While the crisper drawer of our fridge is the best way to keep our produce fresh, epigenetic editing research now brings forth CRISPR-based manipulation of DNA methylation to keep our crops crisp. This tasty treat comes at you in the form of two new publications from the lab of Steven Jacobsen (UCLA), where the talented team expand on their plant epigenetic editing toolkit.
Although sunshine has long been known to be crucial for crops, the Jacobsen lab has been experimenting with a different perspective through the dCas9-SunTag system. Previously, the group reported precision DNA demethylation in Arabidopsis via different approaches, where precision targeting was achieved using an artificial zinc finger or the dCas9-SunTag system and editing was accomplished with a TET1 effector domain. However, systems for precision DNA methylation in plants had remained unexplored.
Now, Gallego-Bartolomé et al. let their DNA methylation toolkit blossom and hijacked machinery from the RNA-directed DNA methylation (RdDM) pathway in plants. The group targeted the promoter of an imprinted gene (FWA) in an Arabidopsis line with a known heritable epiallele for a loss of DNA methylation. This FWA epiallele creates a late flowering phenotype and represents a perfect target for testing precision DNA methylation.
By tethering effector domains from the RdDM pathway to artificial zinc fingers (ZF-RdDM), they were able to:
- Identify a suite of RdDM effectors that promote DNA methylation
- Utilize different mutant backgrounds to gain insight into the hierarchal events behind RdDM
- Examine the effects at thousands of loci using genome-wide screens
- Uncover that co-targeting the two arms of the RdDM pathway, Pol IV (biogenesis of siRNAs) and Pol V (longer non-coding RNAs and DNA methyltransferase recruitment), produces a dramatic enhancement in targeted DNA methylation
Overall, the above study provides fundamental insights into the RdDM pathway and offers new effector domains for epigenetic editing in plants. Although artificial zinc fingers are the original precision epigenetic editors and a great system, they are much more time consuming to create and more prone to off-target effects than the newer dCas9 epigenetic editing systems. Therefore, Papikian et al. sought to bring CRISPR to your crisper and utilized the dCas9-SunTag system to help spread some of their California sunshine.
Here’s what flowered from dCas9-SunTag’s budding effector domains in Arabidopsis:
- VP64 transcriptional activator effector domains drive targeted gene expression at several diverse loci
- The wild-type (repressed) FWA epiallele can be activated and also shows a decrease in DNA methylation
- Targeted activation achieved at transposable elements, regions with different chromatin states, and different protein-coding genes
- The catalytic domain of the tobacco plant DRM methyltransferase deposits DNA methylation at select loci
- An earlier flowering phenotype can be triggered and meiotically inherited across generations by targeting the FWA promoter in a plant background with the epiallele that has lost promoter DNA methylation
- They also used this system to target the promoter of another flowering-associated gene (SUPERMAN)
Taken together, these two manuscripts offer a much-needed expansion of the plant epigenetic editing toolkit. They have not only enabled insight into the fundamentals of the funky world of DNA methylation in plants, but also have much to offer to industry as these systems can be used to target agriculturally important genes.
Senior author Steven Jacobsen shares, “Epigenetic science has many applications, with one of the most promising areas being agriculture.” Jacobsen is also the scientific co-founder of Inari, a plant breeding company that has licensed his labs patents and is focused on creating crops resilient to climate change.
Roger Wakimoto, UCLA vice chancellor for research, adds, “Discoveries that take place in our laboratories directly help solve global issues, and the fragility of the food system has been an issue of concern for some time now. Through Inari, we’re able to apply high-impact research and scientific techniques to the private sector and watch the benefits unfold.”
Ponsi Trivisvavet, CEO of Inari, concludes, “Collaboration and partnerships drive change that addresses the critical problems we face globally in agriculture. Licensing this technology from UCLA provides us with a robust new approach that strengthens our efforts to create a winning food system.”