. In addition, sixteen novel microRNAs were identified. Integrative analysis of microRNA and mRNA expression revealed that microRNAs contribute to muscle aging possibly through the positive regulation of transcription, metabolic process, and kinase activity. Many of the age-related microRNAs were implicated in human muscular diseases. We suggest that genome-wide microRNA profiling helps to expand our knowledge of microRNA function in the muscle aging process.
2014-08-08 | GSE55163 | GEO
Project description:A genome-wide approach to delineate novel MLL4 targets involved in skeletal muscle metabolism
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Project description:Genome-wide maps of IRF2 targets
| PRJNA433012 | ENA
Project description:Skeletal muscle degenerates progressively, loses mass (sarcopenia) along in years, and leads to reduced physical ability, often causing secondary diseases such as diabetes and obesity. It is known that regulation of gene expression by microRNAs is a key event in muscle development and disease. To understand genome-wide changes in microRNAs and mRNAs during muscle aging, we sequenced microRNAs as well as mRNAs from mouse gastrocnemius muscles at two different ages (6 versus 24-month-old). Thirty-four microRNAs (15 up-regulated and 19 down-regulated) were differentially expressed with age among which were microRNAs such as miR-206 or -434 which were differentially expressed in aged muscle in previous studies. Interestingly, seven microRNAs in a microRNA cluster at imprinted Dlk1-Dio3 locus on chromosome 12 were coordinately down-regulated. In addition, sixteen novel microRNAs were identified. Integrative analysis of microRNA and mRNA expression revealed that microRNAs contribute to muscle aging possibly through the positive regulation of transcription, metabolic process, and kinase activity. Many of the age-related microRNAs were implicated in human muscular diseases. We suggest that genome-wide microRNA profiling helps to expand our knowledge of microRNA function in the muscle aging process. miRNA profiles of gastrocnemius muscle tissues (n=10) were generated by deep sequencing using Illumina Hiseq-2000
2014-08-08 | E-GEOD-55164 | biostudies-arrayexpress
Project description:To investigate the structure of the bodywall muscle differentiation network, we sought to both identify what these transcription factors regulate in bodywall muscle. Through loss of function analysis, we identified genome-wide regulatory targets of hlh-1 and unc-120 using RNA-seq. 1445 targets of hlh-1 and 3674 targets of unc-120 were identified, with 760 of these genes being targets of both. Crosstalk was identified between the networks of hlh-1 and hlh-8, which is involved in non-bodywall muscle development. In the process, we quantified bodywall muscle RNA. Our data suggest that shared target genes and overlapping regulation buffer the hlh-1 and unc-120 mutant phenotypes. RNA expression genome-wide in the early embryo
2012-06-21 | E-GEOD-28562 | biostudies-arrayexpress