Project description:This GEO submission accompanies the RNA-seq data of human-chimp and human-gorilla hybrid cells in the study “The Gene Regulatory Evolution of the Human Skeleton”. Changes in gene regulation are key drivers of human evolution. However, which regulatory changes shaped human adaptations, and especially how, remains largely unknown. Skeletal alterations have been particularly central in human evolution, facilitating upright locomotion and large brains, and influencing child- birth and our distinctive faces. Here, we generated human-chimp and human-gorilla hybrid osteochondral progenitor cells to study the cis-regulatory expression changes that distinguish humans from other great apes. We identified 4152 chimpanzee-specific, and 4463 human-specific cis-regulatory expression changes.

2026-04-28 | GSE316892 | GEO

The Gene Regulatory Evolution of the Human Skeleton (Massively parallel reporter assay (MPRA))

Project description:This GEO submission accompanies the massively parallel reporter assay (MPRA) data in the study “The Gene Regulatory Evolution of the Human Skeleton”. Changes in gene regulation are key drivers of human evolution. However, which regulatory changes shaped human adaptations, and especially how, remains largely unknown. Skeletal alterations have been particularly central in human evolution, facilitating upright locomotion and large brains, and influencing child- birth and our distinctive faces. Here, we employed MPRAs in key skeletal cells - chondrocytes - to uncover the functional role of the 574,290 enhancer and promoter substitutions that distinguish humans from their ape relatives. Using this atlas, we identified 15,077 sequences whose activity has diverged since our split from chimpanzees.

2026-04-28 | GSE316891 | GEO

The Gene Regulatory Evolution of the Human Skeleton (human-chimp and human-gorilla hybrid cells)

Project description:The Gene Regulatory Evolution of the Human Skeleton (human-chimp and human-gorilla hybrid cells)

| PRJNA1405491 | ENA

Molecular features driving cellular and regulatory complexity of human brain evolution [ATAC-seq]

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

The Gene Regulatory Evolution of the Human Skeleton (Massively parallel reporter assay (MPRA))

Project description:The Gene Regulatory Evolution of the Human Skeleton (Massively parallel reporter assay (MPRA))

| PRJNA1405493 | ENA

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

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