我们认为,以单细胞分辨率解开基因组调节元件的可及性和基因表达的动态变化将为肾脏发生的基本机制提供信息。
我们分别进行了单细胞ATAC-seq和RNA-seq(单体;Six2GFP细胞),并在相同的细胞(多体;肾脏)中联合进行,以在小鼠胚胎和新生儿肾祖细胞中产生整合的染色质和转录图。
我们证明了单体和多体在分配大多数细胞状态方面是可比的,鉴定新的细胞类型标记,并定义驱动细胞同一性的转录因子。然而,多体在定义祖先群体时更精确。多体在肾单位祖细胞中鉴定出“先驱”bHLH/Fox基序特征。此外,我们确定了足细胞中具有高染色质活性的Fox因子的子集。福克斯因素之一,Foxp1对肾脏发生很重要。关键的肾病因子通过相关基因调控元件和基因表达之间的强相关性来区分。
以单细胞分辨率绘制调控景观图可告知肾脏发生的调控等级。肾单位祖细胞配对的单细胞表观基因组和转录组应该为理解产前编程提供基础。损伤后的再生,和离体肾发生。
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.
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.
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.
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.