CTCF ChIP-Seq from Primate iPSC derived Astrocytes (iAstrocytes)
Ontology highlight
ABSTRACT: CTCF ChIP-Seq experiment was performed to map and compare potential evolutionary changes of CTCF binding, chimpanzee and macaque iAstrocytes.
Project description:H3K4me3 ChIP-Seq experiment was performed to map and compare potential evolutionary changes in active promoters of human, chimpanzee and macaque iAstrocytes.
Project description:H3K27ac ChIP-Seq experiment was performed to map and compare potential evolutionary changes in active promoters and enhancer elements of human, chimpanzee and macaque iAstrocytes.
Project description:ATAC-seq experiments were performed to map the open chromatin regions of human, chimpanzee and macaque iAstrocytes. This experiment allowed to compare evolutionary changes according to chromatin activity.
Project description:CTCF ChIP-Seq experiment was performed to map and compare potential changes of CTCF binding, in mouse embryonic stem cell and ES derived neural stem cells.
Project description:RNA-Seq experiment to detect transcriptional differences in iPSC derived astrocytes between 3 primate species, humans, chimpanzees and macaques. The goal of the experiment is to characterise genome-wide evolutionary changes in transcriptional and regulatory systems across the primate lineage in astrocytes
Project description:H3K27ac ChIP-Seq experiment was performed to map and compare potential changes in elements of mouse embryonic stem cells and their derived neural stem cells
Project description:Hi-C experiment was performed to map and compare potential evolutionary changes in chromatin structural organisation of human, chimpanzee and macaque iAstrocytes.
Project description:Astrocytes play essential roles in neuronal development, function, and disease, yet existing methods to derive astrocytes from human pluripotent stem cells (hPSCs) are complex and can involve months of in vitro maturation. We developed a genomic safe-harbor knock-in system for inducible expression of the astrogenic transcription factors NFIA, NFIB, and SOX9, enabling rapid and robust generation of functional induced astrocytes (iAstrocytes). Across five hPSC lines, NFIB-SOX9 and NFIA-NFIB-SOX9 combinations efficiently generated highly pure populations expressing astrocyte-specific and synaptogenic genes. iAstrocytes displayed cytokine-induced expression of complement factors C3 and C4 and were amenable to CRISPR interference (CRISPRi) gene expression knockdown. Optimization of culture conditions enabled survival of NFIB-SOX9 iAstrocytes in co-culture with human induced neurons (iNeurons). Through pharmacological and genetic perturbations, we uncovered a previously undescribed phenomenon in which co-culture with iAstrocytes promoted the development of synchronized iNeuron network calcium activity mediated by specific gap junction proteins. This rapid and genetically tractable iAstrocyte platform provides a robust model to dissect human genetic and environmental effects on astrocyte-neuron interactions.
Project description:Astrocytes are key regulators of CNS homeostasis and their dysfunction is implicated in neurological and neurodegenerative disorders. Here, we describe a two-step protocol to generate astrocytes from iPSCs using a bankable neural progenitor cell (NPC) intermediate, followed by low-density passaging and overexpression of the gliogenic transcription factor NFIA. A bankable NPC intermediates allows for facile differentiation into both purified neuronal and astrocyte cell types in parallel from the same genetic background, depending on the experimental needs. This article presents a protocol to generate NPCs from iPSCs (Basic Protocol 1), which are then differentiated into iPSC-derived astrocytes, termed iAstrocytes (Basic Protocol 2). The resulting iAstrocytes express key markers of astrocyte identity at transcript and protein levels by bulk RNA-seq and immunocytochemistry respectively. Additionally, they respond to the inflammatory stimuli poly(I:C) and generate waves of calcium activity in response to either physical activity or addition of ATP. Our approach offers a simple and robust method to generate and characterize human astrocytes which can be used to model human disease affecting this cell type.