Chromatin and gene-regulatory dynamics of mouse nephron progenitors at single-cell resolution [Single cell Multiome ATAC + Gene Expression]. Chromatin and gene-regulatory dynamics of mouse nephron progenitors at single-cell resolution [Single cell Multiome ATAC + Gene Expression]

Background: Unraveling the dynamic accessibility of regulatory chromatin at single-cell resolution is key to understanding stem/progenitor cell fate choices in health and disease. Nephron progenitor cells (NPCs) are a multipotent population giving rise to all cell types of the nephron, from the glomerular epithelium to the distal tubule. At any given time, the NPC’s choice to self-renew or differentiate and gain a new identity is determined not only by its transcription factor repertoire but also by the genome accessibility of the cognate cis-regulatory elements. Methods: We performed singleome and multiome analysis of chromatin accessibility and gene expression in thousands of embryonic and neonatal NPCs toward defining the regulatory landscape driving fate choices during nephrogenesis. Results: We show that chromatin accessibility recovers the diverse states of NPCs and precursor states of proximal and distal nephron epithelial cells. We define the key cell type-specific transcriptional regulators across pseudotime and NPC age. We find that chromatin accessibility in the podocyte lineage is established early in the trajectory and identify a subset of Forkhead factors exhibiting high chromatin activity in podocyte precursors. We also determined that strong linkages between cis-regulatory elements and expression levels distinguish fate-determining TFs. Conclusions: Single-cell mapping of accessible and active chromatin defines the regulatory landscape of nephrogenesis and provides a foundation for future studies in disease states characterized by abnormal nephrogenesis. Overall design: (2) Single cell Multiome ATAC + Gene Expression Sequencing and anaylsis of whole kidneys from E16.5.

研究背景：解析单细胞分辨率下调控染色质的动态可及性，是理解健康与疾病状态下干细胞/祖细胞命运抉择的关键。肾单位祖细胞（Nephron progenitor cells, NPCs）是一类多能细胞群，可分化产生肾单位的全部细胞类型，涵盖从肾小球上皮细胞到远端肾小管的所有谱系。在任意时刻，肾单位祖细胞自我更新或分化并获得新细胞身份的选择，不仅取决于其转录因子组，还受同源顺式调控元件的基因组可及性调控。
研究方法：我们对数千个胚胎期及新生期肾单位祖细胞开展单组学与多组学分析，检测染色质可及性与基因表达水平，旨在明确驱动肾发生过程中细胞命运抉择的调控图谱。
研究结果：本研究证实，染色质可及性可精准反映肾单位祖细胞的多样状态，以及近端与远端肾单位上皮细胞的前体状态。我们界定了拟时间轴及肾单位祖细胞不同发育阶段的关键细胞类型特异性转录调控因子。研究发现，足细胞谱系的染色质可及性在发育轨迹早期即已建立，并鉴定出一组在足细胞前体中呈现高染色质活性的叉头框（Forkhead）转录因子家族成员。此外，我们明确顺式调控元件与基因表达水平间的强关联可区分决定细胞命运的转录因子。
研究结论：可及染色质与活性染色质的单细胞图谱，明确了肾发生的调控网络，为后续异常肾发生相关疾病的研究奠定了坚实基础。
整体实验设计：（2）对E16.5时期的全肾脏开展单细胞多组学ATAC+基因表达测序与分析。