The construction of living organisms begins with embryonic development, and its regulation is highly dynamic and complex
Development schema (developmental patterning) how to build, how each fertilized egg cell that is produced to obtain a specific destiny and build a fully functional form tissues and organs, is the core issue of embryonic development
In the 1970s and 1980s, the pioneer of developmental biology, John Sulston, by mapping the developmental origin and lineage relationship of all the somatic cells of C.
elegans, for the first time revealed the cell atlas of the entire developmental process of a multicellular animal , at the single-cell level.
The ground describes the developmental schema establishment process, and nematodes have become the leading model animals for high-precision analysis of developmental dynamic regulation
Compared with a clear and comprehensive cell map, the internal molecular dynamic regulation process still needs to be deepened.
An entry point is to clarify the gene expression and regulation of each cell at all times
At present, it is possible to determine the transcriptome of a single cell, but it is still very difficult to accurately correspond the transcriptome to the cell identity and achieve single-cell annotation accuracy
How to further improve the time accuracy and dimensionality of expression analysis, and achieve in-situ, real-time, and continuous analysis of the dynamic changes of proteins remains to be explored
2021 Nian 7 Yue 26 Ri, Nature Methods published online Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Du Zhuo research new set of laws on the regulatory analytic schema based on dynamic expression of transcription factors and the fate of single cell protein, "A 4D single- cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis"
Focusing on the key genes of developmental regulation -transcription factors, this study has constructed hundreds of fluorescent reporter lines that can indicate the dynamic expression of proteins, integrated in vivo imaging, cell identification, real-time lineage tracking, single-cell fluorescence quantitative analysis, in situ, 4D , The single cell level analyzes the dynamic protein expression of transcription factors in each cell
This study uses a non-invasive method to accurately determine cell identity through imaging and cell tracking, and systematically integrates the single-cell expression levels of multiple proteins to achieve true protein dynamic expression analysis with single-cell annotation accuracy
Using this map, this study first analyzed the molecular regulatory framework established by the cell fate map in a multi-dimensional manner
The study found that transcription factors are at four levels, lineage source, body axis positioning, cell type, and development time.
Through partial overlap and staggered combination in time and space, different cells are gradually given different regulatory states .
Each level of distinction involves multiple different transcription factors with similar expression parts, which endows the regulation process with a high degree of stability.
Calculation simulations show that removing dozens of transcription factors will only have a limited impact on the accuracy of schema establishment .
The result initially reveals the control logic of the intricate fate schema gradual establishment process .
In order to understand the developmental function of transcription factors, this study integrated single-cell expression similarity and transcription factor - target gene information based on experimental data , and constructed a spatiotemporal specific regulatory loop, covering the regulation of more than 8000 transcription factors in 161 developmental spatiotemporal modules Based on this, it reveals the new functions of classical regulatory genes and the new developmental regulation process .
For example, this study found that in addition to the classic regulation of epidermal cell fate, ELT-1/GATA3 also controlled the fate of neural precursor cells of the same lineage, suggesting that the essence of ELT-1 function is to regulate both epidermal and neural fate at the lineage level .
In another analysis, this study revealed the key function of M03D4.
4/VEZF1 in the convergent differentiation of muscle subtype cells.
Different upstream regulatory signals of the body wall and throat muscle cells converge in M03D4.
4 , which is activated and combined It functions in coordination with it, and regulates muscle function genes to mediate the process of convergence and differentiation of cells of the same type that are located in different parts of the body and have different developmental origins .
Accordingly, high-precision " expression Implications type '(expression The-at Informed ) paradigm can efficiently resolved developmentally regulated .
The integration of molecules and cell maps with high temporal and spatial precision provides help for simulating and analyzing the dynamic relationship between cell regulation and cell fate
This study then systematically explored the diversity and complexity of the regulatory state
The study found that the state is highly differentiated with the unfolding of the pedigree.
Although the similar tissues and cells subsequently converge, they still present a high degree of state diversity that depends on the source of the pedigree
Therefore, the developmental history of a cell has a non-negligible influence on the shaping of its final function, and the organization of the lineage determines the diversity of similar cell states and functions
Furthermore, this study found that the regulatory state of cells continued to change with development, until the end of division, and its transition trajectory was highly non-directional, suggesting that the developmental landform of Waddington was winding and tortuous.
Cells went through multiple intermediate states and reached the end through a long “ detour ”.
In conclusion, the present study provides for the analytical molecular regulation of embryonic development law complete, accurate, and standardized reference information for the " revelation expression " function of developmental genes, regulatory status - Quantitative Biological Function, a single cell - the whole embryo - Lay the foundation for multi-dimensional systems biology research .
For " higher " model animals, single-cell analysis may be an emerging field, and nematode developmental biology has entered the single-cell era for more than 40 years .
This research suggests that even for " simple " organisms composed of only a thousand cells , the cognition of the dynamics, diversity and complexity of its developmental regulation has just begun .
The research team Ma Xuehua, Zhao Zhiguang and Xiao Long are the co-first authors of this paper.
Xu Weina, Kou Yahui, Wang Yangyang and Zhang Yanping and Wu Gang of the Dong Mengqiu Laboratory of Beijing Institute of Life Sciences participated in some of the work.
Researcher Du Zhuo is the corresponding author of this article
Nature Methods magazine published a review article " The long and winding road of development: a coordinated song of transcription factors " in the News & Views column at the same time to recommend this work .
This research was funded by the Strategic Leading Science and Technology Project of the Chinese Academy of Sciences ( Category B ) , the National Natural Science Foundation of China and the State Key Laboratory of Molecular Developmental Biology .
Figure: The dynamic map of transcription factor single-cell protein expression reveals the basic framework of molecular regulation for the establishment of developmental fate schemes