Integrated ATAC-seq and RNA-seq Analysis of In Vitro Cultured Skeletal Muscle Satellite Cells to Understand Changes in Cell Proliferation.

Publisher: MDPI Country of Publication: Switzerland NLM ID: 101600052 Publication Model: Electronic Cited Medium: Internet ISSN: 2073-4409 (Electronic) Linking ISSN: 20734409 NLM ISO Abbreviation: Cells Subsets: MEDLINE

Original Publication: Basel, Switzerland : MDPI

Satellite Cells, Skeletal Muscle*/metabolism ; Satellite Cells, Skeletal Muscle*/cytology ; Cell Proliferation*/genetics ; RNA-Seq*; Animals ; Cells, Cultured ; Swine ; Chromatin/metabolism ; Transcriptome/genetics ; Gene Expression Regulation ; Chromatin Immunoprecipitation Sequencing

Skeletal muscle satellite cells, the resident stem cells in pig skeletal muscle, undergo proliferation and differentiation to enable muscle tissue repair. The proliferative and differentiative abilities of these cells gradually decrease during in vitro cultivation as the cell passage number increases. Despite extensive research, the precise molecular mechanisms that regulate this process are not fully understood. To bridge this knowledge gap, we conducted transcriptomic analysis of skeletal muscle satellite cells during in vitro cultivation to quantify passage number-dependent changes in the expression of genes associated with proliferation. Additionally, we explored the relationships between gene transcriptional activity and chromatin accessibility using transposase-accessible chromatin sequencing. This revealed the closure of numerous open chromatin regions, which were primarily located in intergenic regions, as the cell passage number increased. Integrated analysis of the transcriptomic and epigenomic data demonstrated a weak correlation between gene transcriptional activity and chromatin openness in expressed genic regions; although some genes (e.g., GNB4 and FGD5 ) showed consistent relationships between gene expression and chromatin openness, a substantial number of differentially expressed genes had no clear association with chromatin openness in expressed genic regions. The p53-p21-RB signaling pathway may play a critical regulatory role in cell proliferation processes. The combined transcriptomic and epigenomic approach taken here provided key insights into changes in gene expression and chromatin openness during in vitro cultivation of skeletal muscle satellite cells. These findings enhance our understanding of the intricate mechanisms underlying the decline in cellular proliferation capacity in cultured cells.

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32130102 National Natural Science Foundation of China; 32002173 National Natural Science Foundation of China; No.D20221603 Science and Technology Research Program of Hubei Provincial Department of Education; CJGJZD20210408092402006 Science and Technology Program of Shenzhen

Keywords: ATAC-seq; cell proliferation; pig; satellite cells

0 (Chromatin)

Date Created: 20240626 Date Completed: 20240626 Latest Revision: 20240628

20240628

PMC11201436

10.3390/cells13121031

38920660