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| 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
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| 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.
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| 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.
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| 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 |
| E-mail(s) |
stephen.taylor@imm.ox.ac.uk
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| Phone |
+44 1865 222640
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| Organization name |
CBRG
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| Street address |
Headington
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| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
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| Platforms (2) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA159587 |
| SRA |
SRP012261 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE37333_RAW.tar |
342.0 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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