Single-Cell Chromatin and Gene-Regulatory Dynamics of Mouse Nephron Progenitors

Sylvia Hilliard; Giovane Tortelote; Hongbing Liu; Chao-Hui Chen; Samir S. El-Dahr

doi:10.1681/ASN.2021091213

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Significance Statement

Nephron progenitor cells (NPCs) give rise to all epithelial cell types of the nephron. Single-cell transcriptomics have defined the diverse cell states of NPCs, but how cell fate choices are established and maintained requires knowledge of the gene regulatory landscape. This study integrated open chromatin domains representing promoters and enhancers with gene expression in the same single cells. These paired regulatory maps unraveled the dynamics and hierarchy of fate-determining transcription factors along the developmental trajectory of NPCs. These findings have implications for understanding mechanisms of nephrogenesis in health and disease.

Abstract

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; Six2^GFP cells) and jointly in the same cells (multiomes; kidneys) to generate integrated chromatin and transcriptional maps in mouse embryonic and neonatal nephron progenitor cells.

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 nephron progenitor cells. 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 after injury, and ex vivo nephrogenesis.

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