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| Status |
Public on May 23, 2023 |
| Title |
Cell type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells [RNA-seq] |
| Organisms |
Pan troglodytes; Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Although gene expression divergence has long been postulated to be the primary driver of human evolution, identifying the genes and genetic variants underlying uniquely human traits has proven to be quite challenging. Theory suggests that cell type-specific cis-regulatory variants may fuel evolutionary adaptation due to the specificity of their effects. These variants can precisely tune the expression of a single gene in a single cell type, avoiding the potentially deleterious consequences of trans-acting changes and non-cell type-specific changes that can impact many genes and cell types, respectively. It has recently become possible to quantify human-specific cis-acting regulatory divergence by measuring allele-specific expression in human-chimpanzee hybrid cells—the product of fusing induced pluripotent stem (iPS) cells of each species in vitro. However, these cis-regulatory changes have only been explored in a limited number of tissues and cell types. Here, we quantify human-chimpanzee cis-regulatory divergence in gene expression and chromatin accessibility across six cell types, enabling the identification of highly cell type-specific cis-regulatory changes. We find that cell type-specific genes and regulatory elements evolve faster than those shared across cell types. Furthermore, we identify several instances of lineage-specific natural selection that may have played key roles in specific cell types, such as coordinated changes in the cis-regulation of dozens of genes involved in neuronal firing in motor neurons. Finally, using novel metrics and a machine learning model, we identify genetic variants that likely alter chromatin accessibility and transcription factor binding, leading to neuron-specific changes in the expression of the neurodevelopmentally important genes FABP7 and GAD1. Overall, our results demonstrate that integrative analysis of cis-regulatory divergence in chromatin accessibility and gene expression across cell types is a promising approach to identify the specific genes and genetic variants that make us human.
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| Overall design |
RNA sequencing of human-chimpanzee hybrid iPS cells derived six cell types
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| Contributor(s) |
Wang B, Starr AL, Fraser HB |
| Citation(s) |
37292820, 38358392 |
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| Submission date |
May 19, 2023 |
| Last update date |
Mar 20, 2024 |
| Contact name |
Hunter Fraser |
| Organization name |
Stanford University
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| Street address |
327 Campus Drive
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| City |
Stanford |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL27803 |
Illumina HiSeq 4000 (Homo sapiens; Pan troglodytes) |
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| Samples (25)
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| GSM7398433 |
Hybrid Skeletal myocyte, Hybrid2, rep1 |
| GSM7398434 |
Hybrid Hepatocyte progenitor, Hybrid1, rep1 |
| GSM7398435 |
Hybrid Hepatocyte progenitor, Hybrid2, rep1 |
| GSM7398436 |
Hybrid Pancreatic progenitor, Hybrid1, rep1 |
| GSM7398437 |
Hybrid Pancreatic progenitor, Hybrid2, rep1 |
| GSM7398438 |
Hybrid Cardiomyocte, Hybrid1, rep2 |
| GSM7398439 |
Hybrid Motor neuron, Hybrid2, rep1 |
| GSM7398440 |
Hybrid Cardiomyocte, Hybrid2, rep2 |
| GSM7398441 |
Hybrid Skeletal myocyte, Hybrid1, rep2 |
| GSM7398442 |
Hybrid Skeletal myocyte, Hybrid2, rep2 |
| GSM7398443 |
Hybrid Hepatocyte progenitor, Hybrid1, rep2 |
| GSM7398444 |
Hybrid Hepatocyte progenitor, Hybrid2, rep2 |
| GSM7398445 |
Hybrid Pancreatic progenitor, Hybrid1, rep2 |
| GSM7398446 |
Hybrid Pancreatic progenitor, Hybrid2, rep2 |
| GSM7398447 |
Hybrid Retinal pigment epithelium, Hybrid1, rep1 |
| GSM7398448 |
Hybrid Retinal pigment epithelium, Hybrid1, rep2 |
| GSM7398449 |
Hybrid Retinal pigment epithelium, Hybrid2, rep1 |
| GSM7398450 |
Hybrid Retinal pigment epithelium, Hybrid2, rep2 |
| GSM7398451 |
Hybrid Skeletal myocyte, Hybrid2, rep3 |
| GSM7398452 |
Hybrid Motor neuron, Hybrid1, rep1 |
| GSM7398453 |
Hybrid Motor neuron, Hybrid2, rep2 |
| GSM7398454 |
Hybrid Motor neuron, Hybrid1, rep2 |
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| This SubSeries is part of SuperSeries: |
| GSE232949 |
Cell type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells |
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| Relations |
| BioProject |
PRJNA974466 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE232948_RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt.gz |
3.5 Mb |
(ftp)(http) |
TXT |
| GSE232948_RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt.gz |
3.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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