|
| Status |
Public on Nov 09, 2018 |
| Title |
Widespread conservation of chromatin accessibility and transcription factor binding in human and chimpanzee induced pluripotent stem cells |
| Organisms |
Pan troglodytes; Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Changes in gene regulation have been shown to contribute to phenotypic differences between closely related species, most notably in primates. It is likely that a subset of inter-species regulatory differences can be explained by changes in chromatin accessibility and transcription factor binding, yet there is a paucity of comparative data sets with which to investigate this. Using ATAC-seq, we profiled genome-wide chromatin accessibility in a matched set of 6 human and 6 chimpanzee (Pan troglodytes, our closest living relative) induced pluripotent stem cells from which we have previously collected gene expression data. We examined chromatin accessibility patterns near 20,745 orthologous transcriptions start sites and used a footprinting algorithm to predict transcription factor binding activity in each species. We found that the majority of chromatin accessibility patterns and transcription factor activity are conserved between these two closely related species. Interestingly, interspecies divergence in chromatin accessibility and transcription factor binding in pluripotent cells appear to contribute not to differences in the pluripotent state, but to downstream developmental processes. Put together, our findings suggest that the pluripotent state is extremely stable and potentially subject to stronger evolutionary constraint than other somatic tissues.
|
| |
|
| Overall design |
ATAC-seq of 6 chimpanzee iPSC lines (biological reps) and 6 human iPSC lines (biological reps)
|
| |
|
| Contributor(s) |
Gallego Romero I, Gopalakhrisnan S, Gilad Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Nov 08, 2018 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Irene Gallego Romero |
| E-mail(s) |
ireneg@uchicago.edu
|
| Phone |
773 834 1984
|
| Organization name |
University of Chicago
|
| Department |
Human Genetics
|
| Lab |
Gilad
|
| Street address |
920 E 58th St, 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 (12)
|
|
| Relations |
| BioProject |
PRJNA504642 |
| SRA |
SRP168246 |
Less...
More...