Data from: Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment
Data files
Mar 03, 2025 version files 5.87 MB
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HAR_interactions_cNSCs.txt
1.78 MB
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HAR_interactions_hNSCs.txt
2.64 MB
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HAR_interactions_human_neurons.txt
1.45 MB
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README.md
3.53 KB
Abstract
Human accelerated regions (HARs) have been implicated in human brain evolution. However, insight into the genes and pathways they control is lacking, hindering the understanding of their function. Here, we identify 2,963 conserved gene targets for 1,590 HARs and their orthologs in human and chimpanzee neural stem cells (NSCs). Conserved gene targets are enriched for neurodevelopmental functions and are overrepresented among differentially expressed genes (DEGs) identified in human NSCs (hNSCs) and chimpanzee NSCs (cNSCs) as well as in human versus non-human primate brains. Species-specific gene targets do not converge on any function and are not enriched among DEGs. HAR targets also show cell-type-specific expression in the human fetal brain, including in outer radial glia, which are linked to cortical expansion. Our findings support that HARs influence brain evolution by altering the expression of ancestral gene targets shared between human and chimpanzee rather than by gaining new targets in human and facilitate hypothesis-directed studies of HAR biology.
https://doi.org/10.5061/dryad.c59zw3rkj
Description of the data and file structure
These files list HAR and HGE interactions in human and chimpanzee neural stem cells, and in human neurons, along with CHiCAGO scores as described in Pal et al. Cell 2025.
Files and variables
File: HAR_interactions_cNSCs.txt
Description: List of HAR and HGE interactions in iPSC-derived chimpanzee neural stem cells as detected by Capture-HiC.
Variables
- Bait_chr: Chromosome on which the DpnII fragment containing the HAR or HGE (or its chimpanzee ortholog) is located (hg38 or panTro6 genomes)
- Bait_start: Start position for the DpnII fragment containing the HAR or HGE (or its chimpanzee ortholog)
- Bait_end: End position for the DpnII fragment containing the HAR or HGE (or its chimpanzee ortholog)
- Bait_name: Name of HAR or HGE
- OtherEnd_chr: Chromosome on which the interacting region with the HAR or HGE (or its chimpanzee ortholog) is located
- OtherEnd_start: Start position for the interacting region with the HAR or HGE (or its chimpanzee ortholog)
- OtherEnd_end: End position for the interacting region with the HAR or HGE (or its chimpanzee ortholog)
- CHiCAGO_score: measure of significance of interaction (-log(weighted P-value), computed by CHiCAGO package in R)
File: HAR_interactions_human_neurons.txt
Description: List of HAR and HGE interactions in human iPSC-derived neurons as detected by Capture-HiC.
Variables
- Bait_chr: Chromosome on which the DpnII fragment containing the HAR or HGE (or its chimpanzee ortholog) is located (hg38 or panTro6 genomes)
- Bait_start: Start position for the DpnII fragment containing the HAR or HGE (or its chimpanzee ortholog)
- Bait_end: End position for the DpnII fragment containing the HAR or HGE (or its chimpanzee ortholog)
- Bait_name: Name of HAR or HGE
- OtherEnd_chr: Chromosome on which the interacting region with the HAR or HGE (or its chimpanzee ortholog) is located
- OtherEnd_start: Start position for the interacting region with the HAR or HGE (or its chimpanzee ortholog)
- OtherEnd_end: End position for the interacting region with the HAR or HGE (or its chimpanzee ortholog)
- CHiCAGO_score: measure of significance of interaction (-log(weighted P-value), computed by CHiCAGO package in R)
File: HAR_interactions_hNSCs.txt
Description: List of HAR and HGE interactions in human iPSC-derived neural stem cells as detected by Capture-HiC.
Variables
- Bait_chr: Chromosome on which the DpnII fragment containing the HAR or HGE (or its chimpanzee ortholog) is located (hg38 or panTro6 genomes)
- Bait_start: Start position for the DpnII fragment containing the HAR or HGE (or its chimpanzee ortholog)
- Bait_end: End position for the DpnII fragment containing the HAR or HGE (or its chimpanzee ortholog)
- Bait_name: Name of HAR or HGE
- OtherEnd_chr: Chromosome on which the interacting region with the HAR or HGE (or its chimpanzee ortholog) is located
- OtherEnd_start: Start position for the interacting region with the HAR or HGE (or its chimpanzee ortholog)
- OtherEnd_end: End position for the interacting region with the HAR or HGE (or its chimpanzee ortholog)
- CHiCAGO_score: measure of significance of interaction (-log(weighted P-value), computed by CHiCAGO package in R)