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| Status |
Public on Apr 26, 2018 |
| Title |
Epigenomic conservation of transposable element silencing [RNA-seq] |
| Organisms |
Pan troglodytes; Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Transposable elements (TEs) comprise a substantial proportion of primate genomes. Because of the potential deleterious effects of TEs during development, TEs are targeted for silencing by sequence-specific KRAB-ZNF proteins, which recruit the TRIM28-SETDB1 complex, to deposit the repressive histone modification H3K9me3. TEs, in turn, acquire mutations to evade detection by the host, and hence KRAB-ZNF proteins need to rapidly evolve to counteract them. To investigate the short-term evolution of TE silencing, we profiled the genome-wide distribution of H3K9me3 in both human and chimpanzee induced pluripotent stem cells. We performed chromatin immunoprecipitation followed by high-throughput sequencing for H3K9me3, as well as total RNA sequencing in ten human and seven chimpanzee individuals. H3K9me3 enrichment was quantified in 141,642 regions determined to be orthologous between the two species. These H3K9me3-enriched regions were overlaid on a compiled set of 4 million orthologous TEs that can be mapped in both species.
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| Overall design |
We collected RNA-seq data from 10 human and 7 chimpanzee iPSC lines.
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| Contributor(s) |
Ward MC |
| Citation(s) |
29648536 |
| |
| Submission date |
Mar 16, 2017 |
| Last update date |
Jun 22, 2021 |
| Contact name |
Michelle C Ward |
| Organization name |
University of Chicago
|
| Department |
Human Genetics
|
| Lab |
Gilad
|
| Street address |
920 E. 58th Street, CLSC 317
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL19148 |
Illumina HiSeq 2500 (Pan troglodytes) |
|
| Samples (17)
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| This SubSeries is part of SuperSeries: |
| GSE96712 |
Epigenomic conservation of transposable element silencing |
|
| Relations |
| BioProject |
PRJNA379443 |
| SRA |
SRP102015 |
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