Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

The DNA methylomes of a newborn and a centenarian

ABSTRACT: We have developed Whole Genome Bisulfite Sequencing (WGBS) of a newborn and a centenarian to address the epigenetic drifts in human aging, which might be an alternative pathway to explain the age-associated alterations. In addition, we have analyzed the methylome of a middle-age donor (26 years). Examination of two DNA methylomes at the most extreme points of their lives to see differences that might contribute to explain the aged phenotype. The methylome of a middle-age donor (26 years) was also analyzed.

ORGANISM(S): Homo sapiens

SUBMITTER: Antonio GM-CM-3mez

PROVIDER: E-GEOD-31263 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Distinct DNA methylomes of newborns and centenarians.

Heyn Holger H Li Ning N Ferreira Humberto J HJ Moran Sebastian S Pisano David G DG Gomez Antonio A Diez Javier J Sanchez-Mut Jose V JV Setien Fernando F Carmona F Javier FJ Puca Annibale A AA Sayols Sergi S Pujana Miguel A MA Serra-Musach Jordi J Iglesias-Platas Isabel I Formiga Francesc F Fernandez Agustin F AF Fraga Mario F MF Heath Simon C SC Valencia Alfonso A Gut Ivo G IG Wang Jun J Wang Jun J Esteller Manel M

Proceedings of the National Academy of Sciences of the United States of America 20120611 26

Human aging cannot be fully understood in terms of the constrained genetic setting. Epigenetic drift is an alternative means of explaining age-associated alterations. To address this issue, we performed whole-genome bisulfite sequencing (WGBS) of newborn and centenarian genomes. The centenarian DNA had a lower DNA methylation content and a reduced correlation in the methylation status of neighboring cytosine--phosphate--guanine (CpGs) throughout the genome in comparison with the more homogeneous ...[more]

PMID: 22689993

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Project description:Cytosine methylation in the genome of Drosophila melanogaster has been elusive and controversial: methylcytosine has been detected at very low levels in early embryos, but the genomic location and function of methylation has not been established. We have mapped cytosine methylation genomewide in Stage 5 Drosophila embryo DNA by combining immuno-enrichment for 5-methylcytosine, bisulfite conversion, and deep sequencing. Unlike methylation patterns observed in other eukaryotic species, methylation in Drosophila is punctate and highly strand-asymmetrical; we confirmed this by direct PCR amplification and sequencing of bisulfite-converted DNA. Despite the locally asymmetric nature of methylation, large-scale patterns of methylation are symmetric. Methylated regions make up ~1% of the genome, and within these regions methylation of individual cytosines averages 2-10%. Methylation is concentrated in specific 5-base sequence motifs that are CA- and CT-rich but depleted of guanine. It is depleted from promoters, coding sequences, and most retrotransposons, and enriched in introns and in certain simple sequence repeats containing the commonly methylated motifs. Comparison with available gene expression data indicates that methylation in a gene is associated with lower expression; the X chromosome, which is subject to gene dosage compensation, is more densely methylated than the autosomes. This study firmly establishes the presence of cytosine methylation in Drosophila; the temporal overlap of methylation with the maternal-zygotic transition raises the possibility that methylation participates in the transition to zygotic gene expression. To enrich for rare cytosine methylation in Drosophila at embryonic Stage 5 (2-3 hours post-fertilization), we enriched sonicated Stage 5 genomic DNA for methylcytosine by immunoprecipitation with antibody to 5-methylcytosine. The immunoprecipitated DNA was then bisulfite converted and Illumina sequenced to obtain direct evidence for the presence of methylation. The presence and extent of DNA methylation was confirmed by Illumina sequencing of bisulfite-converted PCR amplicons.

Dataset Information

The DNA methylomes of a newborn and a centenarian

Publications

Distinct DNA methylomes of newborns and centenarians.

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