Zoom in on the leaf of a corn plant, and you’ll find a patchwork of about 20 different cell types. A recent study, published in Cell, provides an atlas of critical genomic regions that control cell identity in six different corn organs, and perhaps the organs of other plant species.
While molecular biologists can already distinguish gene expression levels in plant cells, this new work pinpoints where expression is regulated on the genome in different cell types. “For the first time, we can understand what parts of the genome are important for identifying the type of plant cell,” says lead author Alexandre Marand, a postdoctoral geneticist at the University of Georgia in Athens. The results could one day enable researchers to control and change cell identity, for instance engineering plants with more cell types that produce medicinal compounds or starches for food.
“This is an impressive paper that greatly advances our view of transcriptional regulation not just in plants, but any organism,” says molecular biologist Detlef Weigel at the Max Planck Institute for Developmental Biology in Tübingen, Germany, who was not involved in the work.
To build the atlas, Marand and coauthors began with fresh tissue from 7-day-old corn seedlings, washed clean and chopped up with a razor blade. Breaking open the seedlings’ cell walls released the cell nuclei into a solution of liquid and debris. Most of the DNA from nuclei was tightly coiled and packed away, making these stretches of the genome much less accessible to binding by transcription proteins. But a small fraction of the DNA, about 3 to 4%, was accessible. Marand wanted to identify these open stretches across cell types.
To do so, he isolated more than 72,000 nuclei and then used a microfluidics device and enzymes to tag a characteristic 16-base-pair barcode to every open, accessible stretch of the genome in every nucleus. Each of the thousands of nuclei received a different 16-base-pair tag sequence. Finally, Marand and coauthors sequenced the contents of all the nuclei to identify which stretches of the genome had been tagged. Comparing the location of the tags across cell types revealed that mesophyll cells, for instance, had one unique and predictable set of open transcription factor binding sites, while bundle sheath cells—cells involved in a key type of photosynthesis that allows corn to grow rapidly in hot and dry conditions—had another. There was a strong correlation between accessible binding sites and the regions controlling gene expression, Marand says.
Identifying where proteins bind is a critical step for understanding how cells differ in their control of certain responses, says plant developmental biologist Philip Benfey at Duke University in Durham, NC. The first step was identifying cell-type specific mRNA expression patterns, he says. Down the road, understanding where cell responses are controlled could have practical benefits, such as altering a plant’s response to help it better handle stress. Benfey coauthored past work showing differences in RNA expression between plant cells types, particularly in the root. But those studies didn’t indicate why a certain region of the genome causes one sequence to be expressed versus another.
Consider, for example, a researcher trying to make a drought-resistant plant. Knowing just the RNA expression, they could try to do so by modifying every relevant gene, Benfey says. But if, instead, the researcher knew which stretches of the genome regulated the majority of those drought genes, then they could “change expression of all the downstream genes in one fell swoop,” Benfey adds.
While the techniques in this latest paper are not novel, applying them to the identification of distinct plant cell types is new, Marand notes. He and coauthors also built a predictive model of plant cell types based on the data. Now, “we can easily say, ‘Oh, this cell is enriched for these transcription factors; this is definitely bundle sheath’,” he explains.
Marand and collaborators now plan to use the same methods in other types of corn, as well as other crops, to build richer maps of the genomic regions that regulate plant cell identity. Learning how natural variation in local climate and elevation might lead to variation in cell-type–specific binding regions could help explain regional differences in corn phenotypes. For instance, if tropical corn varieties consistently share the same open binding regions, “those plants may give us a big clue to what genes control the ability to deal with hot, dry environments,” explains developmental biologist Kenneth Birnbaum at New York University in Manhattan. Longer term, Marand imagines gene editing could tweak protein-binding regions, possibly to increase crop yields or change the angle of leaf growth so that crops can be planted more densely. “What we envision, our lab and collaborators,” Marand says, “is using CRISPR-Cas9 to edit these regions to create new types of phenotypic diversity.”
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