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Potential roles of DNA methylation in the initiation and establishment of replicative senescence revealed by array-based methylome and transcriptome analyses

ABSTRACT: Potential roles of DNA methylation in the initiation and establishment of replicative senescence revealed by array-based methylome and transcriptome analyses

PROVIDER: PRJNA322553 | ENA |

REPOSITORIES: ENA

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Potential roles of DNA methylation in the initiation and establishment of replicative senescence revealed by array-based methylome and transcriptome analyses [methylation]

Project description:Cellular senescence is classified into two types; replicative and premature senescence. Gene expression and epigenetic changes are different in types of senescence, replicative and premature senescence, and cell types. Normal human diploid fibroblast TIG-3 cells were often used in cellular senescence research, however, their epigenetic profiles were not fully understood. To elucidate how cellular senescence is epigenetically regulated in TIG-3 cells, we analyzed gene expression and DNA methylation profiles among three types of senescent cells, namely, replicative senescent, RAS-induced senescent (RIS) and non-permissive temperature-induced senescent SVts8 cells, using gene expression and methylation microarrays. The expression of genes involved in cell cycle and immune response were commonly either down- or up-regulated among three types of senescent cells, respectively. The sequential alteration of DNA methylation level was observed only in replicative senescent cells in a time-dependent manner, but not in premature senescent cells. The integrated analysis of gene expression and methylation in replicative senescent cells demonstrated that the expression of 759 genes involved in cell cycle and immune response was associated with methylation. Furthermore, hypomethylation occurred at non-CpG island regions (open sea) on the genes with increased expression as well as non-CpG promoter of the genes related to immune response. Several miRNAs regulated by DNA methylation were found to affect the expression of their target genes. Taken together, these results indicate that DNA methylation contributes to introduction and establishment of replicative senescence partly by regulating gene expression.

2017-02-12 | GSE81788 | GEO

Potential roles of DNA methylation in the initiation and establishment of replicative senescence revealed by array-based methylome and transcriptome analyses [expression]

2017-02-12 | GSE81786 | GEO

Potential roles of DNA methylation in the initiation and establishment of replicative senescence revealed by array-based methylome and transcriptome analyses [methylation 450K]

2017-02-12 | GSE81797 | GEO

Potential roles of DNA methylation in the initiation and establishment of replicative senescence revealed by array-based methylome and transcriptome analyses

Project description:Cellular senescence is classified into two groups; replicative and premature senescence. The gene expression and epigenetic changes differ between two groups of senescence, replicative and premature senescence, and cell types. Normal human diploid fibroblast TIG-3 cells have often been used in cellular senescence research, however, their epigenetic profiles are not fully understood. To elucidate how cellular senescence is epigenetically regulated in TIG-3 cells, we analyzed the gene expression and DNA methylation profiles of three types of senescent cells, namely, replicative senescent, ras-induced senescent (RIS), and non-permissive temperature-induced senescent SVts8 cells, using gene expression and methylation microarrays. The expression of genes involved in the cell cycle and immune response was commonly either down- or up-regulated in the three types of senescent cells, respectively. The sequential alteration of the DNA methylation level in a time-dependent manner was observed in replicatively senescent cells, but not in premature senescent cells. The integrated analysis of gene expression and methylation in replicatively senescent cells demonstrated that the expression of 759 genes involved in the cell cycle and immune response was associated with methylation. Furthermore, hypomethylation occurred in non-CpG island regions (open sea) of the genes exhibiting increased expression as well as non-CpG island promoters of the genes related to the immune response. Several miRNAs regulated through DNA methylation were found to affect the expression of their target genes. Taken together, these results indicate that DNA methylation contributes to the introduction and establishment of replicative senescence partly by regulating gene expression.

2017-02-12 | GSE90942 | GEO

Potential roles of DNA methylation in the initiation and establishment of replicative senescence revealed by array-based methylome and transcriptome analyses.

Project description: Not available

| S-EPMC5291461 | biostudies-literature

Potential roles of DNA methylation in the initiation and establishment of replicative senescence revealed by array-based methylome and transcriptome analyses

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-02-12 | GSE81798 | GEO

Transcription initiation drives dosage compensation establishment and maintenance in male Drosophila

Project description:Transcription initiation drives dosage compensation establishment and maintenance in male Drosophila

| PRJNA1321782 | ENA

Transcription initiation drives dosage compensation establishment and maintenance in male Drosophila

Project description:Dosage compensation (DC) in Drosophila equalizes X chromosome-linked gene expression via the Male-Specific Lethal (MSL) complex, which acetylates histone 4 lysine 16 on the male X-chromosome. How DC is established during early embryogenesis remains obscure, largely due to the difficulty of obtaining sufficient sex-specific material at early embryonic stages. Here, we developed a high-throughput embryo sorting strategy and combined newly synthesized RNA-sequencing and RNA-polymerase II (Pol II) profiling to investigate the mechanisms underlying the onset of DC in vivo. We found that changes in transcription initiation occur prior to detectable differences in transcriptional pausing or elongation and represent the primary determinant of enhanced mRNA output during DC establishment. It had hitherto been unclear whether DC establishment and maintenance exerted similar or distinct effects on transcriptional kinetics. Extending genomewide profiling to S2 cells we uncovered Pol II initiation as a general principle underlying both inception and perpetuation of DC-driven transcriptional upregulation.

2026-05-28 | GSE307467 | GEO

Transcription initiation drives dosage compensation establishment and maintenance in male Drosophila [TTSeq_Embryos]

2026-05-28 | GSE307585 | GEO

Transcription initiation drives dosage compensation establishment and maintenance in male Drosophila [TTseq_S2_MSL1_MSL2]

2026-05-28 | GSE307582 | GEO