E-GEOD-41273 - Genome-wide analysis identifies aberrant methylation in Fragile X syndrome is specific to the FMR1 locus

Status
Released on 15 April 2013, last updated on 22 April 2013
Organism
Homo sapiens
Samples (62)
Array (1)
Protocols (7)
Description
Fragile X syndrome (FXS) is a common form of inherited intellectual disability and is caused by an expansion of CGG repeats located in the 5Õ untranslated region (UTR) of the FMR1 gene, leading to hypermethylation and silencing of this locus. While the dramatic increase in DNA methylation (DNAm) of the FMR1 full mutation allele is well documented, the extent that these changes affect DNAm throughout the entire gene and the rest of the genome remains unexplored. Here, we examine the genome-wide methylation in peripheral blood (N = 9) as well as induced pluripotent stem cells (iPSCs; N = 10) from FXS individuals and controls (N = 53 and 9, respectively) and find the expected significant DNAm differences in the FMR1 promoter and 5Õ UTR, but also that these changes inversely persist throughout the FMR1 gene body. Importantly, we find there are no additional differential methylated loci (DML) throughout the remainder of the genome, indicating that the aberrant methylation of the FMR1 in FXS is locus-specific and does not change DNAm genome-wide. This study provides a comprehensive methylation profile of FXS and refines mechanistic considerations of FMR1 silencing. A total of 62 blood (53 controls + 9 Fragile X) samples analyzed using a linear regression model.
Experiment type
methylation profiling by array 
Contacts
Citation
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-41273.idf.txt
Sample and data relationshipE-GEOD-41273.sdrf.txt
Processed data (2)E-GEOD-41273.processed.1.zip, E-GEOD-41273.processed.2.zip
Array designA-GEOD-13534.adf.txt
Links