A Single-Cell RNA-Seq-Based Approach for Genome-Wide Identification of Cell Essential Genes.
A Single-Cell RNA-Seq-Based Approach for Genome-Wide Identification of Cell Essential Genes.
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基于单细胞 RNA-Seq 的细胞必需基因全基因组鉴定方法。
DOI：
10.1007/978-1-0716-1720-5_18
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发表时间：
2021
影响因子：
--
通讯作者：
S. Shi
中科院分区：
文献类型：
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作者：
Yuqiu Lu;S. Shi
识别对一种细胞类型的结构、功能和生存至关重要的基因，对于理解潜在的机制是至关重要的。不幸的是，目前还没有有效的方法来识别这些基因。单细胞RNA测序研究表明，同一类型的单个细胞的基因表达具有高度的异质性。因此，我们推测，在同一类型的所有单个细胞中表达的基因是该细胞类型所必需的，包括管家基因和特定细胞类型的必需基因。基于这一原理，我们设计了一种高通量的方法来识别足细胞必需基因。在这种方法中，小鼠足细胞受到超深单细胞RNA-SEQ的影响，所有单个足细胞表达的基因都被筛选出来，被认为是足细胞必需基因的候选者。这些基因对足细胞的重要性通过生物信息学、跨物种保守表达、与损伤/疾病的关联、包含已知的必需基因和实验验证来评估。通过与其他细胞类型的必需基因的比较，可以区分足细胞特有的必需基因。这种方法适用于任何单元格类型。在这一章中，我们描述了方法和具体的方法。
Identification of genes essential for structure, function, and survival of a cell type is critical for understanding of the underlying mechanisms. Unfortunately, there is no efficient way to identify such genes. Studies by single-cell RNA sequencing have shown that gene expressions of single cells of the same type are highly heterogeneous. We therefore speculate that the genes expressed in all individual cells of the same type are essential for the cell type, including the housekeeping genes and cell type-specific essential genes. Based on this rationale, we design a high-throughput approach to identify podocyte essential genes. In this approach, mouse podocytes are subjected to ultra-deep single-cell RNA-seq, and the genes expressed in all single podocytes are sorted out and considered as the candidates of podocyte essential genes. The essentiality of these genes for podocytes is assessed by bioinformatics, cross-species conserved expression, association with injury/disease, inclusion of known essential genes, and experimental validation. By comparison with the essential genes of other cell types, podocyte-specific essential genes can be distinguished. This approach applies to any cell types. In this chapter, we describe the approach and detailed methods.