Integration of Single-Cell RNA- and CAGE-seq Reveals Tooth-Enriched Genes
Integration of Single-Cell RNA- and CAGE-seq Reveals Tooth-Enriched Genes
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DOI：
10.1177/00220345211049785
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发表时间：
2021-11-20
影响因子：
7.6
通讯作者：
Fukumoto, S.
中科院分区：
文献类型：
--
作者：
Chiba, Y.;Yoshizaki, K.;Fukumoto, S.
器官发育是由组织或细胞类型中优先表达的基因的调节决定的。基因表达谱和器官中特定基因的鉴定可以提供对器官发生的见解。因此，全基因组分析是阐明器官发生和牙齿发育过程中发育机制的有力工具。单细胞 RNA 测序 (scRNA-seq) 是揭示牙细胞基因表达谱的合适工具。使用scRNA-seq，我们可以获得大量关于基因表达的信息；然而，通过这种方法鉴定功能基因（牙齿发育的关键分子）仍然具有挑战性。在本研究中，我们使用小鼠牙胚进行基因表达序列（CAGE-seq）的帽分析，以鉴定在牙齿中优先表达的基因。 CAGE-seq 对转录本 5' 端的短读进行计数；因此，该方法可以量化转录本的数量，而不会出现与转录本长度相关的偏差。我们假设这个 CAGE 数据集对于通过 scRNA-seq 进一步了解基因表达谱有很大帮助。我们的目的是结合使用 scRNA-seq 和 CAGE-seq，通过生物信息学分析来识别参与牙齿发育的重要基因。我们获得了出生后第 1 天小鼠磨牙的 12,212 个细胞的 scRNA-seq 数据集和出生后第 1 天磨牙的 CAGE-seq 数据集。 scRNA-seq 分析揭示了细胞类型特异性基因的时空表达，CAGE-seq 有助于确定这些基因是优先在牙齿中表达还是普遍表达。此外，我们确定了候选基因作为新型牙齿富集和牙齿细胞类型特异性标记。我们的结果表明，scRNA-seq 和 CAGE-seq 的整合突出了众多基因表达谱中对牙齿发育重要的基因。这些发现应有助于解决牙齿发育的机制，并为未来牙齿再生奠定基础。
Organ development is dictated by the regulation of genes preferentially expressed in tissues or cell types. Gene expression profiling and identification of specific genes in organs can provide insights into organogenesis. Therefore, genome-wide analysis is a powerful tool for clarifying the mechanisms of development during organogenesis as well as tooth development. Single-cell RNA sequencing (scRNA-seq) is a suitable tool for unraveling the gene expression profile of dental cells. Using scRNA-seq, we can obtain a large pool of information on gene expression; however, identification of functional genes, which are key molecules for tooth development, via this approach remains challenging. In the present study, we performed cap analysis of gene expression sequence (CAGE-seq) using mouse tooth germ to identify the genes preferentially expressed in teeth. The CAGE-seq counts short reads at the 5 '-end of transcripts; therefore, this method can quantify the amount of transcripts without bias related to the transcript length. We hypothesized that this CAGE data set would be of great help for further understanding a gene expression profile through scRNA-seq. We aimed to identify the important genes involved in tooth development via bioinformatics analyses, using a combination of scRNA-seq and CAGE-seq. We obtained the scRNA-seq data set of 12,212 cells from postnatal day 1 mouse molars and the CAGE-seq data set from postnatal day 1 molars. scRNA-seq analysis revealed the spatiotemporal expression of cell type-specific genes, and CAGE-seq helped determine whether these genes are preferentially expressed in tooth or ubiquitously. Furthermore, we identified candidate genes as novel tooth-enriched and dental cell type-specific markers. Our results show that the integration of scRNA-seq and CAGE-seq highlights the genes important for tooth development among numerous gene expression profiles. These findings should contribute to resolving the mechanism of tooth development and establishing the basis for tooth regeneration in the future.