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| Status |
Public on Jul 06, 2018 |
| Title |
LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation |
| Organisms |
Mus musculus; Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
De novo DNA methylation (DNAme) occurs coincident with transcription during mouse oogenesis. As many oocyte transcripts originate in Long Terminal Repeats (LTRs), which are divergent across species, we examined whether polymorphic LTR-initiated transcription units (LITs) shape the oocyte methylome. We identified thousands of syntenic regions in mouse, rat and human, including CpG islands (CGIs), that show divergent DNAme associated with polymorphic LITs. Notably, many CGI promoters methylated exclusively in mouse and/or rat are embedded within rodent-specific LITs, and show persistent maternal methylation in the blastocyst. Polymorphic LITs are also responsible for divergent methylation of CGI promoters in distantly related mouse strains, revealing that LITs also promote intra-species diversification of promoter DNAme.
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| |
|
| Overall design |
Total RNA-seq in mouse and rat oocytes; H3K36me3 ChIP-seq in mouse oocytes
|
| Web link |
https://www.nature.com/articles/s41467-018-05841-x
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| |
|
| Contributor(s) |
Brind'Amour J, Kobayashi H, Albert JR, Shirane K, Sakashita A, Bogutz AB, Koike T, Karimi MM, Lefebvre LL, Kono T, Lorincz MC |
| Citation(s) |
30127397 |
| |
| Submission date |
Apr 03, 2018 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Matthew C Lorincz |
| Organization name |
University of British Columbia
|
| Department |
Medical Genetics
|
| Street address |
2350 Health Sciences Mall
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V6T 1Z3 |
| Country |
Canada |
| |
|
| Platforms (3) |
| GPL18694 |
Illumina HiSeq 2500 (Rattus norvegicus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL20084 |
Illumina NextSeq 500 (Rattus norvegicus) |
|
| Samples (10)
|
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| Relations |
| BioProject |
PRJNA448528 |
| SRA |
SRP136995 |
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