How plants transmit genetic memories

COLD SPRING HARBOR, NY, December 21, 2023 /PRNewswire/ — When organisms pass their genes on to future generations, they include more than just the code laid out in DNA. Some also transmit chemical signals that teach cells how to use that code. The transmission of these markers to future generations is known as epigenetic inheritance. It is common in plants. So, the important findings here may have implications for agriculture, food supply, and the environment.

Arabidopsis thaliana is a plant species widely used to make fundamental biological discoveries. With the help of this versatile test subject, CSHL scientists have now unearthed the secrets of a process that helps control inheritance.

Cold Spring Harbor Laboratory (CSHL) Professors and HHMI Investigators Rob Martienssen and Leemor Joshua-Tor researched how plants pass markers that keep transposons inactive. Transposons are also known as jumping genes. When turned on, they can act and interfere with other genes. To silence it and protect the genome, cells add regulatory markers to specific areas of DNA. This process is called methylation.

Martienssen and Joshua-Tor have now shown how the protein DDM1 makes way for the enzyme that places these marks on new DNA strands. Plant cells need DDM1 because their DNA is tightly packed. To keep their genomes compact and orderly, cells wrap their DNA in proteins called histones. “But that restricts access to the DNA for all kinds of important enzymes,” Martienssen explained. Before methylation can happen, “you have to remove or slide the histones out of the way.”

Martienssen and former CSHL teammate Eric Richards first discovered DDM1 30 years ago. Since then, researchers have learned that it slides DNA over its packaging proteins to expose sites that require methylation. Martienssen likened the movement to a yo-yo going through a string. Histones “can move up and down the DNA, exposing parts of the DNA at a time, but never falling off,” he explained.

Through genetic and biochemical experiments, Martienssen pinpointed the exact histones transferred by DDM1. Used by Joshua-Tor cryo-electron microscopy to obtain detailed images of the enzyme interacting with DNA and associated packing proteins. They saw how DDM1 grabs specific histones to change the packaging of the DNA. “An unexpected bond that binds DDM1 together turns out to correspond to the first mutation found all those years ago,” says Joshua-Tor.

The experiments also revealed how DDM1’s affinity for certain histones preserves epigenetic controls across generations. The team showed that a histone found only in pollen was resistant to DDM1 and acted as a placeholder during cell division. “It remembers where the histone was during plant development and stores that memory in the next generation,” says Martienssen.

Plants may not be alone here. Humans also depend on DDM1 proteins to maintain DNA methylation. The new discovery may help explain how proteins keep our genomes functional and intact.

About Cold Spring Harbor Laboratory
Founded in 1890, Cold Spring Harbor Laboratory has shaped contemporary biomedical research and education with programs in cancer, neuroscience, plant biology and quantitative biology. Home to eight Nobel Prize winners, the private, non-profit Laboratory employs 1,000 people including 600 scientists, students and technicians. For more information, visit



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