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Series GSE37333 Query DataSets for GSE37333
Status Public on Oct 15, 2012
Title Smchd1 dependent and independent pathways determine developmental dynamics of CpG island methylation on the inactive X chromosome.
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary X chromosome inactivation involves multiple levels of chromatin modification, established progressively and in a stepwise manner during early development. The chromosomal protein Smchd1 has recently been shown to play an important role in DNA methylation of CpG islands (CGIs), a late step in the X inactivation pathway required for long-term stability of gene silencing. Here we show that inactive X chromosome (Xi) CGI methylation can occur via either Smchd1 dependent or independent pathways. Smchd1 dependent CGI methylation, the primary pathway, is acquired gradually over an extended period, whereas Smchd1 independent CGI methylation occurs rapidly after the onset of X inactivation. The de novo methyltransferase Dnmt3b is required for methylation of both classes of CGI, whereas Dnmt3a and Dnmt3L are dispensable. Xi CGIs methylated by these distinct pathways differ in respect to their sequence characteristics and immediate chromosomal environment. We discuss the implications of these results for understanding CGI methylation during development.
Overall design Examination of CpG methylated DNA from wild type and smchd1 null male and female somatic cells and female ES cells differentiated for either 7 or 10 days. Duplicate samples of each type were generated.
Contributor(s) Gendrel A, Apedaile A, Coker H, Zvetkova I, Tang YA, Huntley D, Montana G, Taylor S, Giannoulatou E, Termanis A, Stancheva I, Leleu M, Brockdorff N
Citation(s) 22841499
Submission date Apr 17, 2012
Last update date May 15, 2019
Contact name Stephen Taylor
Phone +44 1865 222640
Organization name CBRG
Street address Headington
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (6)
BioProject PRJNA159587
SRA SRP012261

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Supplementary file Size Download File type/resource
GSE37333_RAW.tar 342.0 Mb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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