Researchers at the University of Washington Health Sciences (UW Medicine), at the Brotman Baty Institute, in the United States, in collaboration with other centers, have created two atlases of cells that track gene expression and chromatin accessibility during the development of types of human cells and tissues.
One atlas maps gene expression within individual cells in 15 fetal tissues, while the second refers to the chromatin accessibility of individual genes within cells, according to the researchers in the journal Science.
Together, both atlases provide a critical resource for understanding gene expression and chromatin accessibility in unprecedented human development. In addition, the techniques described in the two articles make it possible to generate data on gene expression and chromatin accessibility for millions of cells.
The Illumina company, the University of Arizona, the Fred Hutchinson Cancer Research Center, the Max Planck Institute of Germany and the University of Rochester have also participated in the creation of these atlases.
Gene expression is the process in which a cell uses instructions stored in its DNA to direct protein synthesis. These proteins, in turn, determine the structure and function of a cell. The gene expression atlas maps where and when gene expression occurs in different types of cells as they grow and develop.
“From this data, we can directly generate a catalog of all the major cell types in human tissues, including how those cell types can vary in their gene expression in tissues,” explains lead author Junyue. Cao, who completed this work as a postdoctoral fellow in the lab of Jay Shendure, professor of genome sciences at UW Medicine, and now an assistant professor at Rockefeller University.
“There is a general goal of the field to outline the genetic programs that are present in a human being on such a wide scale and with the highest resolution possible,” adds Shendure.
To create the atlas, the researchers profiled gene expression in 15 types of fetal tissue using a technique called sci-RNA-seq3. This technique labels each cell with a unique combination of three DNA 'barcodes', allowing researchers to track cells without physically separating them.
Once the sequences were obtained, they used computer algorithms to retrieve the information from a single cell, group the cells by type and subtype, and identify their developmental trajectories. The scientists profiled more than 4 million individual cells and identified 77 major cell types and approximately 650 cell subtypes.
They also compared the atlas with another existing one of mouse embryonic development. Co-lead author Cole Trapnell, associate professor of genome sciences at the University of Washington School of Medicine and a researcher at the Brotman Baty Institute, explains: “When we combine these data with previously published data, we can directly delineate the developmental path of the cell for all major cell types. “
The second atlas, DNA Accessibility, maps a material called chromatin that allows DNA to pack tightly into the cell nucleus. Chromatin can be open and “accessible” to the molecular machinery that reads the genetic instructions encoded in DNA or closed and “inaccessible”. Knowing the regions of DNA that are open and closed can indicate how a cell chooses to turn genes on and off.
“Studying chromatin gives you insight into the regulatory 'grammar' of the cell,” says co-lead author Darren Cusanovich, a former postdoctoral fellow in Shendure's lab and now an assistant professor at the University of Arizona. DNA that is open, or accessible, is enriched for certain 'words', which are, in turn, the basis for the cell to specify that it wants certain genes in them. “
The scientists generated nearly 800,000 single-cell chromatin accessibility profiles at approximately 1 million sites in 15 fetal tissues in this study. They wondered what proteins might interact with accessible DNA sites in each cell and how those interactions might explain the cell type. This analysis defines the control switches for development within the genome. They also identified chromatin hotspots that could be associated with disease.
“This tells us what part of the genome could be functional. We do not yet know what percentage of the genome that does not encode genes may be involved in genetic regulation. Our atlas now provides that information for many types of cells,” acknowledges Silvia Domcke, co-lead author. of the article of the accessibility atlas and postdoctoral fellow in the Shendure laboratory.