Scientists use calibration genes to understand how animals are born from single-celled eggs. Harvard researchers now use genetic sequencing techniques to analyze how a single egg develops within 24 hours of birth and embryogenesis.
The egg cells differentiated from a complex embryo into a group of cells and eventually became a zebrafish. The team study showed how the genes involved in embryonic development are regulated, allowing individuals to develop sophisticated organ tissue from a single cell.
Whether it is insects, humans or blue whale, it is formed from a single egg cell. With the extremely complicated development of egg cells and the precise regulation and control of a large number of different genes, it is possible to allow cells that have undergone division and differentiation to coordinate and cooperate with each other, enabling various physiological functions to operate.
The ontogeny process has always been a major mystery in the natural world, but despite decades of accumulated research knowledge, scientists are still unable to get a glimpse of the entire development process; however, a study recently published in the Science journal shows developmental biology. Great progress. Researchers at Harvard Medical School and Harvard University systematically analyzed the development of each cell in zebrafish and Xenopus tropicalis embryos and constructed how a single egg can be transformed into a complete organism.
The team used single-cell sequencing technology to track the division of each cell 24 hours before the embryo began to develop. The results of the analysis grasped the timing of the opening and closing of each gene and the differentiation of cells into the next stage.
Professor Sean Megason, co-author of the study, said that scientists want to understand how the genes regulate when cells differentiate to determine the fate of each cell. It is necessary to understand how the whole organism is formed and not rely solely on genetic sequence analysis to analyze the statistical results. The results of the new study are the first time scientists have used systematic and quantitative techniques to analyze this complex problem.
In summary, this study presents the development of two species of embryos, using genes that allow the cells to differentiate into different functional “modulators.”
Allon Klein, an assistant professor of systems biology at Harvard Medical School, said that with the single cell gene sequencing technology, researchers can complete the onerous task that could take decades to complete in one day, and the system technology used in the research may be in the future. It can change the direction of research in the field of developmental biology and turn it to quantified big data-oriented science.
In addition, the research co-author Alexander Schier, a professor of molecular and cell biology at Harvard University, said that these findings also allow us to understand more about the causes of certain diseases. Scientists currently only use this technique to analyze cells during embryonic development. Gene expression changes, but the same technique can also be used to study the process of cancer cells producing divisions or brain degeneration.
Alexander Schier described the study as a way for scientists to see the entire universe from a few stars that could have only seen the night sky.
When the fertilized egg begins to divide and grow into a mature individual, each cell in the individual has exactly the same complete genetic body, but as the embryo develops, the originally identical cells will differentiate and begin to exhibit different functions. That is, although the DNA in each cell is the same, each cell only expresses the necessary genes that it needs to make the embryo develop normally.
Klein collaborated with Marc Kirschner, a professor of systems biology at Harvard Medical School, and associate professor Sean Megason, to collect gene expression information for each cell of the embryo one by one, using the single-cell gene sequencer InDrops developed by the team. Finally, the research team got two types of Bio-embryos have a total of 200,000 cells within 24 hours and their gene expression status at different time points.
The research team also introduced another research and calculation technology called TracerSeq to send artificial DNA “barcodes” into cells to track the kinship between cells.
Megason said that if you want to understand the composition of an organism, you need to know which genes are turned on or off when the cells differentiate, and then the cells have their own fate and role. It is not enough to understand only the sequence of the static genome. The team analyzed more than 38,000 cells to construct a “genealogy” of cells, and analyzed the gene expression trends in 25 cell differentiation processes. Combined with information on the spatial distribution of cells in the embryos, the research team was able to reconstruct the origin of various cells in the embryo.
The embryonic development information discovered by the new technology can correspond to our previously known process of embryonic development, but in fact it underestimates the power of new technologies because the analysis of development details is unprecedented and the events within the cells take place successively. It is also very specific, showing all the details of the cells from the very first stage of the process to the functional stage of differentiation.
The research team also clarified the relationship between cell division and evolution with extremely accurate gene expression trends. Through this previously difficult-to-detect detail, some of the more sparse cell types and branches were found. Not only were the classifications made even finer, they also found that we did not know in the past. Cell type.
This technique can also be used to study what effect gene development can have on embryonic development. The team used the CRISPR / Cas9 technology to mutate several genes in the zebrafish, and the gene was originally involved in determining the anterior and posterior steps of embryonic development. Then the gene expression trend of the embryo cells with the mutation was detected. After analyzing the results, the research team was able to confirm whether our previous understanding of the gene was correct or not, as well as being able to depict or even predict the overall impact on the developing cell and the entire embryonic tissue.
▲ Zebrafish embryo development. (Source: Fengzhu Xiong / Sean Megason)
It is worth noting that the research team also found that although the genetic DNA sequences and protein product structures exhibited by embryo development are almost identical between different species, the performance trends are quite different. Klein said that this finding contradicts our current developmental biology theory and challenges our identification of “cell types.”
Since no one had systematically analyzed the gene expression in cells before, the research team also found that in the past the scientists studied deviations from the logic. In the past, scientists often referenced the same parts of different species as the reference, but they neglected that they still have different performance characteristics. Now with these research data, we can revisit and correct the biases of past studies.
The results of this study also suggest another unexpected discovery. In fact, the cell differentiation process may not only be like a dendrogram, but merely branching down one layer to the next, but it can form a cycle. For example, neural crest cells were first developed from neural and skin precursor cells, but neural crest cells can differentiate into smooth muscle cells, specific nerve cells, or craniofacial sacrum, and they are almost similar to bone and chondrocyte precursors. .
This finding also indicates that the two cells in the same state may have differentiated from each other via different routes, and the “family genealogy” of the dendrogram is obviously insufficient to depict the upstream and downstream relationships of cell differentiation.
The team also found that there are specific “fate points” in the cell differentiation process that can change cell differentiation pathways. Some cells also have genes that activate two different developmental pathways at the same time. Cells in the transitional phase will eventually choose one of them. One way, differentiate into this kind of cell.
This finding also shows that the factors that determine the ultimate fate of the cell, in addition to the genes that are turned on, also have parts that we have not yet understood. The team hopes to understand the cells that have opened multiple differentiation pathways at the same time, and in what way ultimately determine the direction of cell differentiation. In addition to gene expression methods, whether there are some decisive factors or environmental interactions involved, it leads to different differentiation routes.
This research on cell differentiation makes scientists like a traveler who already has a map, but there are no marks on the map. What the scientists are now doing is to find the factors that let the cells decide where to go and understand the process mechanism.
The research results will advance future disease-related research. For example, in the field of regenerative medicine, it has been hoped for decades to repair or replace damaged cell tissues or organs through the regulation of stem cell differentiation. Klein said that such information is just like recipe recipes. If the researchers want to produce specific cell functions, they can systematically reconstruct the process of gene expression by referring to the cell’s performance in each stage of the embryo.