Project description:Genomic changes acquired in human evolution contribute to the unique abilities of human brain. However, characterizing the molecular underpinnings of human-specific traits is a multifaceted challenge due to the cellular heterogeneity of human brain and complex regulation of gene expression. Here, we performed single-nuclei RNA-sequencing (snRNA-seq) and single-nuclei ATAC-seq (snATAC-seq) in human, chimpanzee, and rhesus macaque brain tissue (brodmann area 23, posterior cingulate cortex). Human-specific changes were distinct among neuronal subtypes indicating that human brain evolution was accompanied by molecular alterations in finer cellular resolution. We also observed more human-specific alterations in epigenome compared to transcriptome. Interestingly, human-specific accessibility changes in neurons were not as concordant with gene expression changes in comparison to other species, partially explaining this discrepancy. These cis-regulatory elements were enriched for immediate early gene motifs, identifying accelerated evolution of activity regulated genes in humans. We also uncovered associations between human evolution and brain disease genes at the cell type level. Together, these results reveal multiple mechanisms for human brain evolution at cell type resolution and establish the first direct evidence for accelerated human-specificity of activity-dependent molecular changes.

2023-04-26 | GSE192772 | GEO

ATAC-seq of human (Homo sapiens) and cynomolgus macaque (Macaca fascicularis) iPSC and iPSC-derived NPC cell lines

Project description:ATAC-seq samples from 2 species and 2 cell types were generated to study cis-regulatory element evolution. Briefly, previously generated urinary stem cell derived iPS-cells (Homo sapiens) of 2 human individuals and fibroblast derived cynomolgus macaque iPSCs (Macaca fascicularis) of 2 individuals (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009; Ohnuki et al. 2014). The NPC lines were cultured in NPC proliferation medium and passaged 2 - 4 times until they were dissociated and subjected to ATAC-seq together with the respective iPSC clones. ATAC-seq libraries were generated using the Omni-ATAC protocol (Corces et al. 2017) with minor modifications.

2023-10-25 | E-MTAB-13373 | biostudies-arrayexpress

A Multi-omic Atlas of Human Embryonic Skeletal Development -Multiome GEX+ATAC

Project description:Two distinct and anatomically restricted modes of ossification, which are endochondral ossification and intramembranous ossification, govern osteogenesis and joint formation throughout the human skeleton and, to our knowledge, the cellular bases by which they form and mature remain incompletely described in human development at single-cell resolution. To address this, we apply single-nuclei paired RNA and ATAC sequencing to decipher the molecular gene regulatory programmes that mediate maturation of the distinct bone and joint-forming niches in the cranium and appendicular skeleton across space and time from 5-11 PCW.

2024-10-09 | E-MTAB-14385 | biostudies-arrayexpress

Pre-Hypertrophic Chondrogenic Enhancer Landscape of Limb and Axial Skeleton Development [ATAC-seq]

Project description:Pre-Hypertrophic Chondrogenic Enhancer Landscape of Limb and Axial Skeleton Development [ATAC-seq]

| PRJNA958101 | ENA

Evolution of the human autopod skeleton [ATAC-seq]

Project description:We investigate the genetic architecture of autopod development at the regulatory and transcriptomic level.

2025-08-20 | GSE283854 | GEO

ATAC-seq of iPSC and human dermal fibroblasts

Project description:ATAC-seq of iPSC and human dermal fibroblasts, used to compare open chromatin and transcription signal.

2021-05-02 | E-MTAB-10381 | biostudies-arrayexpress

Human senescence ATAC-seq [II]

Project description:Human senescence ATAC-seq [II]