|
| Status |
Public on Nov 23, 2022 |
| Title |
De novo enhancer function in divergent hominin haplotypes |
| Organisms |
Mus musculus; synthetic construct |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
Identifying functional changes in gene regulatory elements in the human lineage is essential to understanding how humans emerged as a species. We performed genome-wide comparative genomic analysis of humans and great apes to identify 1581 Human Ancestor Quickly-Evolved Regions (HAQERs), which we identify as the fastest-evolved regions of the human genome (hg38). To detect how rapid sequence divergence contributed to divergent gene regulatory functionality in HAQERs, we designed in vivo STARR-seq as a multiplex single-cell assay of enhancer activity in the developing mouse brain. We tested multiple haplotypes from hominins (Human/Neanderthal/Denisova) and non-hominins (Chimpanzee and the inferred Human-Chimpanzee ancestor) for 13 HAQERs to assess their enhancer activity in the developing brain. We found significant differences in enhancer activity between hominins and non-hominins in 8 of these sequences.
|
| |
|
| Overall design |
In this assay, STARR-seq plasmids along with an EGFP transfection reporter plasmid are delivered to the developing mouse cerebral cortex via in utero electroporation. Following 18 hours of incubation, mouse brains are harvested and GFP+ cells are isolated via Fluorescent Activated Cell Sorting. Single cell sequencing is then performed to recover gene expression, EGFP transfection reporter plasmid expression, and STARR-seq reporter expression. We performed two independent STARR-seq experiments (V4.2 = E14.5 injection, V4.1 = E15.5 injection) with the same input library, which we sequenced for input normalization.
|
| |
|
| Contributor(s) |
Lowe CB, Mangan RJ |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Aug 26, 2022 |
| Last update date |
Nov 25, 2022 |
| Contact name |
Craig Barrett Lowe |
| Organization name |
Duke University School of Medicine
|
| Department |
Molecular Genetics and Microbiology
|
| Street address |
213 Research Dr
|
| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL17769 |
Illumina MiSeq (synthetic construct) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
|
| Samples (3) |
| GSM6510409 |
Output mouse scSTARR-seq, E15.5 Injection; scRNA-seq |
| GSM6510410 |
Output mouse scSTARR-seq, E14.5 Injection; scRNA-seq |
| GSM6510411 |
Input library sequencing; RNA-seq |
|
| Relations |
| BioProject |
PRJNA874114 |
