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ScATAC-seq data of pig brains

ABSTRACT: Pig brains are valuable models for studying brain diseases due to their structural similarities to human brains. However, understanding the regulatory mechanisms in pig brains is challenging due to cellular heterogeneity. This study aimed to investigate the heterogeneity of pig brains and uncover the underlying regulatory mechanisms at single-cell resolution. We created the first single-cell chromatin accessibility atlas of the cerebral cortex and cerebellum in domestic pigs and wild boars using single-cell ATAC-seq (scATAC-seq). We profiled 71,798 cells, identifying nine cell types, and integrated single-cell RNA sequencing (scRNA-seq) data to characterize cell type-specific regulatory landscapes and oligodendrocyte development. Our analysis revealed that oligodendrocyte progenitor cells exhibit the fastest evolutionary rate between domestic pigs and wild boars. Additionally, cross-species comparison showed that pig regulatory elements are more conserved with humans than those in mice. Notably, genetic variant enrichment studies found that regulatory elements associated with Alzheimer’s disease were significantly enriched in pigs but not in mice, suggesting pigs as a potentially superior model for this condition. Conversely, neurological diseases like schizophrenia and bipolar disorder showed higher enrichment in mice.

ORGANISM(S): Sus scrofa

PROVIDER: GSE281568 | GEO | 2025/05/11

REPOSITORIES: GEO

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Project description:We investigated the nutritional effects on gene expression in testes of F0 boars from a three generation Large White pig feeding experiment. A group of experimental (E) F0 boars were fed a standard diet supplemented with high amounts of methylating micronutrients whereas a control (C) group of F0 boars received a standard diet. These differentially fed F0 boars sired F1 boars which then sired 60 F2 pigs which were investigated in a previous study. The aim of this project was to investigate if the nutrition affects gene expression in testis of differentially fed boars and thus impact on spermatogenesis. We found a small number of 70 genes that were differentially expressed (fc ≥ 1) on the P<0.01 significance level. The false discovery rate (FDR) was 0.82 indicating that only a small portion of these genes are real positives. Nevertheless, we performed a pathway analysis and found this moderate differential expression associated with pathways maps of development_A2B receptor: action via G-protein alpha s, cell adhesion_Tight junctions and cell adhesion_Endothelial cell contacts by junctional mechanisms. The gene ontology (GO) processes that matched the gene expression data in boars’ testes were positive regulation of nucleobase-containing compound metabolic process, cellular response to hormone stimulus and cellular process. The pathway maps and GO processes associated with gene expression differences do not indicate a simple relationship between nutritional influences and gene expression in testes. Nevertheless the Adenosine A2B receptor influences cell differentiation and proliferation and has thus far reaching consequences. Similar applies to those GO processes positive regulation of nucleobase-containing compound metabolic process, cellular response to hormone stimulus and cellular process that were associated with differentially expressed genes between the testes samples. The expression result is thus not conclusive of whether the diet affects processes related to transmittable epigenetic marks. The results, however, indicate that the extreme supplementation of methylating micronutrients from month one to month ten of age has a very moderate (if any) effect on gene expression in boar testes as measured by microarray analysis. Gene expression in testes from differentially fed F0 boars was measured. F0 boars received either a standard diet or a standard diet supplemented with methylating micronutrients. These boars were used to study transgenerational epigenetic inheritance in a three generation pig pedigree. Therefore it was of interest if the diet affects gene expression in testes and so could impact spermatogenesis.

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ScATAC-seq data of pig brains

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