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Series GSE50837 Query DataSets for GSE50837
Status Public on Sep 13, 2013
Title DNA methylation profiling in X;autosome translocations supports a role for L1 repeats in the spread of X chromosome inactivation
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary In order to test the hypothesis that X chromosome inactivation shows sequence specificity, we have analysed the spread of XCI into autosomal chromatin by performing DNA methylation profiling in six unbalanced X;autosome translocations. Using promoter hypermethylation as an epigenetic signature of XCI, we have determined the inactivation status of 1,050 autosomal genes after translocation onto the inactive X. By performing a comparative sequence analysis of autosomal genes that are either subject to or escape the X inactivation signal, we identified a number of common repetitive elements, including LINEs, and DNA motifs that are significantly enriched around inactive autosomal genes. We show that these same motifs predominantly map to L1P elements, are significantly enriched on the X chromosome versus the autosomes, and also occur at higher densities around X-linked genes that are subject to X inactivation compared to those that escape X inactivation. These results are consistent with a potential causal relationship between DNA sequence features such as L1s and the spread of XCI, lending strong support to Mary Lyon's 'repeat hypothesis'.
Overall design Genome-wide measurement of CpG methylation levels by hybridizing bisulphite-converted DNA to Infinium HumanMethylation450 BeadChips. Eight DNA samples extracted from individuals carrying X;autosome translocations were processed according to manufacturer's recommended protocols, and array data processed using the Methylation Module of GenomeStudio v1.8 software with default parameters.
Contributor(s) Bala-Tannan N, Brahmachary M, Garg P, Borel C, Sharp AJ
Citation(s) 24186870
Submission date Sep 12, 2013
Last update date Mar 22, 2019
Contact name Andrew Sharp
Organization name Icahn School of Medicine at Mount Sinai
Department Genetics and Genomics
Street address Hess CSM Building Floor Floor 8 Room 116
City New York
State/province NY
ZIP/Postal code 10029
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (8)
GSM1230994 Genomic DNA from peripheral blood sample 1
GSM1230995 Genomic DNA from peripheral blood sample 2
GSM1230996 Genomic DNA from peripheral blood sample 3
BioProject PRJNA219131

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE50837_RAW.tar 183.1 Mb (http)(custom) TAR
GSE50837_methylated_unmethylated_signal_intensities.txt.gz 19.7 Mb (ftp)(http) TXT
GSE50837_raw_data.txt.gz 87.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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