DOI: 10.5061/dryad.c59zw3rkj
title: Data from: Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment

description: 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.
description: # Data from: Resolving the three-dimensional interactome of human
 accelerated regions during human and chimpanzee neurodevelopment
 [https://doi.org/10.5061/dryad.c59zw3rkj](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)