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Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites.

Hänzelmann S, Beier F, Gusmao EG, Koch CM, Hummel S, Charapitsa I, Joussen S, Benes V, Brümmendorf TH, Reid G, Costa IG, Wagner W - Clin Epigenetics (2015)

Bottom Line: DNA hypermethylation was significantly enriched in the vicinity of genes that are either up- or downregulated at later passages.Furthermore, specific transcription factor binding motifs (e.g. EGR1, TFAP2A, and ETS1) were significantly enriched in differentially methylated regions and in the promoters of differentially expressed genes.Senescence-associated DNA hypermethylation occurs at specific sites in the genome and reflects functional changes in the course of replicative senescence.

View Article: PubMed Central - PubMed

Affiliation: Interdisciplinary Centre for Clinical Research (IZKF), RWTH University Medical School, Aachen, Germany ; Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany.

ABSTRACT

Background: Primary cells enter replicative senescence after a limited number of cell divisions. This process needs to be considered in cell culture experiments, and it is particularly important for regenerative medicine. Replicative senescence is associated with reproducible changes in DNA methylation (DNAm) at specific sites in the genome. The mechanism that drives senescence-associated DNAm changes remains unknown - it may involve stochastic DNAm drift due to imperfect maintenance of epigenetic marks or it is directly regulated at specific sites in the genome.

Results: In this study, we analyzed the reorganization of nuclear architecture and DNAm changes during long-term culture of human fibroblasts and mesenchymal stromal cells (MSCs). We demonstrate that telomeres shorten and shift towards the nuclear center at later passages. In addition, DNAm profiles, either analyzed by MethylCap-seq or by 450k IlluminaBeadChip technology, revealed consistent senescence-associated hypermethylation in regions associated with H3K27me3, H3K4me3, and H3K4me1 histone marks, whereas hypomethylation was associated with chromatin containing H3K9me3 and lamina-associated domains (LADs). DNA hypermethylation was significantly enriched in the vicinity of genes that are either up- or downregulated at later passages. Furthermore, specific transcription factor binding motifs (e.g. EGR1, TFAP2A, and ETS1) were significantly enriched in differentially methylated regions and in the promoters of differentially expressed genes.

Conclusions: Senescence-associated DNA hypermethylation occurs at specific sites in the genome and reflects functional changes in the course of replicative senescence. These results indicate that tightly regulated epigenetic modifications during long-term culture contribute to changes in nuclear organization and gene expression.

No MeSH data available.


Related in: MedlinePlus

Scheme of chromosomal changes in replicative senescence. Nuclear size increases; telomeres shorten and shift towards the nuclear center; DNA hypermethylation is rather observed in regions with the repressive histone mark H3K27me3 and with the activating histone marks H3K4me3 and H3K4me1, whereas hypomethylation is associated with H3K9me3 and LADs; gene expression changes are particularly observed in hypermethylated regions. DNAm changes and differentially expressed genes coincide with binding motifs for specific TFs.
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Fig6: Scheme of chromosomal changes in replicative senescence. Nuclear size increases; telomeres shorten and shift towards the nuclear center; DNA hypermethylation is rather observed in regions with the repressive histone mark H3K27me3 and with the activating histone marks H3K4me3 and H3K4me1, whereas hypomethylation is associated with H3K9me3 and LADs; gene expression changes are particularly observed in hypermethylated regions. DNAm changes and differentially expressed genes coincide with binding motifs for specific TFs.

Mentions: In this study, we demonstrate various facets of the impact replicative senescence has on nuclear organization (Figure 6). This complex picture suggests that different mechanisms are involved in senescence-associated changes, with hypomethylation enriched in inactivated LADs, whereas hypermethylation is reflected by specific changes in gene expression.Figure 6


Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites.

Hänzelmann S, Beier F, Gusmao EG, Koch CM, Hummel S, Charapitsa I, Joussen S, Benes V, Brümmendorf TH, Reid G, Costa IG, Wagner W - Clin Epigenetics (2015)

Scheme of chromosomal changes in replicative senescence. Nuclear size increases; telomeres shorten and shift towards the nuclear center; DNA hypermethylation is rather observed in regions with the repressive histone mark H3K27me3 and with the activating histone marks H3K4me3 and H3K4me1, whereas hypomethylation is associated with H3K9me3 and LADs; gene expression changes are particularly observed in hypermethylated regions. DNAm changes and differentially expressed genes coincide with binding motifs for specific TFs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4356053&req=5

Fig6: Scheme of chromosomal changes in replicative senescence. Nuclear size increases; telomeres shorten and shift towards the nuclear center; DNA hypermethylation is rather observed in regions with the repressive histone mark H3K27me3 and with the activating histone marks H3K4me3 and H3K4me1, whereas hypomethylation is associated with H3K9me3 and LADs; gene expression changes are particularly observed in hypermethylated regions. DNAm changes and differentially expressed genes coincide with binding motifs for specific TFs.
Mentions: In this study, we demonstrate various facets of the impact replicative senescence has on nuclear organization (Figure 6). This complex picture suggests that different mechanisms are involved in senescence-associated changes, with hypomethylation enriched in inactivated LADs, whereas hypermethylation is reflected by specific changes in gene expression.Figure 6

Bottom Line: DNA hypermethylation was significantly enriched in the vicinity of genes that are either up- or downregulated at later passages.Furthermore, specific transcription factor binding motifs (e.g. EGR1, TFAP2A, and ETS1) were significantly enriched in differentially methylated regions and in the promoters of differentially expressed genes.Senescence-associated DNA hypermethylation occurs at specific sites in the genome and reflects functional changes in the course of replicative senescence.

View Article: PubMed Central - PubMed

Affiliation: Interdisciplinary Centre for Clinical Research (IZKF), RWTH University Medical School, Aachen, Germany ; Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany.

ABSTRACT

Background: Primary cells enter replicative senescence after a limited number of cell divisions. This process needs to be considered in cell culture experiments, and it is particularly important for regenerative medicine. Replicative senescence is associated with reproducible changes in DNA methylation (DNAm) at specific sites in the genome. The mechanism that drives senescence-associated DNAm changes remains unknown - it may involve stochastic DNAm drift due to imperfect maintenance of epigenetic marks or it is directly regulated at specific sites in the genome.

Results: In this study, we analyzed the reorganization of nuclear architecture and DNAm changes during long-term culture of human fibroblasts and mesenchymal stromal cells (MSCs). We demonstrate that telomeres shorten and shift towards the nuclear center at later passages. In addition, DNAm profiles, either analyzed by MethylCap-seq or by 450k IlluminaBeadChip technology, revealed consistent senescence-associated hypermethylation in regions associated with H3K27me3, H3K4me3, and H3K4me1 histone marks, whereas hypomethylation was associated with chromatin containing H3K9me3 and lamina-associated domains (LADs). DNA hypermethylation was significantly enriched in the vicinity of genes that are either up- or downregulated at later passages. Furthermore, specific transcription factor binding motifs (e.g. EGR1, TFAP2A, and ETS1) were significantly enriched in differentially methylated regions and in the promoters of differentially expressed genes.

Conclusions: Senescence-associated DNA hypermethylation occurs at specific sites in the genome and reflects functional changes in the course of replicative senescence. These results indicate that tightly regulated epigenetic modifications during long-term culture contribute to changes in nuclear organization and gene expression.

No MeSH data available.


Related in: MedlinePlus