Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment

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 tar..., , , # 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)
* Bai...

人类加速区域（Human accelerated regions, HARs）已被证实参与人类大脑演化过程。然而，目前学界对其所调控的基因及通路仍缺乏深入认知，这极大阻碍了对其功能机制的解析。本研究针对人类与黑猩猩的神经干细胞（neural stem cells, NSCs），鉴定出1590个人类加速区域及其直系同源序列对应的2963个保守基因靶标。保守基因靶标显著富集于神经发育相关功能类别，且在人类神经干细胞（hNSCs）、黑猩猩神经干细胞（cNSCs）以及人类与非人灵长类大脑的差异表达基因（differentially expressed genes, DEGs）中显著过量存在。物种特异性基因靶标则未集中于任何功能类别，且未在差异表达基因中呈现富集现象。人类加速区域靶标在人类胎儿脑中还展现出细胞类型特异性表达模式，包括与大脑皮层扩张相关的外放射状胶质细胞。本研究结果支持：人类加速区域通过调控人类与黑猩猩共有的祖先基因靶标的表达，而非通过获得新的靶标……来影响大脑演化。

# 数据来源：
《Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment》
DOI: https://doi.org/10.5061/dryad.c59zw3rkj

## 数据与文件结构
本批文件收录了人类与黑猩猩神经干细胞、人类神经元中的人类加速区域（HARs）与HGE的相互作用数据，同时包含Pal等人2025年发表于《Cell》的研究中提及的CHiCAGO评分。

### 文件与变量
#### 文件：HAR_interactions_cNSCs.txt
**描述**：通过捕获Hi-C（Capture-HiC）技术检测得到的由诱导多能干细胞（induced pluripotent stem cells, iPSC）分化得到的黑猩猩神经干细胞中的人类加速区域与HGE相互作用列表。
##### 变量
* Bait_chr：包含人类加速区域或HGE（或其黑猩猩同源序列）的DpnII酶切片段所在染色体（对应hg38或panTro6基因组版本）
* Bait_start：包含人类加速区域或HGE（或其黑猩猩同源序列）的DpnII酶切片段的起始位置
* Bait_end：包含人类加速区域或HGE（或其黑猩猩同源序列）的DpnII酶切片段的终止位置
* Bai...