Transcriptomics

Dataset Information

4

H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells [twins]


ABSTRACT: In differentiated cells, aging is associated with hypermethylation of DNA regions enriched in repressive histone posttranslational modifications. However, the chromatin marks associated with changes in DNA methylation in adult stem cells during lifetime are still largely unknown. Here, DNA methylation profiling of mesenchymal stem cells obtained from individuals aged 2 to 92 identified 18735 hypermethylated and 45407 hypomethylated CpG sites associated with aging. As in differentiated cells, hypermethylated sequences were enriched in chromatin repressive marks. Most importantly, hypomethylated CpG sites were strongly enriched in the active chromatin mark H3K4me1 in stem and differentiated cells, suggesting this is a cell type-independent chromatin signature of DNA hypomethylation during aging. Analysis of scedasticity showed that interindividual variability of DNA methylation increased during aging in MSCs and differentiated cells, providing a new avenue for the identification of DNA methylation changes over time. DNA methylation profiling of genetically identical individuals showed that both the tendency of DNA methylation changes and scedasticity depended on non-genetic as well as genetic factors. Our results indicate that the dynamics of DNA methylation during aging depend on a complex mixture of factors that include the DNA sequence, cell type and chromatin context involved, and that, depending on the locus, the changes can be modulated by genetic and/or external factors. Total DNA isolated by standard procedures from peripheral blood of 24 samples obtained from 12 pairs of MZ twins aged 21 to 66.

ORGANISM(S): Homo sapiens  

SUBMITTER: Sonia Brescianini   Rocío G Urdinguio  Agustin F Fernandez  Lorenza Nisticò  Manel Esteller  Anouk Mentink  Sebastián Moran  Maria G Garcia  Flor M Perez-Campo  Katia Mareschi  Corrado Fagnani  Jan de Boer  Pablo Menendez  Mario F Fraga  Isabel Cubillo  Maria A Stazi  Jesús Delgado-Calle  Clara Bueno  Antonella Carella  Gustavo F Bayón  Javier García-Castro  José A Riancho  Alexandra Stolzing  Fabian Claire  Pablo Martinez-Camblor  Cecilia Ferrero  Estela G Toraño  Sandra Petrus-Reurer  Virgilia Toccaceli  Emanuela Medda 

PROVIDER: E-GEOD-52113 | ArrayExpress | 2014-09-25

SECONDARY ACCESSION(S): GSE52113PRJNA226710

REPOSITORIES: GEO, ArrayExpress

Dataset's files

Source:
Action DRS
E-GEOD-52113.additional.1.zip Other
E-GEOD-52113.idf.txt Idf
E-GEOD-52113.processed.1.zip Processed
E-GEOD-52113.sdrf.txt Txt
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