|
| Status |
Public on Jul 31, 2013 |
| Title |
Default DNA Methylation is Preceded by Broad, Low-Level Transcription in Fetal Male Germ Cells and Is Inversely Patterned by Dynamic H3K4 Methylation (RNA-Seq) |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
To understand what dictates the emerging patterns of de novo DNA methylation, we mapped DNA methylation, chromatin, and transcription changes in purified fetal mouse germ cells using MIRA-chip, ChIP-chip, and strand-specific RNA-seq, respectively. De novo methylation occurred without any apparent trigger from preexisting repressing chromatin marks but was preceded by broad, low-level transcription along the entire genome in prospermatogonia. Only distinct short sequences remained unmethylated, precisely aligned with constitutive or emerging peaks of H3K4me2. Establishment of methylation at differentially methylated regions (DMRs) of imprinted genes, CpG islands, and IAPs followed these same default rules. Transcription run-through occurred at paternal DMRs with no- or diminishing H3K4me2 peaks. Maternal DMRs remained unmethylated among highly methylated DNA at precisely aligned H3K4me2 peaks with transcription initiating at least in one strand. Our results suggest that the pattern of de novo DNA methylation in prospermatogonia is dictated by opposing actions of broad, low-level transcription and dynamic patterns of active chromatin.
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| |
|
| Overall design |
Strand-specific RNA-seq was done in male and female fetal germ cells and somatic gonadal cells at 15.5 dpc to map transcription.
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| |
|
| Contributor(s) |
Singh P, Wu X, Szabo PE |
| Citation(s) |
23810559 |
| Submission date |
May 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiwei Wu |
| E-mail(s) |
xwu@coh.org
|
| Organization name |
City of Hope National Medical Center
|
| Department |
Computational and Quantitative Medicine
|
| Street address |
1500 E. Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (4)
|
| GSM1142599 |
RNA in the male germ cells at 15.5 dpc |
| GSM1142600 |
RNA in the female germ cells at 15.5 dpc |
| GSM1142601 |
RNA in the male somatic cells at 15.5 dpc |
| GSM1142602 |
RNA in the female somatic cells at 15.5 dpc |
|
| This SubSeries is part of SuperSeries: |
| GSE46954 |
Default DNA Methylation is Preceded by Broad, Low-Level Transcription in Fetal Male Germ Cells and Is Inversely Patterned by Dynamic H3K4 Methylation |
|
| Relations |
| BioProject |
PRJNA203213 |
| SRA |
SRP022767 |
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