Tracing embryonic development through single-cell sequencing analysis

The gradual formation of varies tissues and organs from a single fertilized egg is precisely regulated in spatial and tem-poral manner during the embryonic development. A comprehensive understanding about the cell fate decision of differ-ent cell types is one of the key questions in developmental biology. However, limitations in biotechnology have severely restricted us to well understand the whole process of embryonic development in the past decades, leading to many unresolved questions that still need further exploration. In the last few years, rapid development of emerging technologies, which are represented by single-cell sequencing, gene editing and computational biology have immensely expanded our accessibility to many challenging questions that could hardly be resolved in the past. Continuous modifications of these methods also make it possible for us to reveal the key regulatory processes in embryonic development and disease progression more comprehensively. Meanwhile, the combination of these different biotechnologies is providing us a more flexible way to carry out in-depth investigations of many basic problems in embryonic development and even the occurrence of diseases. Recently, researchers from three different groups applied high throughput single-cell RNA sequencing methods com-bined with computational tools to trace the transcriptional changes during vertebrate embryo development. In a study on zebrafish embryo development, through analyzing more than 90000 single cells, researchers highlighted the cell transition process during body axis patterning, different germ layer formation as well as organogenesis. Meanwhile, an-other zebrafish study constructed a branching tree based on large scale single-cell RNA-seq data, revealing the transcriptome trajectories during the formation of the 25 different cell types, highlighting how progenitor cells gradually differentiate to specific cell types. Besides, another group applied microfluidics based single-cell sequencing method and analyzed above 130000 cells from whole frog embryo. They identified 259 gene expression clusters that were corresponded to 10 different time points, providing a landscape of cell states during the formation of all cell lineages. These studies combined single-cell sequencing and computation tools or gene editing tools to track the cell fate transition in zebrafish and frog embryo development. By recording the gene expression atlas of each single cell that collected from multiple fetal stages, they tracked the cell type formation and cell fate decision cell-by-cell, constructing entire cell lineages in embryonic development. In recent years, the emerging of new technologies greatly expanded our insights in many key biological events, leading us a more comprehensive understanding of development and human disease. The constantly development of single-cell RNA-seq and computational tools play very important roles in life science, especially in embryo development and cell differentiation, identifying novel sub-cell types as well as their function in development. In disease pathology analysis, especially in cancer studies, applying single-cell RNA-seq immensely revealed the heterogeneity of cancer cells, highlighted the molecular features of these disease related cells, paving new ways to better understand the pathogenesis of human disease. These studies revealed the great potential of single-cell sequencing in solving important biological questions, and they also provided a novel approach to investigate the onset and progression of many diseases.