A revolutionary technique for studying gene expression takes root in plants

An open-source RNA analysis platform was successfully used for the first time on plant cells – a breakthrough that could pave the way for a new era of basic research and strengthen efforts to to design more efficient food and biofuel crops.

The technology, called Drop-seq, is a method of measuring RNA present in individual cells. It allows scientists to see what genes are expressed and how it relates to the specific functions of different types of cells. Developed at Harvard Medical School in 2015, the freely shared protocol was previously only used in animal cells.

"This is very important for understanding plant biology," said lead researcher Diane Dickel, a researcher at the Berkeley Lab's Lawrence Berkeley National Lab. "Like humans and mice, plants contain many types of cells and tissues, but knowing more about plants at the cellular level is a bit more difficult because unlike animals, cell walls make it difficult Opening cells to the genetics study. "

Dickel explained that for many genes present in plants, we misunderstand what they actually do. "But by knowing exactly the type of cell or stage of development in which a specific gene is expressed, we can begin to take control of its function.In our study, we have shown that Drop-seq can help us achieve this. . "

"We have also shown that these technologies can be used to understand how plants respond to different environmental conditions at the cellular level.What is of interest to many biologists in the Berkeley Lab laboratory is the ability to develop crops under poor environmental conditions. such as drought, which is essential for our continued production of food resources and biofuels, "she said.

Dickel, who studies mammal genomics in the Berkeley Lab's Environmental Genomics and Systems Biology Division, has been using Drop-seq on animal cells for several years. Immediate adept of the ease of use and efficiency of the platform, she quickly began talking to her colleagues working on plants to try to use it on cells plant.

However, some were skeptical that such a project would work so easily. First, to analyze plant cells in a monocrystalline RNA-seq assay, they must be protoplasted, which means that they have to be rid of their cell walls with the help of one. cocktail of enzymes. This process is not easy because different species cells and even different parts of the same plant require unique enzymatic cocktails.

Secondly, some plant biologists fear that protoplasty will change the cells too much to give an idea of ​​normal functioning. Finally, some cells of the plant are simply too big to go through existing single-celled RNA-seq cell platforms. These technologies, which have emerged in the past five years, allow scientists to evaluate RNA in thousands of cells per cycle; Previous approaches could only scan tens to hundreds of cells at a time.

Undeterred by these challenges, Dickel and his colleagues at the DOE Joint Genome Institute (JGI) teamed up with UC Davis researchers who had developed a technique for the protoplasty of Arabidopsis thaliana root tissue ear), a species of small, flourishing flower. which serves as a plant model organism.

After preparing samples of over 12,000 Arabidopsis root cells, the group was delighted when the Drop-seq process went off more smoothly than expected. Their full results were published this week in Cell reports.

"When we proposed the idea of ​​doing this in the factories, people came up with a list of reasons why it would not work," Dickel said. "And we were saying" ok, but just try and see if it works. "And then it really worked, and we were honestly surprised at how simple it was."

The open-source nature of Drop-seq technology was critical to the success of this project, according to co-author Benjamin Cole, plant genomics scientist at JGI. Drop-seq being inexpensive and using easy-to-assemble components, researchers had a low-risk, inexpensive way of experimenting. Already, a wave of interest is being built. In the run-up to the publication of their article, Dickel and his colleagues began to receive requests for advice, from other Berkeley Lab scientists, from JGI and beyond, on how to "get the job done." adapt the platform to other projects.

"When I spoke with Diane for the first time of the Drop-seq trial in plants, I recognized the huge potential, but I thought it would be difficult to separate the plant cells quickly enough to get useful data, "said John Vogel, chief scientist for plant functional genomics at JGI. "I was shocked to see how well it worked and how well they had learned from their initial experience.This technique will change the game for plant biologists because it allows us to explore Gene expression without destroying whole organs, and the results are not confused by the signals of the few most common cell types. "

The authors predict that the platform, along with other similar technologies based on RNA-seq, will eventually become a routine in facilities surveys. Mr Dickel said that the main obstacle to the development of protoplast methods for the plant of interest of each project.

"Part of the Berkeley Lab's mission is to better understand how plants respond to changing environmental conditions and how we can apply that understanding to better use plants for bioenergy," said lead author Christine Shulse, currently affiliated with JGI. "In this work, we generated a map of gene expression in individual cell types from one plant species under two environmental conditions, which is an important first step."