Single-cell chromatin and gene-regulatory dynamics of mouse nephron progenitors [ChIP-seq]

Background: We reasoned that unraveling the dynamic changes in accessibility of genomic regulatory elements and gene expression at single-cell resolution will inform the basic mechanisms of nephrogenesis. Methods: We performed single-cell ATAC-seq and RNA-seq both individually (Singleomes; Six2GFP cells) and jointly in the same cells (Multiomes; kidneys) to generate integrated chromatin and transcriptional maps in mouse embryonic and neonatal nephron progenitor cells (NPCs). Results: We demonstrate that singleomes and multiomes are comparable in assigning most cell states, identification of new cell type markers, and defining the transcription factors driving cell identity. However, multiomes are more precise in defining the progenitor population. Multiomes identified a “pioneer” bHLH/Fox motif signature in NPCs. Moreover, we identified a subset of Fox factors exhibiting high chromatin activity in podocytes. One of these Fox factors, Foxp1, is important for nephrogenesis. Key nephrogenic factors are distinguished by strong correlation between linked gene-regulatory elements and gene expression. Conclusion: Mapping the regulatory landscape at single-cell resolution informs the regulatory hierarchy of nephrogenesis. Paired single-cell epigenomes and transcriptomes of nephron progenitors should provide a foundation to understand prenatal programming, regeneration following injury, and ex vivo nephrogenesis. Chip-seq from E13.5 and P0 Nephron Progenitor Cells with H3K4me1, H3K27me3 and H3K27ac. Nephron Progenitor cells (NPCs) were isolated by Magnetic Activated Cell Sorting (MACS) from E13.5 and P0 CD1 mouse kidneys. The NPCs were cultured in nephron progenitor expansion medium (NPEM) and passaged twice before the cells were subjected to ChIP-seq for H3K4me1, H3K27me3, and H3K27ac.