Dynamic enhancer interactome promotes senescence and aging [Hi-ChIP I]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA974457 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24661423_1.fastq.gz | Fastqsanger.gz | |||
| SRR24661423_2.fastq.gz | Fastqsanger.gz | |||
| SRR24661424_1.fastq.gz | Fastqsanger.gz | |||
| SRR24661424_2.fastq.gz | Fastqsanger.gz | |||
| SRR24661425_1.fastq.gz | Fastqsanger.gz |
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Project description:Dynamic enhancer interactome promotes senescence and aging [Hi-ChIP II]
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Project description:Dynamic enhancer interactome promotes senescence and aging
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Project description:Gene expression programs are regulated by enhancers which act in a context-specific manner, and can reside at great distances from their target genes. Extensive three-dimensional (3D) genome reorganization occurs in senescence, but how enhancer interactomes are reconfigured during this process is just beginning to be understood. Here we generated high-resolution contact maps of active enhancers and their target genes, assessed chromatin accessibility, and established one-dimensional maps of various histone modifications and transcription factors to comprehensively understand the regulation of enhancer configuration during senescence. Hyper-connected enhancer communities/cliques formed around genes that are highly expressed and within essential gene pathways in each cell state. In addition, motif analysis indicates the involvement of specific transcription factors in hyper-connected regulatory elements in each condition; importantly, MafK, a bZIP family transcription factor, was upregulated in senescence, and reduced expression of MafK ameliorated the senescence phenotypes. Because the accumulation of senescent cells is a key feature of aging, we further investigated enhancer connectomes in the liver of young and aged mice. Hyper-connected enhancer communities were identified during aging, which regulate essential genes that maintain cell differentiation and homeostasis. These findings reveal that hyper-connected enhancer communities correlate with high gene expression in senescence and aging and provide potential hotspots for therapeutic intervention in aging and age-associated diseases.
2023-06-20 | GSE232942 | GEO
Project description:Gene expression programs are regulated by enhancers which act in a context-specific manner, and can reside at great distances from their target genes. Extensive three-dimensional (3D) genome reorganization occurs in senescence, but how enhancer interactomes are reconfigured during this process is just beginning to be understood. Here we generated high-resolution contact maps of active enhancers and their target genes, assessed chromatin accessibility, and established one-dimensional maps of various histone modifications and transcription factors to comprehensively understand the regulation of enhancer configuration during senescence. Hyper-connected enhancer communities/cliques formed around genes that are highly expressed and within essential gene pathways in each cell state. In addition, motif analysis indicates the involvement of specific transcription factors in hyper-connected regulatory elements in each condition; importantly, MafK, a bZIP family transcription factor, was upregulated in senescence, and reduced expression of MafK ameliorated the senescence phenotypes. Because the accumulation of senescent cells is a key feature of aging, we further investigated enhancer connectomes in the liver of young and aged mice. Hyper-connected enhancer communities were identified during aging, which regulate essential genes that maintain cell differentiation and homeostasis. These findings reveal that hyper-connected enhancer communities correlate with high gene expression in senescence and aging and provide potential hotspots for therapeutic intervention in aging and age-associated diseases.
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Project description:Skeletal muscle allows voluntary movement and plays a key role in regulating metabolism and homeostasis in the organism. Adult muscle stem cells, MuSCs, are responsible for muscle growth and regeneration. Skeletal muscle suffers from sarcopenia (muscle mass and function loss) during the aging process. Burgeoning evidence suggests that cellular senescence drives MuSC dysfunction in muscle aging. Activation of senescence-associated secretory phenotype (SASP) factors, which is one of the hallmarks of senescence, may be a driving mechanism of sarcopenia but no study so far has clearly defined cellular senescence atlas and SASP components in aging human muscles. Here in this study we propose to profile aging and senescence atlases in aging muscles using the state-of-art multiomics approaches. Our pilot results demonstrate the prevalence of cellular senescence and the dynamics/heterogeneity of SASPs in aging human muscle. Furthermore, regulators governing senescence state and SASP induction were defined. Moreover, we demonstrated the potential of senotherapeutic targeting for sarcopenia treatment. In the project we propose (1) To complete single cell multiomics mapping of aging muscle atlas. (2) To further elucidate cellular senescence in aging muscle. (3) To investigate JUNB regulation of MuSC SASP induction in aging muscle. (4) To test the potential use of senotherapeutics on aging muscle. Once completed, findings from this study will uncover novel knowledge of how MuSC senescence is involved in niche alteration and muscle aging through SASPs and demonstrate the possibility of developing senotherapeutics for treating sarcopenia.
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Project description:Epigenetic alterations are among the prominent drivers of cellular senescence and/or aging. In this study, we show that histone lactylation plays a pivotal role in counteracting senescence and mitigating dysfunctions of skeletal muscle in aged mice. Mechanistically, histone lactylation and lactyl-CoA levels markedly decrease during cellular senescence but are restored under hypoxic conditions primarily due to elevated glycolytic activity. The enrichment of histone lactylation at promoters is essential for sustaining the expression of genes involved in the cell cycle and DNA repair pathways, thereby inhibiting cellular senescence. Furthermore, the modulation of enzymes crucial for histone lactylation, including p300 and HDAC1, leads to reduced histone lactylation and accelerated cellular senescence. Consistently, the suppression of glycolysis and the depletion of histone lactylation are also observed during skeletal muscle aging. Modulating the enzymes also leads to the loss of histone lactylation in skeletal muscle, downregulating DNA repair and proteostasis pathways and accelerating muscle aging. Running exercise increases the levels of glycolysis and histone lactylation, thereby helping to preserve the proper function of skeletal muscle. Our study highlights the significant roles of histone lactylation in modulating cellular senescence and muscle aging, suggesting that this modification may serve as an innovative biomarker for senescence.
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Project description:Epigenetic alterations are among the prominent drivers of cellular senescence and/or aging. In this study, we show that histone lactylation plays a pivotal role in counteracting senescence and mitigating dysfunctions of skeletal muscle in aged mice. Mechanistically, histone lactylation and lactyl-CoA levels markedly decrease during cellular senescence but are restored under hypoxic conditions primarily due to elevated glycolytic activity. The enrichment of histone lactylation at promoters is essential for sustaining the expression of genes involved in the cell cycle and DNA repair pathways, thereby inhibiting cellular senescence. Furthermore, the modulation of enzymes crucial for histone lactylation, including p300 and HDAC1, leads to reduced histone lactylation and accelerated cellular senescence. Consistently, the suppression of glycolysis and the depletion of histone lactylation are also observed during skeletal muscle aging. Modulating the enzymes also leads to the loss of histone lactylation in skeletal muscle, downregulating DNA repair and proteostasis pathways and accelerating muscle aging. Running exercise increases the levels of glycolysis and histone lactylation, thereby helping to preserve the proper function of skeletal muscle. Our study highlights the significant roles of histone lactylation in modulating cellular senescence and muscle aging, suggesting that this modification may serve as an innovative biomarker for senescence.
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