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| Status |
Public on Oct 09, 2020 |
| Title |
Mapping the regulatory potential of fixed variants in modern humans |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The Neanderthal and Denisovan genomes enabled the discovery of sequences that differ between modern and archaic humans, the majority of which are noncoding. However, our understanding of the regulatory consequences of these differences remains limited, in part due to the decay of regulatory marks in ancient samples. Here, we used a massively parallel reporter assay in embryonic stem cells, neural progenitor cells and bone osteoblasts to investigate the regulatory effects of the 14,042 single-nucleotide modern human-specific variants. Overall, 1,791 (13%) of sequences containing these variants showed active regulatory activity, and 407 (23%) of these drove differential expression between human groups. Differentially active sequences were associated with divergent transcription factor binding motifs, and with genes enriched for vocal tract and brain anatomy and function. This work provides insight into the regulatory function of variants that emerged along the modern human lineage and the recent evolution of human gene expression.
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| Overall design |
Massively parallel reporter assay (MPRA) conducted on 14,042 pairs of modern and archaic human alleles in three cell types (ESCs, NPCs and osteoblasts) in three replicates each.
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| Contributor(s) |
Weiss C, Harshman L, Inoue F, Fraser HB, Petrov DA, Ahituv N, Gokhman D |
| Citation(s) |
33885362 |
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| Submission date |
Jun 12, 2020 |
| Last update date |
May 06, 2021 |
| Contact name |
David Gokhman |
| E-mail(s) |
david.gokhman@mail.huji.ac.il
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| Organization name |
The Hebrew University of Jerusalem
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| Street address |
Givat Ram, Safra Campus
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| City |
Jerusalem |
| ZIP/Postal code |
91904 |
| Country |
Israel |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (19)
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| Relations |
| BioProject |
PRJNA639170 |
| SRA |
SRP267550 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE152404_Oligos_library_joint_noDups.fasta.gz |
1.3 Mb |
(ftp)(http) |
FASTA |
| GSE152404_ProcessedData.xlsx |
3.0 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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