New molecular atlases reveal how human cells grow and develop

UW Medicine researchers at Seattle’s Brotman Baty Institute have created two cell atlases that track gene expression and chromatin accessibility during the development of human cell types and tissues.

An atlas maps gene expression within single cells in 15 fetal tissues. The second atlas maps the chromatin accessibility of individual genes within cells.

Together, the atlases provide a critical resource for understanding gene expression and chromatin accessibility in human development at an unprecedented scale. Furthermore, the techniques described in the two articles allow to generate data on gene expression and chromatin accessibility for millions of cells.

The atlases are featured in back-to-back publications in the November 13 issue of the journal Science. In addition to BBI and UW Medicine, other contributors from Illumina, Inc., University of Arizona, Fred Hutchinson Cancer Research Center, Max Planck Institute for Molecular Genetics, and University of Rochester Medical Center contributed to these studies.

Atlas of gene expression

Gene expression is the process in which a cell uses the 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 cell types as they grow and develop.

“From these data, we can directly generate a catalog of all major cell types in human tissues, including how these cell types might vary in their gene expression in tissues,” said lead author Junyue Cao. He completed this work as a postdoctoral fellow in the lab of Jay Shendure, a professor of genome sciences at UW Medicine, a researcher at the Howard Hughes Medical Institute and scientific director of the Brotman Baty Institute. Cao is now an assistant professor at Rockefeller University.

“There is an overall goal of the field to profile the genetic programs that are present in a human on a larger scale and with the highest possible resolution,” Shendure said.

To create the atlas, the researchers profiled gene expression on 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”, thus allowing researchers to keep track of cells without physically separating them.

Once the sequences were obtained, they used computer algorithms to retrieve information about the single cell, group the cells by type and subtype, and identify their development trajectories. Scientists profiled over 4 million single cells and identified 77 major cell types and around 650 cell subtypes.

They also compared the atlas to an existing atlas of mouse embryonic development. Senior co-author Cole Trapnell, associate professor of genome sciences at the UW School of Medicine and researcher at the Brotman Baty Institute, explained, “When we combine this data with previously published data, we can directly map the development path of the cell for all major cell types. “

Atlas of DNA accessibility

The second atlas, DNA accessibility, maps material called chromatin that allows DNA to be securely packed 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 tell how a cell chooses to turn genes on and off.

Studying chromatin gives you a sense of the regulatory “grammar” of the cell, “said senior co-author Darren Cusanovich, formerly a postdoctoral fellow in the Shendure lab and now an assistant professor at the University of Arizona. open, or accessible, is enriched with certain “words”, which in turn are the basis for the cell to specify that it wants to turn on certain genes.

To profile the accessibility of DNA in individual cells, scientists developed a new method, called sci-ATAC-seq3. Like sci-RNA-seq3, this technique also uses three different DNA “barcodes” in each cell to label and track individual cells. However, rather than identifying all currently expressed sequences, sci-ATAC-seq3 acquires and sequences opens the chromatin sites.

In this study, scientists generated nearly 800,000 single-cell chromatin accessibility profiles at approximately 1 million sites in 15 fetal tissues. They asked which proteins could interact with the accessible DNA sites in each cell and how these interactions can explain the cell type. This analysis defines the control switches for development within the genome. They also identified chromatin accessibility sites that could be associated with disease.

“This tells us what part of the genome might be functional. We don’t yet know what percentage of the genome that doesn’t code for genes may be involved in gene regulation. Our atlas now provides this information for many cell types,” said Silvia Domcke. , co-author of the Atlas paper on accessibility and postdoctoral fellow in the Shendure lab. The other lead authors of the DNA accessibility study are Andrew Hill, formerly a computational biologist in the Shendure lab and now a scientist at 10x Genomics, and Riza Daza, a researcher in the Shendure lab.