A cell's identity is based on the genes it expresses, and scientists have been studying gene expression mechanisms for many years. But the process involves molecules that are too small to see, until the recent development of a technique called expansion microscopy. With expansion microscopy, scientists preserve tissue, and then enlarge it; this can make very small structures much easier to see. Researchers have now improved the technology, and even after increasing the size of zebrafish embryonic cell nuclei by 4,000 times, they were able to see the influence of individual molecules on gene expression. The findings, which have enhanced our understanding of gene regulation, have been reported in Science.
With this technique, investigators can now visualize the fundamental processes of the cell that form the basis of life. "We can see processes that we could only imagine before," said co-senior study author Antonio Giraldez, Ph.D., Fergus F. Wallace Professor of Genetics at Yale School of Medicine.
When an egg is fertilized by sperm, the genome remains silent at first, until the egg transforms into a transient pluripotent stem cell that can become many different types of cells. The genome has to get started before this cell can be programmed to become other cell types. The Giraldez lab has learned a lot about this process. "But we had never seen the genome activating for ourselves," noted Giraldez.
Co-senior study author Professor Joerg Bewersdorf, Ph.D. previously created a technique that used an expandable gel to preserve cellular features while making them 64 times larger. Researchers then added a second expansion step to increase the cells' size 4,000 times. The Giraldez and Bewersdorf labs came together to develop ChromExM, which could dramatically increase the cells' size while also keeping resolution intact. Once the samples were enlarged, the team used a confocal microscope to analyze the specimens.
The fundamental mechanisms of the genome could then be seen. The scientists saw regulatory regions of DNA interacting with the starts of genes to trigger gene expression, and how the regulatory regions are separated to stop expression after transcription has occurred. More questions can now be answered as well, such as how various genes are turned on or off, where genes are positioned, or how mutations alter the positions of genes.
This method is also not very expensive, so most labs will be able to use ChromExM if they want to. "Our work will democratize a method to see how molecular processes happen within the nucleus, which will open up new areas of research," said Giraldez.
Now the researchers want to make ChromExM even better by improving its resolution more, and they may soon be able to see individual genes in action.
Sources: Yale University, Science