Chromatin profiling reveals many transcriptional regulators of proliferation and differentiation of bovine satellite cells
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ABSTRACT:
PROVIDER: PRJNA1065453 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27585844_1.fastq.gz | Fastqsanger.gz | |||
| SRR27585844_2.fastq.gz | Fastqsanger.gz | |||
| SRR27585845_1.fastq.gz | Fastqsanger.gz | |||
| SRR27585845_2.fastq.gz | Fastqsanger.gz | |||
| SRR27585846_1.fastq.gz | Fastqsanger.gz |
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Project description:Satellite cells are myogenic precursor cells in adult skeletal muscle and play a crucial role in skeletal muscle repair, remodeling, and maintenance. Like myoblasts, satellite cells have the ability to proliferate, differentiate, and fuse to form multinucleated myofibers. In this study we aimed to identify the enhancers and the transcription factors binding to these enhancers that control gene expression in proliferating and differentiating bovine satellite cells. Using ChIP-seq, we identified 56,973 and 54,470 active enhancers, genomic regions marked with both H3K4me1 and H3K27ac, and 50,956 and 59,174 repressed enhancers, genomic regions marked with H3K27me3, in proliferating and differentiating bovine satellite cells, respectively. Motif enrichment analyses revealed many transcription factors including the AP-1 family transcription factors that regulate gene expression in proliferating bovine satellite cells and many transcription factors besides MyoG that regulate gene expression in differentiating bovine satellite cells.
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Project description:In this study we isolated satellite cells from skeletal muscle from two Angus-crossbred steers, initially cultured them in growth medium for proliferation, and then in differentiation medium to induce them to differentiate and fuse into myotubes. We used ChIP-seq to identify enhancers marked with H3K27ac, i.e., active enhancers, from these cells immediately before and two days after induction of differentiation. Nearly 20,000 and 50,000 H3K27ac-marked enhancers were consistently identified from two biological replicates of before- and during-differentiation bovine satellite cells, respectively.
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Project description:In this study we analyzed the bovine satellite cells with single-cell RNA sequencing (scRNA-seq). We isolated muscle satellite cells from a male calf, cultured them in growth medium for a week, and then constructed two scRNA-seq libraries from them using the 10x Genomics platform. Next generation sequencing yielded 860 million reads. Cell calling analyses revealed that these reads represented 15 cell clusters that differed in gene expression profile from a total of 19,096 individual cells.
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Project description:In this study, we directly compared turkey muscle satellite cell gene expression between satellite cells with the gene Matrix Gla Protein (MGP) knocked down by siRNA transfection and those transfected with a lipofectamine control using our 6K Turkey Skeletal Muscle Long Oligo (TSKMLO) microarray (GPL9788). The MGP gene was previously identified as differentially expressed by genetic line and during development of turkey skeletal muscle (Sporer et al., 2011). Gene expression changes were investigated in satellite cells after 72 h of proliferation and after 48 h of differentiation. We identified novel candidate genes and pathways as playing potentially crucial roles in the MGP-mediated effects on the normal processes of proliferation and differentiation in turkey satellite cells previously identified by Velleman et al. (submitted). This experiment was designed to investigate the role of MGP expression in turkey satellite cells during two crucial processes in muscle development: proliferation and differentiation. Satellite cells were isolated from 7-week-old turkeys from the RBC2 line. Cells were transfected with either MGP siRNA or a lipofectamine control; MGP expression was knocked down by over 50% with siRNA transfection (Velleman et al., submitted). Satellite cells were then induced to proliferate for 72h or differentiate for 48h; culture plates from each stage (n=4) were frozen until RNA extraction. Microarrays directly compared the MGP -knockdown to control from each of 4 culture plates and utilized a dye swap to equal 8 arrays for each of the cell developmental stages, proliferation and differentiation, and 16 arrays for the overall experiment investigating the role of MGP expression in satellite cell development and function. Hybridizations were performed in random order.
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Project description:In this study, we directly compared turkey muscle satellite cell gene expression between satellite cells with the gene versican (VCAN) knocked down by siRNA transfection and those transfected with a lipofectamine control using our 6K Turkey Skeletal Muscle Long Oligo (TSKMLO) microarray (GPL9788). The VCAN gene was previously identified as differentially expressed by genetic line and during development of turkey skeletal muscle (Sporer et al., 2011). Gene expression changes were investigated in satellite cells after 72 h of proliferation and after 48 h of differentiation. We identified novel candidate genes and pathways as playing potentially crucial roles in the VCAN-mediated effects on the normal processes of proliferation and differentiation in turkey satellite cells previously identified by Velleman et al. (submitted). This experiment was designed to investigate the role of VCAN expression in turkey satellite cells during two crucial processes in muscle development: proliferation and differentiation. Satellite cells were isolated from 7-week-old turkeys from the RBC2 line. Cells were transfected with either VCAN siRNA or a lipofectamine control; VCAN expression was knocked down by over 50% with siRNA transfection (Velleman et al., submitted). Satellite cells were then induced to proliferate for 72h or differentiate for 48h; culture plates from each stage (n=4) were frozen until RNA extraction. Microarrays directly compared the VCAN-knockdown to control from each of 4 culture plates and utilized a dye swap to equal 8 arrays for each of the cell developmental stages, proliferation and differentiation, and 16 arrays for the overall experiment investigating the role of VCAN expression in satellite cell development and function. Hybridizations were performed in random order.
2012-05-31 | E-GEOD-36365 | biostudies-arrayexpress
Project description:In this study, we directly compared turkey muscle satellite cell gene expression between satellite cells with the gene Death-Associated Protein (DAP) knocked down by siRNA transfection and those transfected with a lipofectamine control using our 6K Turkey Skeletal Muscle Long Oligo (TSKMLO) microarray (GPL9788). The DAP gene was previously identified as differentially expressed by genetic line and during development of turkey skeletal muscle (Sporer et al., 2011). Gene expression changes were investigated in satellite cells after 72 h of proliferation and after 48 h of differentiation. We identified novel candidate genes and pathways as playing potentially crucial roles in the DAP-mediated attenuation of the normal processes of proliferation and differentiation in turkey satellite cells previously identified by Velleman et al. (submitted). This experiment was designed to investigate the role of DAP expression in turkey satellite cells during two crucial processes in muscle development: proliferation and differentiation. Satellite cells were isolated from 7-week-old turkeys from the RBC2 line. Cells were transfected with either DAP siRNA or a lipofectamine control; DAP expression was knocked down by over 50% with siRNA transfection (Velleman et al., submitted). Satellite cells were then induced to proliferate for 72h or differentiate for 48h; culture plates from each stage (n=4) were frozen until RNA extraction. Microarrays directly compared the DAP-knockdown to control from each of 4 culture plates and utilized a dye swap to equal 8 arrays for each of the cell developmental stages, proliferation and differentiation, and 16 arrays for the overall experiment investigating the role of DAP expression in satellite cell development and function. Hybridizations were performed in random order.
2012-05-31 | E-GEOD-35660 | biostudies-arrayexpress
Project description:scRNA-seq analysis of cultured bovine satellite cells
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Project description:DNA methylation is an essential form of epigenetic regulation responsible for cellular identity. In muscle stem cells, termed satellite cells, DNA methylation patterns are tightly regulated during differentiation. However, it is unclear how these DNA methylation patterns affect the function of satellite cells. We demonstrate that a key epigenetic regulator, ubiquitin like with PHD and RING finger domains 1 (Uhrf1), is activated in proliferating myogenic cells but not expressed in quiescent satellite cells or differentiated myogenic cells in mice. Ablation of Uhrf1 in mouse satellite cells impairs their proliferation and differentiation, leading to failed muscle regeneration. Uhrf1-deficient myogenic cells exhibited aberrant up-regulation of transcripts, including Sox9, with the reduction of DNA methylation level of their promoter and enhancer region. These findings show that Uhrf1 is a critical epigenetic regulator of proliferation and differentiation in satellite cells, by controlling cell type-specific gene expression via maintenance of DNA methylation.
2022-02-04 | GSE169193 | GEO
Project description:DNA methylation is an essential epigenetic regulation for cellular identity. In muscle stem cells, termed satellite cells, DNA methylation patterns are dynamically changed during muscle regeneration. However, how these DNA methylation patterns are maintained remain unclear. Here, we demonstrate that a key epigenetic regulator Uhrf1 (ubiquitin-like with PHD and RING finger domains 1) is activated in proliferating but not expressed in quiescent or differentiated satellite cells. Ablation of Uhrf1 in satellite cell impairs the proliferation and differentiation of satellite cells, leading to failure of muscle regeneration. Loss of Uhrf1 in satellite cells alters transcriptional programs and leads to DNA hypomethylation with the activation of Cdkn1a and Notch signalling. Down-regulation of Cdkn1a and Notch signalling rescued the proliferation and differentiation defect in Uhrf1-deficient satellite cells. Therefore, this study suggest that Uhrf1 can regulate the self-renewal and differentiation of satellite cells through DNA methylation patterning.
2022-02-04 | GSE169192 | GEO