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YY1 stabilizes super enhancer-promoter loops and gene expression during mesenchymal stem cell aging (ChIP-Seq)

ABSTRACT: Stem cell aging leads to a progressive functional decline in self-renewal and differentiation capacity. How chromatin architecture impacts the gene expression changes that underlie altered stem cell function remains to be fully understood. Here, by integrative analyses of transcriptomic, epigenomic and Hi-C data in young and old in vitro aged human mesenchymal stem cells (MSCs), we identified super enhancer (SE)-promoter pairs and delineated changes in these loops during aging. SE target genes are associated with GO categories involved in key MSC functions and are enriched among genes with altered expression during aging, suggesting that changes in SE activity contribute to the functional decline of aged MSCs. YY1 is highly enriched at promoters and SEs and is lost from these regions in old cells. Loss of YY1 from SE-promoter loops correlates with reduced Hi-C contacts, and YY1 knockdown in young cells recapitulates age-associated transcriptomic changes, particularly among SE target genes. Our analyses provide novel insights into the role of altered chromatin loops in stem cell aging and highlight the function of YY1 in maintaining super enhancer-promoter loops and promoting gene expression stability during this process.

ORGANISM(S): Homo sapiens

PROVIDER: GSE261008 | GEO | 2025/06/24

REPOSITORIES: GEO

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Project description:Mesenchymal stromal cells (MSCs) are of high relevance for the regeneration of mesenchymal tissues such as bone and cartilage. The promising role of MSCs in cell-based therapies and tissue engineering appears to be limited due to a decline of their regenerative potential with increasing donor age, their limited availability in human tissues and the need of in vitro expansion prior to treatment. We therefore aimed to determine to which degree in vitro aging and chronological aging may be similar processes or if in vitro culture-related changes at the cellular and molecular level are at least altered as a function of donor age. For that purpose we established MSCs cultures from young (yMSCs) and aged (aMSCs) rats that were cultured for more than 100 passages. These long-term MSCs cultures were non-tumorigenic and exhibited similar surface marker patterns as primary MSCs of passage 2. During in vitro expansion, but not during chronological aging, MSCs progressively lose their progenitor characteristics, e.g., complete loss of osteogenic differentiation potential, diminished adipogenic differentiation, altered cell morphology and increased susceptibility towards senescence. Transcriptome analysis revealed that long-term in vitro MSCs cultivation leads to down-regulation of genes involved in cell differentiation, focal adhesion organization, cytoskeleton turnover and mitochondria function. Accordingly, functional analysis demonstrated altered mitochondrial morphology, decreased antioxidant capacities and elevated ROS levels in long-term cultivated yMSCs as well as aMSCs. Notably, only the MSC migration potential and their antioxidative capacity were altered by in vitro as well as chronological aging. Based on specific differences observed between the impact of chronological and in vitro MSC aging we conclude that both are distinct processes. Total mRNA obtained from MSCs from 12 month and three week old Sprague Dawley rats of passage 2, 30 and 100. Total RNA was isolated using Trizol® (Invitrogen) reagent as describes previously and purified using Qiagen RNeasy® mini kit (Qiagen, Germany, www.qiagen.com) according to manufacturers instruction. Illumina® BeadChip hybridization: Biotinylated cRNA was produced from 500ng total RNA using llumina® TotalPrep™ RNA amplification kit (Invitrogen). Illumina® RatRef-12 Expression BeadChips hybridization, washing, Cy3 streptavidin staining, and scanning were performed using Illumina® BeadStation 500 platform.

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YY1 stabilizes super enhancer-promoter loops and gene expression during mesenchymal stem cell aging (ChIP-Seq)

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