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DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns

ABSTRACT: Background: DNA epigenetic modifications, such as methylation, are important regulators of tissue differentiation, contributing to processes of both development and cancer. Profiling the tissue-specific DNA methylome patterns will provide novel insights into normal and pathogenic mechanisms, as well as help in future epigenetic therapies. In this study, 17 somatic tissues from four autopsied humans were subjected to functional genome analysis using the Illumina Infinium HumanMethylation450 BeadChip, covering 486 428 CpG sites. Results: Only 2% of the CpGs analyzed are hypermethylated in all 17 tissue specimens; these permanently methylated CpG sites are located predominantly in gene-body regions. In contrast, 15% of the CpGs are hypomethylated in all specimens and are primarily located in regions proximal to transcription start sites. A vast number of tissue-specific differentially methylated regions are identified and considered likely mediators of tissue-specific gene regulatory mechanisms since the hypomethylated regions are closely related to known functions of the corresponding tissue. Finally, a clear inverse correlation is observed between promoter methylation within CpG islands and gene expression data obtained from publicly available databases. Conclusions: This genome-wide methylation profiling study identified tissue-specific differentially methylated regions in 17 human somatic tissues. Many of the genes corresponding to these differentially methylated regions contribute to tissue-specific functions. Future studies may use these data as a reference to identify markers of perturbed differentiation and disease-related pathogenic mechanisms.

ORGANISM(S): Homo sapiens

PROVIDER: GSE50192 | GEO | 2014/02/26

SECONDARY ACCESSION(S): PRJNA217218

REPOSITORIES: GEO

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Project description:Background: DNA epigenetic modifications, such as methylation, are important regulators of tissue differentiation, contributing to processes of both development and cancer. Profiling the tissue-specific DNA methylome patterns will provide novel insights into normal and pathogenic mechanisms, as well as help in future epigenetic therapies. In this study, 17 somatic tissues from four autopsied humans were subjected to functional genome analysis using the Illumina Infinium HumanMethylation450 BeadChip, covering 486 428 CpG sites. Results: Only 2% of the CpGs analyzed are hypermethylated in all 17 tissue specimens; these permanently methylated CpG sites are located predominantly in gene-body regions. In contrast, 15% of the CpGs are hypomethylated in all specimens and are primarily located in regions proximal to transcription start sites. A vast number of tissue-specific differentially methylated regions are identified and considered likely mediators of tissue-specific gene regulatory mechanisms since the hypomethylated regions are closely related to known functions of the corresponding tissue. Finally, a clear inverse correlation is observed between promoter methylation within CpG islands and gene expression data obtained from publicly available databases. Conclusions: This genome-wide methylation profiling study identified tissue-specific differentially methylated regions in 17 human somatic tissues. Many of the genes corresponding to these differentially methylated regions contribute to tissue-specific functions. Future studies may use these data as a reference to identify markers of perturbed differentiation and disease-related pathogenic mechanisms. DNA methylation analysis of the total 72 tissue samples and controls was performed with the Illumina Infinium HumanMethylation450 BeadChip. The 17 post-mortem human somatic tissues used in this study were collected at the time of autopsy. Controls for unmethylated and methylated DNA were represented, respectively, by whole-genome amplified DNA from subcutaneous adipose tissue (using the GenomiPhi DNA amplification kit; GE Healthcare, Piscataway, NJ, USA) and the universal methylated human DNA standard (Zymo Research). We had two technical and two biological replicates processed by chip technique.

Project description:Background Chronological aging-associated changes in the human DNA methylome are studied by multiple epigenome-wide association studies (EWAS); however, the aging-associated DNAmet changes identified among different age groups and tissues vary and especially the rates of aging-associated alterations in the epigenome during adulthood remain unclear. Here, we further explore and characterize CpG-sites where DNA methylation levels alter at a constant rate during adulthood and are also independent of blood cell type heterogeneity. Results In the study, we observed 1,202 aging-associated CpG-sites (a-CpGs), of which 48% were hypermethylated with advancing age in whole blood with an especially narrow age range (40 - 49 years). Repeatedly reported a-CpGs in ELOVL2, FHL2, PENK and KLF14 were also identified. Regions with aging-associated hypermethylation were enriched to several gene ontology terms (especially on the cluster of developmental processes), while hypomethylated sites showed no enrichment. The genes with a higher number of a-CpG hits were more often hypermethylated. Of the 1,202 aging-associated CpG-sites in the present study, 987 were identified in previous study (Vitality 90+) as differentially methylated also between nonagenarians and young adults in a previous study, and importantly, the directions of changes were identical in the previous and in the present study. Conclusions The set of 987 replicated a-CpGs presented here are altered in strong association with chronological aging in the whole range of adulthood. Consequently, future studies should note the variability of the types of a-CpGs, and the a-CpGs presented here should be dissociated from the environmental-sensitive CpG-sites or from regions that are associated with aging in a non-linear manner due to the accumulation of senescence-related features. This report offers detailed and verified pool of a-CpGs in which DNAmet levels associate linearly with chronological age and of which are different from the non-linearly changing ones.

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DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns

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