Plants rely on the CLASSY gene family to diversify their epigenomes

"There have been many observations that one cell or tissue type has a different DNA methylation pattern than another, but how the methylation pathways are modulated to end up with different outcomes in different tissues has remained poorly understood," says senior author Julie Law, associate professor in Salk's Plant Molecular and Cellular Biology Laboratory. "We found that whichCLSYs是表达了在给定的组织机制controlling how the core DNA methylation machinery is directed to different genomic locations in different tissues."

The study of DNA methylation falls under the field of epigenetics -- molecular modifications that change how the DNA functions without changing the DNA sequence itself. It's both a necessary process and a dangerous one. For instance, it helps establish cell identity in a developing embryo but can cause cancer later in life. In plants, defects in DNA methylation can cause developmental defects and negatively impact crop yields.

DNA methylation is regulated by many factors, including certain types of small RNAs. Working with the model plantArabidopsis thaliana,Salk team discovered that the CLASSY gene family (CLSY1-4) acts at different locations depending on the tissue, revealing how diverse patterns of methylation are generated during plant development.

The current work expands on a previous study by Law and her team in which they found that inArabidopsis,CLSYgenes determine which sites in the genome are methylated, via small RNAs. The current study addresses the larger question of whether this process can result in different methylation patterns in differentArabidopsistissues: leaf, flower bud, ovule, and rosette.

The researchers found thatCLSYgenes were expressed differently depending on the plant tissue type. For example, all fourCLSYgenes were expressed in flower buds, whileCLSY3was strongly expressed in ovules andCLSY1was expressed in leaf and rosette tissues.

然后,研究人员将植物与突变CLSYgenes against wild-type plants. They found that depending on the tissue, different combinations ofCLSYfamily members, or even individual CLSY proteins, controlled small RNA and DNA methylation patterns at thousands of sites throughout the genome. These findings demonstrate theCLSYgenes' role in shaping the tissues' epigenetic landscape.

The team's findings may open the door to advances in many areas, from boosting crop yields in plants to informing precision medicine in humans. "Before knowing how a diversity of DNA methylation patterns was generated during development, we didn't have the ability to manipulate that system. Finding that theCLSYs control methylation in a tissue-specific manner represents a major advance as it provides scientists a way to alter DNA methylation patterns with much higher precision," says Law.

Other authors included Ceyda Coruh, Guanghui Xu, Laura M. Martins, Clara Bourbousse and Alice Lambolez of Salk; and Ming Zhou of Zhejiang University in China.

This work was supported by the NIH, the Hearst Foundation, the Hundred-Talent Program of Zhejiang University, the Paul F. Glenn Center for Biology of Aging Research at the Salk Institute, the Chapman Foundation, and the Helmsley Charitable Trust.