|
| 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 |
| GSM1230997 |
Genomic DNA from peripheral blood sample 4 |
| GSM1230998 |
Genomic DNA from peripheral blood sample 5 |
| GSM1230999 |
Genomic DNA from peripheral blood sample 6 |
| GSM1231000 |
Genomic DNA from peripheral blood sample 7 |
| GSM1231001 |
Genomic DNA from peripheral blood sample 8 |
|
| Relations |
| BioProject |
PRJNA219131 |
Less...
More...